Starting phenix.real_space_refine on Sat Feb 24 20:29:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0f_9314/02_2024/6n0f_9314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0f_9314/02_2024/6n0f_9314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0f_9314/02_2024/6n0f_9314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0f_9314/02_2024/6n0f_9314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0f_9314/02_2024/6n0f_9314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0f_9314/02_2024/6n0f_9314.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 198 5.16 5 C 29148 2.51 5 N 8229 2.21 5 O 8643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA ARG 78": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 202": "NH1" <-> "NH2" Residue "M ARG 148": "NH1" <-> "NH2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "N ARG 202": "NH1" <-> "NH2" Residue "O ARG 148": "NH1" <-> "NH2" Residue "O ARG 202": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "T ARG 148": "NH1" <-> "NH2" Residue "T ARG 202": "NH1" <-> "NH2" Residue "U ARG 148": "NH1" <-> "NH2" Residue "U ARG 202": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46218 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "B" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "C" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "E" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "F" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "GA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "ID" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1484 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 10, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1484 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 10, 'TRANS': 186} Chain breaks: 1 Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "M" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "N" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "O" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "S" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "T" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "U" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1489 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Time building chain proxies: 24.46, per 1000 atoms: 0.53 Number of scatterers: 46218 At special positions: 0 Unit cell: (154.5, 268.83, 251.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 198 16.00 O 8643 8.00 N 8229 7.00 C 29148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.90 Conformation dependent library (CDL) restraints added in 9.3 seconds 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11424 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 67 sheets defined 41.1% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 47 through 57 removed outlier: 4.032A pdb=" N ASP A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.932A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.521A pdb=" N ILE A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.816A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.539A pdb=" N ARG A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 46 through 59 removed outlier: 4.436A pdb=" N ARG B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 96 removed outlier: 4.013A pdb=" N VAL B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.239A pdb=" N ILE B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.752A pdb=" N ALA B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.905A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 removed outlier: 3.568A pdb=" N THR C 25 " --> pdb=" O PHE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.521A pdb=" N VAL C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 removed outlier: 3.889A pdb=" N GLN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.879A pdb=" N ALA C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.748A pdb=" N ARG C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 25 Processing helix chain 'D' and resid 47 through 59 removed outlier: 4.098A pdb=" N VAL D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.513A pdb=" N LEU D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.591A pdb=" N THR D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.718A pdb=" N ALA D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'E' and resid 15 through 25 Processing helix chain 'E' and resid 47 through 59 removed outlier: 3.613A pdb=" N VAL E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 96 removed outlier: 3.580A pdb=" N VAL E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.821A pdb=" N ILE E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 150 through 161 removed outlier: 3.804A pdb=" N ALA E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.538A pdb=" N ARG E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 25 Processing helix chain 'F' and resid 47 through 59 removed outlier: 4.056A pdb=" N VAL F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 96 removed outlier: 3.645A pdb=" N VAL F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 103 removed outlier: 3.729A pdb=" N GLY F 102 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG F 103 " --> pdb=" O GLU F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 103' Processing helix chain 'F' and resid 118 through 126 removed outlier: 4.096A pdb=" N ILE F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.640A pdb=" N ALA F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.627A pdb=" N ARG F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.615A pdb=" N VALGA 24 " --> pdb=" O ALAGA 20 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 4.094A pdb=" N ALAGA 55 " --> pdb=" O ALAGA 51 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLUGA 58 " --> pdb=" O LYSGA 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLUGA 65 " --> pdb=" O GLNGA 61 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.691A pdb=" N METGB 16 " --> pdb=" O GLYGB 12 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VALGB 24 " --> pdb=" O ALAGB 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 4.006A pdb=" N ALAGB 55 " --> pdb=" O ALAGB 51 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 85 removed outlier: 3.934A pdb=" N ASPGB 84 " --> pdb=" O HISGB 80 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALAGB 85 " --> pdb=" O VALGB 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'GB' and resid 80 through 85' Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.699A pdb=" N METGC 16 " --> pdb=" O GLYGC 12 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VALGC 24 " --> pdb=" O ALAGC 20 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.615A pdb=" N ALAGC 55 " --> pdb=" O ALAGC 51 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLUGC 58 " --> pdb=" O LYSGC 54 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAGC 59 " --> pdb=" O ALAGC 55 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 Processing helix chain 'GD' and resid 12 through 27 removed outlier: 3.545A pdb=" N METGD 16 " --> pdb=" O GLYGD 12 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALAGD 27 " --> pdb=" O METGD 23 " (cutoff:3.500A) Processing helix chain 'GD' and resid 49 through 66 removed outlier: 3.853A pdb=" N ALAGD 55 " --> pdb=" O ALAGD 51 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARGGD 62 " --> pdb=" O GLUGD 58 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARGGD 66 " --> pdb=" O ARGGD 62 " (cutoff:3.500A) Processing helix chain 'GD' and resid 80 through 87 removed outlier: 3.794A pdb=" N ASPGD 84 " --> pdb=" O HISGD 80 " (cutoff:3.500A) Processing helix chain 'GE' and resid 12 through 27 removed outlier: 3.867A pdb=" N VALGE 24 " --> pdb=" O ALAGE 20 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSGE 25 " --> pdb=" O ASPGE 21 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 3.866A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARGGE 62 " --> pdb=" O GLUGE 58 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 removed outlier: 3.564A pdb=" N ASPGE 84 " --> pdb=" O HISGE 80 " (cutoff:3.500A) Processing helix chain 'GF' and resid 12 through 26 Processing helix chain 'GF' and resid 49 through 65 removed outlier: 3.914A pdb=" N ALAGF 55 " --> pdb=" O ALAGF 51 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARGGF 62 " --> pdb=" O GLUGF 58 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 25 removed outlier: 3.661A pdb=" N METHA 16 " --> pdb=" O GLYHA 12 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 4.231A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLUHA 65 " --> pdb=" O GLNHA 61 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 87 Processing helix chain 'HB' and resid 12 through 27 removed outlier: 3.579A pdb=" N METHB 16 " --> pdb=" O GLYHB 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VALHB 24 " --> pdb=" O ALAHB 20 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 68 removed outlier: 3.814A pdb=" N LYSHB 54 " --> pdb=" O VALHB 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALAHB 55 " --> pdb=" O ALAHB 51 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARGHB 62 " --> pdb=" O GLUHB 58 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARGHB 66 " --> pdb=" O ARGHB 62 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VALHB 67 " --> pdb=" O ALAHB 63 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 86 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.648A pdb=" N METHC 16 " --> pdb=" O GLYHC 12 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.786A pdb=" N ALAHC 55 " --> pdb=" O ALAHC 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLUHC 58 " --> pdb=" O LYSHC 54 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALAHC 59 " --> pdb=" O ALAHC 55 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARGHC 62 " --> pdb=" O GLUHC 58 " (cutoff:3.500A) Processing helix chain 'HC' and resid 80 through 87 Processing helix chain 'HD' and resid 12 through 27 removed outlier: 3.620A pdb=" N METHD 16 " --> pdb=" O GLYHD 12 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VALHD 24 " --> pdb=" O ALAHD 20 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 4.139A pdb=" N ALAHD 55 " --> pdb=" O ALAHD 51 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGHD 62 " --> pdb=" O GLUHD 58 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALAHD 63 " --> pdb=" O ALAHD 59 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 removed outlier: 3.599A pdb=" N ASPHD 84 " --> pdb=" O HISHD 80 " (cutoff:3.500A) Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.680A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 removed outlier: 3.852A pdb=" N GLUHE 58 " --> pdb=" O LYSHE 54 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAHE 59 " --> pdb=" O ALAHE 55 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARGHE 62 " --> pdb=" O GLUHE 58 " (cutoff:3.500A) Processing helix chain 'HE' and resid 80 through 86 Processing helix chain 'HF' and resid 12 through 27 removed outlier: 3.514A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALAHF 27 " --> pdb=" O METHF 23 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 68 removed outlier: 3.658A pdb=" N ALAHF 55 " --> pdb=" O ALAHF 51 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLUHF 58 " --> pdb=" O LYSHF 54 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARGHF 66 " --> pdb=" O ARGHF 62 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VALHF 67 " --> pdb=" O ALAHF 63 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 removed outlier: 3.549A pdb=" N ASPHF 84 " --> pdb=" O HISHF 80 " (cutoff:3.500A) Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.626A pdb=" N METIA 16 " --> pdb=" O GLYIA 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 65 removed outlier: 3.955A pdb=" N ALAIA 55 " --> pdb=" O ALAIA 51 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARGIA 62 " --> pdb=" O GLUIA 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLUIA 65 " --> pdb=" O GLNIA 61 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.568A pdb=" N METIB 16 " --> pdb=" O GLYIB 12 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 65 removed outlier: 4.045A pdb=" N ALAIB 55 " --> pdb=" O ALAIB 51 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALAIB 59 " --> pdb=" O ALAIB 55 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARGIB 62 " --> pdb=" O GLUIB 58 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 removed outlier: 3.624A pdb=" N ASPIB 84 " --> pdb=" O HISIB 80 " (cutoff:3.500A) Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.562A pdb=" N METIC 16 " --> pdb=" O GLYIC 12 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALIC 24 " --> pdb=" O ALAIC 20 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 4.030A pdb=" N GLUIC 58 " --> pdb=" O LYSIC 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALAIC 59 " --> pdb=" O ALAIC 55 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.530A pdb=" N ALAID 27 " --> pdb=" O METID 23 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 3.696A pdb=" N ALAID 55 " --> pdb=" O ALAID 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALAID 59 " --> pdb=" O ALAID 55 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 86 removed outlier: 3.543A pdb=" N ASPID 84 " --> pdb=" O HISID 80 " (cutoff:3.500A) Processing helix chain 'IE' and resid 12 through 27 removed outlier: 3.538A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 68 removed outlier: 3.942A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARGIE 62 " --> pdb=" O GLUIE 58 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALAIE 63 " --> pdb=" O ALAIE 59 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARGIE 66 " --> pdb=" O ARGIE 62 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VALIE 67 " --> pdb=" O ALAIE 63 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 Processing helix chain 'IF' and resid 49 through 65 removed outlier: 3.812A pdb=" N ALAIF 55 " --> pdb=" O ALAIF 51 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLUIF 58 " --> pdb=" O LYSIF 54 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARGIF 62 " --> pdb=" O GLUIF 58 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.554A pdb=" N METJA 16 " --> pdb=" O GLYJA 12 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 59 removed outlier: 3.554A pdb=" N GLUJA 58 " --> pdb=" O LYSJA 54 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 Processing helix chain 'JB' and resid 12 through 27 removed outlier: 3.522A pdb=" N METJB 16 " --> pdb=" O GLYJB 12 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 65 removed outlier: 3.813A pdb=" N LYSJB 54 " --> pdb=" O VALJB 50 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALAJB 55 " --> pdb=" O ALAJB 51 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARGJB 62 " --> pdb=" O GLUJB 58 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 86 Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.774A pdb=" N METJC 16 " --> pdb=" O GLYJC 12 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 68 removed outlier: 4.017A pdb=" N ALAJC 55 " --> pdb=" O ALAJC 51 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLUJC 58 " --> pdb=" O LYSJC 54 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALAJC 59 " --> pdb=" O ALAJC 55 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARGJC 62 " --> pdb=" O GLUJC 58 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARGJC 66 " --> pdb=" O ARGJC 62 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VALJC 67 " --> pdb=" O ALAJC 63 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.520A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 61 removed outlier: 4.268A pdb=" N ALAJD 55 " --> pdb=" O ALAJD 51 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) Processing helix chain 'JD' and resid 64 through 68 removed outlier: 3.587A pdb=" N GLYJD 68 " --> pdb=" O GLUJD 65 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 85 removed outlier: 3.873A pdb=" N ASPJD 84 " --> pdb=" O HISJD 80 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALAJD 85 " --> pdb=" O VALJD 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'JD' and resid 80 through 85' Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.614A pdb=" N METJE 16 " --> pdb=" O GLYJE 12 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 removed outlier: 3.976A pdb=" N GLUJE 58 " --> pdb=" O LYSJE 54 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALAJE 59 " --> pdb=" O ALAJE 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLUJE 65 " --> pdb=" O GLNJE 61 " (cutoff:3.500A) Processing helix chain 'JE' and resid 66 through 68 No H-bonds generated for 'chain 'JE' and resid 66 through 68' Processing helix chain 'JE' and resid 80 through 87 removed outlier: 3.550A pdb=" N ASPJE 84 " --> pdb=" O HISJE 80 " (cutoff:3.500A) Processing helix chain 'JF' and resid 12 through 26 removed outlier: 4.037A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 68 removed outlier: 4.197A pdb=" N GLUJF 58 " --> pdb=" O LYSJF 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARGJF 66 " --> pdb=" O ARGJF 62 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VALJF 67 " --> pdb=" O ALAJF 63 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 removed outlier: 3.688A pdb=" N ASPJF 84 " --> pdb=" O HISJF 80 " (cutoff:3.500A) Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.608A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VALKA 24 " --> pdb=" O ALAKA 20 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 64 removed outlier: 3.922A pdb=" N ALAKA 55 " --> pdb=" O ALAKA 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALAKA 59 " --> pdb=" O ALAKA 55 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARGKA 62 " --> pdb=" O GLUKA 58 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 removed outlier: 3.549A pdb=" N ASPKA 84 " --> pdb=" O HISKA 80 " (cutoff:3.500A) Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.728A pdb=" N METKB 16 " --> pdb=" O GLYKB 12 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 3.586A pdb=" N ALAKB 59 " --> pdb=" O ALAKB 55 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARGKB 62 " --> pdb=" O GLUKB 58 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 85 removed outlier: 3.957A pdb=" N ASPKB 84 " --> pdb=" O HISKB 80 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALAKB 85 " --> pdb=" O VALKB 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'KB' and resid 80 through 85' Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.645A pdb=" N METKC 16 " --> pdb=" O GLYKC 12 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.849A pdb=" N GLUKC 58 " --> pdb=" O LYSKC 54 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALAKC 59 " --> pdb=" O ALAKC 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLUKC 65 " --> pdb=" O GLNKC 61 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 Processing helix chain 'KD' and resid 12 through 27 removed outlier: 3.522A pdb=" N METKD 16 " --> pdb=" O GLYKD 12 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALAKD 27 " --> pdb=" O METKD 23 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 65 removed outlier: 3.597A pdb=" N ALAKD 55 " --> pdb=" O ALAKD 51 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLUKD 58 " --> pdb=" O LYSKD 54 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALAKD 59 " --> pdb=" O ALAKD 55 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 removed outlier: 3.636A pdb=" N ASPKD 84 " --> pdb=" O HISKD 80 " (cutoff:3.500A) Processing helix chain 'KE' and resid 12 through 26 removed outlier: 3.800A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 4.089A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARGKE 62 " --> pdb=" O GLUKE 58 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 removed outlier: 3.612A pdb=" N METKF 16 " --> pdb=" O GLYKF 12 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.917A pdb=" N ALAKF 55 " --> pdb=" O ALAKF 51 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARGKF 62 " --> pdb=" O GLUKF 58 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.535A pdb=" N METLA 16 " --> pdb=" O GLYLA 12 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 65 removed outlier: 3.911A pdb=" N ARGLA 62 " --> pdb=" O GLULA 58 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 87 Processing helix chain 'LB' and resid 12 through 27 Processing helix chain 'LB' and resid 49 through 65 removed outlier: 3.651A pdb=" N ALALB 55 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARGLB 62 " --> pdb=" O GLULB 58 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 86 removed outlier: 3.542A pdb=" N ASPLB 84 " --> pdb=" O HISLB 80 " (cutoff:3.500A) Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.587A pdb=" N METLC 16 " --> pdb=" O GLYLC 12 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VALLC 24 " --> pdb=" O ALALC 20 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 65 removed outlier: 3.535A pdb=" N LYSLC 54 " --> pdb=" O VALLC 50 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALALC 55 " --> pdb=" O ALALC 51 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALALC 59 " --> pdb=" O ALALC 55 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARGLC 62 " --> pdb=" O GLULC 58 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.533A pdb=" N METLD 16 " --> pdb=" O GLYLD 12 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VALLD 24 " --> pdb=" O ALALD 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 66 removed outlier: 4.367A pdb=" N ALALD 55 " --> pdb=" O ALALD 51 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLULD 58 " --> pdb=" O LYSLD 54 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARGLD 62 " --> pdb=" O GLULD 58 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARGLD 66 " --> pdb=" O ARGLD 62 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 removed outlier: 3.528A pdb=" N ASPLD 84 " --> pdb=" O HISLD 80 " (cutoff:3.500A) Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.639A pdb=" N METLE 16 " --> pdb=" O GLYLE 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 removed outlier: 3.763A pdb=" N GLULE 58 " --> pdb=" O LYSLE 54 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALALE 59 " --> pdb=" O ALALE 55 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARGLE 62 " --> pdb=" O GLULE 58 " (cutoff:3.500A) Processing helix chain 'LE' and resid 80 through 87 removed outlier: 3.518A pdb=" N ASPLE 84 " --> pdb=" O HISLE 80 " (cutoff:3.500A) Processing helix chain 'LF' and resid 12 through 27 removed outlier: 3.805A pdb=" N ALALF 27 " --> pdb=" O METLF 23 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 65 removed outlier: 3.818A pdb=" N ALALF 55 " --> pdb=" O ALALF 51 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLULF 58 " --> pdb=" O LYSLF 54 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLULF 65 " --> pdb=" O GLNLF 61 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 85 removed outlier: 3.505A pdb=" N ASPLF 84 " --> pdb=" O HISLF 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 66 through 82 removed outlier: 3.641A pdb=" N GLY G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 105 removed outlier: 3.744A pdb=" N LEU G 105 " --> pdb=" O TRP G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 143 removed outlier: 3.876A pdb=" N ALA G 132 " --> pdb=" O THR G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 182 removed outlier: 4.087A pdb=" N GLU G 180 " --> pdb=" O GLU G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 44 removed outlier: 3.695A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 82 removed outlier: 4.377A pdb=" N GLY H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 143 removed outlier: 3.577A pdb=" N ALA H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 183 removed outlier: 3.585A pdb=" N GLY H 183 " --> pdb=" O ARG H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 44 removed outlier: 3.552A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 81 Processing helix chain 'I' and resid 100 through 104 removed outlier: 4.132A pdb=" N ARG I 103 " --> pdb=" O GLN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 141 Processing helix chain 'I' and resid 167 through 180 Processing helix chain 'M' and resid 30 through 44 removed outlier: 3.608A pdb=" N ALA M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 81 Processing helix chain 'M' and resid 101 through 105 removed outlier: 4.077A pdb=" N LEU M 105 " --> pdb=" O TRP M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 141 removed outlier: 3.518A pdb=" N LYS M 141 " --> pdb=" O ASP M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 182 removed outlier: 4.055A pdb=" N GLU M 180 " --> pdb=" O GLU M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 44 Processing helix chain 'N' and resid 66 through 82 removed outlier: 4.545A pdb=" N GLY N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 105 removed outlier: 3.945A pdb=" N LEU N 105 " --> pdb=" O TRP N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 141 Processing helix chain 'N' and resid 167 through 182 Processing helix chain 'N' and resid 196 through 200 removed outlier: 3.748A pdb=" N ARG N 200 " --> pdb=" O ASP N 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 removed outlier: 4.066A pdb=" N PHE O 8 " --> pdb=" O PRO O 5 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP O 9 " --> pdb=" O GLU O 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 5 through 9' Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.667A pdb=" N ALA O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 82 removed outlier: 3.595A pdb=" N GLY O 82 " --> pdb=" O ARG O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 105 removed outlier: 4.154A pdb=" N LEU O 105 " --> pdb=" O TRP O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 removed outlier: 3.775A pdb=" N LYS O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 183 removed outlier: 3.752A pdb=" N GLY O 183 " --> pdb=" O ARG O 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 44 removed outlier: 3.815A pdb=" N ALA S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 81 Processing helix chain 'S' and resid 101 through 105 removed outlier: 3.827A pdb=" N LEU S 105 " --> pdb=" O TRP S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 129 through 141 removed outlier: 3.584A pdb=" N LYS S 141 " --> pdb=" O ASP S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 182 removed outlier: 3.928A pdb=" N GLU S 180 " --> pdb=" O GLU S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 44 Processing helix chain 'T' and resid 66 through 82 removed outlier: 3.788A pdb=" N GLY T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 129 through 143 Processing helix chain 'T' and resid 167 through 183 Processing helix chain 'T' and resid 196 through 200 removed outlier: 3.727A pdb=" N ARG T 200 " --> pdb=" O ASP T 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 4.322A pdb=" N PHE U 8 " --> pdb=" O PRO U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 44 removed outlier: 3.542A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 81 Processing helix chain 'U' and resid 101 through 105 removed outlier: 3.789A pdb=" N LEU U 105 " --> pdb=" O TRP U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 141 removed outlier: 4.003A pdb=" N ALA U 132 " --> pdb=" O THR U 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU U 140 " --> pdb=" O ALA U 136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS U 141 " --> pdb=" O ASP U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 183 removed outlier: 3.775A pdb=" N GLY U 183 " --> pdb=" O ARG U 179 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 200 removed outlier: 3.642A pdb=" N ARG U 200 " --> pdb=" O ASP U 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 6.352A pdb=" N GLU A 76 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 114 removed outlier: 6.538A pdb=" N GLU A 144 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS A 111 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE A 142 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 113 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 140 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG A 177 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 169 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.175A pdb=" N VAL B 65 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS B 78 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.860A pdb=" N GLU B 144 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS B 111 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 142 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 113 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG B 177 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 169 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.798A pdb=" N VAL C 65 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS C 78 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 114 removed outlier: 5.136A pdb=" N VAL C 108 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN C 146 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL C 169 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR C 179 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 11 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 114 removed outlier: 5.598A pdb=" N VAL D 108 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN D 146 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 112 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 182 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG D 177 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL D 169 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR D 179 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 11 removed outlier: 4.162A pdb=" N VAL E 65 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N HIS E 78 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 107 through 114 removed outlier: 5.364A pdb=" N VAL E 108 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN E 146 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 112 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG E 177 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL E 169 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 11 removed outlier: 4.253A pdb=" N VAL F 65 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS F 78 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 108 Processing sheet with id=AB4, first strand: chain 'F' and resid 107 through 108 removed outlier: 6.440A pdb=" N ARG F 177 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL F 169 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR F 179 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'GA' and resid 31 through 36 removed outlier: 5.636A pdb=" N LEUGA 31 " --> pdb=" O ARGGA 47 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARGGA 47 " --> pdb=" O LEUGA 31 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLYGA 33 " --> pdb=" O VALGA 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VALGA 45 " --> pdb=" O GLYGA 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALAGA 72 " --> pdb=" O GLUGA 9 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARGGA 11 " --> pdb=" O VALGA 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VALGA 70 " --> pdb=" O ARGGA 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'GB' and resid 30 through 38 removed outlier: 5.423A pdb=" N LEUGB 31 " --> pdb=" O ARGGB 47 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARGGB 47 " --> pdb=" O LEUGB 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYRGB 41 " --> pdb=" O THRGB 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HISGB 74 " --> pdb=" O METGB 7 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALAGB 72 " --> pdb=" O GLUGB 9 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'GC' and resid 31 through 36 removed outlier: 5.975A pdb=" N LEUGC 31 " --> pdb=" O ARGGC 47 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARGGC 47 " --> pdb=" O LEUGC 31 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLYGC 33 " --> pdb=" O VALGC 45 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALGC 45 " --> pdb=" O GLYGC 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALAGC 72 " --> pdb=" O GLUGC 9 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARGGC 11 " --> pdb=" O VALGC 70 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VALGC 70 " --> pdb=" O ARGGC 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'GD' and resid 31 through 36 removed outlier: 4.210A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VALGD 45 " --> pdb=" O GLYGD 33 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALAGD 72 " --> pdb=" O GLUGD 9 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'GE' and resid 31 through 36 removed outlier: 5.869A pdb=" N LEUGE 31 " --> pdb=" O ARGGE 47 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARGGE 47 " --> pdb=" O LEUGE 31 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLYGE 33 " --> pdb=" O VALGE 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALAGE 72 " --> pdb=" O GLUGE 9 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARGGE 11 " --> pdb=" O VALGE 70 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VALGE 70 " --> pdb=" O ARGGE 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'GF' and resid 31 through 36 removed outlier: 6.499A pdb=" N VALGF 45 " --> pdb=" O ILEGF 32 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYRGF 34 " --> pdb=" O THRGF 43 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THRGF 43 " --> pdb=" O TYRGF 34 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYSGF 36 " --> pdb=" O TYRGF 41 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYRGF 41 " --> pdb=" O LYSGF 36 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARGGF 11 " --> pdb=" O VALGF 70 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VALGF 70 " --> pdb=" O ARGGF 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HA' and resid 30 through 38 removed outlier: 5.415A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VALHA 45 " --> pdb=" O GLYHA 33 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYRHA 41 " --> pdb=" O THRHA 37 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALAHA 72 " --> pdb=" O GLUHA 9 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARGHA 11 " --> pdb=" O VALHA 70 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VALHA 70 " --> pdb=" O ARGHA 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'HB' and resid 30 through 36 removed outlier: 5.452A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N METHB 7 " --> pdb=" O HISHB 74 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HISHB 74 " --> pdb=" O METHB 7 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALAHB 72 " --> pdb=" O GLUHB 9 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'HC' and resid 31 through 36 removed outlier: 4.446A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VALHC 45 " --> pdb=" O GLYHC 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HISHC 74 " --> pdb=" O METHC 7 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALAHC 72 " --> pdb=" O GLUHC 9 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARGHC 11 " --> pdb=" O VALHC 70 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VALHC 70 " --> pdb=" O ARGHC 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'HD' and resid 30 through 38 removed outlier: 7.245A pdb=" N VALHD 45 " --> pdb=" O ILEHD 32 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYRHD 34 " --> pdb=" O THRHD 43 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THRHD 43 " --> pdb=" O TYRHD 34 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYSHD 36 " --> pdb=" O TYRHD 41 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N TYRHD 41 " --> pdb=" O LYSHD 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HISHD 74 " --> pdb=" O METHD 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALAHD 72 " --> pdb=" O GLUHD 9 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARGHD 11 " --> pdb=" O VALHD 70 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VALHD 70 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'HE' and resid 30 through 36 removed outlier: 5.522A pdb=" N LEUHE 31 " --> pdb=" O ARGHE 47 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARGHE 47 " --> pdb=" O LEUHE 31 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLYHE 33 " --> pdb=" O VALHE 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALAHE 72 " --> pdb=" O GLUHE 9 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARGHE 11 " --> pdb=" O VALHE 70 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VALHE 70 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'HF' and resid 30 through 36 removed outlier: 5.505A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VALHF 45 " --> pdb=" O GLYHF 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALAHF 72 " --> pdb=" O GLUHF 9 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'IA' and resid 30 through 36 removed outlier: 5.362A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALIA 45 " --> pdb=" O GLYIA 33 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALAIA 72 " --> pdb=" O GLUIA 9 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARGIA 11 " --> pdb=" O VALIA 70 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VALIA 70 " --> pdb=" O ARGIA 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'IB' and resid 30 through 38 removed outlier: 5.209A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRIB 37 " --> pdb=" O TYRIB 41 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEUIB 5 " --> pdb=" O VALIB 75 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VALIB 75 " --> pdb=" O LEUIB 5 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N METIB 7 " --> pdb=" O VALIB 73 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VALIB 73 " --> pdb=" O METIB 7 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLUIB 9 " --> pdb=" O VALIB 71 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'IC' and resid 30 through 36 removed outlier: 5.719A pdb=" N LEUIC 31 " --> pdb=" O ARGIC 47 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARGIC 47 " --> pdb=" O LEUIC 31 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLYIC 33 " --> pdb=" O VALIC 45 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VALIC 45 " --> pdb=" O GLYIC 33 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALAIC 72 " --> pdb=" O GLUIC 9 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARGIC 11 " --> pdb=" O VALIC 70 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VALIC 70 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'ID' and resid 30 through 36 removed outlier: 5.634A pdb=" N LEUID 31 " --> pdb=" O ARGID 47 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARGID 47 " --> pdb=" O LEUID 31 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLYID 33 " --> pdb=" O VALID 45 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VALID 45 " --> pdb=" O GLYID 33 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HISID 74 " --> pdb=" O METID 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALAID 72 " --> pdb=" O GLUID 9 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARGID 11 " --> pdb=" O VALID 70 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VALID 70 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'IE' and resid 30 through 36 removed outlier: 5.532A pdb=" N LEUIE 31 " --> pdb=" O ARGIE 47 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARGIE 47 " --> pdb=" O LEUIE 31 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLYIE 33 " --> pdb=" O VALIE 45 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEUIE 5 " --> pdb=" O VALIE 75 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VALIE 75 " --> pdb=" O LEUIE 5 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N METIE 7 " --> pdb=" O VALIE 73 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VALIE 73 " --> pdb=" O METIE 7 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLUIE 9 " --> pdb=" O VALIE 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'IF' and resid 31 through 36 removed outlier: 5.862A pdb=" N LEUIF 31 " --> pdb=" O ARGIF 47 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARGIF 47 " --> pdb=" O LEUIF 31 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VALIF 45 " --> pdb=" O GLYIF 33 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARGIF 11 " --> pdb=" O VALIF 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VALIF 70 " --> pdb=" O ARGIF 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'JA' and resid 30 through 36 removed outlier: 5.407A pdb=" N LEUJA 31 " --> pdb=" O ARGJA 47 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARGJA 47 " --> pdb=" O LEUJA 31 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VALJA 45 " --> pdb=" O GLYJA 33 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEUJA 5 " --> pdb=" O VALJA 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VALJA 75 " --> pdb=" O LEUJA 5 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N METJA 7 " --> pdb=" O VALJA 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VALJA 73 " --> pdb=" O METJA 7 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLUJA 9 " --> pdb=" O VALJA 71 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'JB' and resid 31 through 36 removed outlier: 5.852A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEUJB 5 " --> pdb=" O VALJB 75 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VALJB 75 " --> pdb=" O LEUJB 5 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N METJB 7 " --> pdb=" O VALJB 73 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VALJB 73 " --> pdb=" O METJB 7 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLUJB 9 " --> pdb=" O VALJB 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'JC' and resid 31 through 36 removed outlier: 3.968A pdb=" N GLYJC 33 " --> pdb=" O VALJC 45 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HISJC 74 " --> pdb=" O METJC 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'JD' and resid 30 through 36 removed outlier: 5.282A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VALJD 45 " --> pdb=" O GLYJD 33 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HISJD 74 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALAJD 72 " --> pdb=" O GLUJD 9 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARGJD 11 " --> pdb=" O VALJD 70 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VALJD 70 " --> pdb=" O ARGJD 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'JE' and resid 30 through 36 removed outlier: 7.614A pdb=" N VALJE 45 " --> pdb=" O ILEJE 32 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYRJE 34 " --> pdb=" O THRJE 43 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THRJE 43 " --> pdb=" O TYRJE 34 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYSJE 36 " --> pdb=" O TYRJE 41 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYRJE 41 " --> pdb=" O LYSJE 36 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLYJE 48 " --> pdb=" O ALAJE 4 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALAJE 72 " --> pdb=" O GLUJE 9 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARGJE 11 " --> pdb=" O VALJE 70 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VALJE 70 " --> pdb=" O ARGJE 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'JF' and resid 30 through 36 removed outlier: 5.544A pdb=" N LEUJF 31 " --> pdb=" O ARGJF 47 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARGJF 47 " --> pdb=" O LEUJF 31 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLYJF 33 " --> pdb=" O VALJF 45 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'KA' and resid 31 through 36 removed outlier: 5.860A pdb=" N LEUKA 31 " --> pdb=" O ARGKA 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARGKA 47 " --> pdb=" O LEUKA 31 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLYKA 33 " --> pdb=" O VALKA 45 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VALKA 45 " --> pdb=" O GLYKA 33 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEUKA 5 " --> pdb=" O VALKA 75 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VALKA 75 " --> pdb=" O LEUKA 5 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N METKA 7 " --> pdb=" O VALKA 73 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VALKA 73 " --> pdb=" O METKA 7 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLUKA 9 " --> pdb=" O VALKA 71 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLUKA 69 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'KB' and resid 30 through 36 removed outlier: 7.087A pdb=" N VALKB 45 " --> pdb=" O ILEKB 32 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYRKB 34 " --> pdb=" O THRKB 43 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THRKB 43 " --> pdb=" O TYRKB 34 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYSKB 36 " --> pdb=" O TYRKB 41 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYRKB 41 " --> pdb=" O LYSKB 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALAKB 72 " --> pdb=" O GLUKB 9 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'KC' and resid 30 through 36 removed outlier: 5.569A pdb=" N LEUKC 31 " --> pdb=" O ARGKC 47 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARGKC 47 " --> pdb=" O LEUKC 31 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLYKC 33 " --> pdb=" O VALKC 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALKC 45 " --> pdb=" O GLYKC 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEUKC 5 " --> pdb=" O VALKC 75 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VALKC 75 " --> pdb=" O LEUKC 5 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N METKC 7 " --> pdb=" O VALKC 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VALKC 73 " --> pdb=" O METKC 7 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLUKC 9 " --> pdb=" O VALKC 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'KD' and resid 30 through 36 removed outlier: 5.651A pdb=" N LEUKD 31 " --> pdb=" O ARGKD 47 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARGKD 47 " --> pdb=" O LEUKD 31 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VALKD 45 " --> pdb=" O GLYKD 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HISKD 74 " --> pdb=" O METKD 7 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALAKD 72 " --> pdb=" O GLUKD 9 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARGKD 11 " --> pdb=" O VALKD 70 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VALKD 70 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KE' and resid 30 through 36 removed outlier: 7.145A pdb=" N VALKE 45 " --> pdb=" O ILEKE 32 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYRKE 34 " --> pdb=" O THRKE 43 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THRKE 43 " --> pdb=" O TYRKE 34 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LYSKE 36 " --> pdb=" O TYRKE 41 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYRKE 41 " --> pdb=" O LYSKE 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALAKE 72 " --> pdb=" O GLUKE 9 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARGKE 11 " --> pdb=" O VALKE 70 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VALKE 70 " --> pdb=" O ARGKE 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'KF' and resid 31 through 36 removed outlier: 5.755A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LA' and resid 30 through 36 removed outlier: 5.662A pdb=" N LEULA 31 " --> pdb=" O ARGLA 47 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARGLA 47 " --> pdb=" O LEULA 31 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALLA 45 " --> pdb=" O GLYLA 33 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALALA 72 " --> pdb=" O GLULA 9 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARGLA 11 " --> pdb=" O VALLA 70 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VALLA 70 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LB' and resid 30 through 36 removed outlier: 5.980A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLYLB 48 " --> pdb=" O ALALB 4 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEULB 5 " --> pdb=" O VALLB 75 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VALLB 75 " --> pdb=" O LEULB 5 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N METLB 7 " --> pdb=" O VALLB 73 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VALLB 73 " --> pdb=" O METLB 7 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLULB 9 " --> pdb=" O VALLB 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LC' and resid 30 through 36 removed outlier: 5.810A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VALLC 45 " --> pdb=" O GLYLC 33 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LD' and resid 30 through 38 removed outlier: 5.589A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THRLD 37 " --> pdb=" O TYRLD 41 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALALD 72 " --> pdb=" O GLULD 9 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LE' and resid 30 through 36 removed outlier: 5.531A pdb=" N LEULE 31 " --> pdb=" O ARGLE 47 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARGLE 47 " --> pdb=" O LEULE 31 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLYLE 33 " --> pdb=" O VALLE 45 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALLE 45 " --> pdb=" O GLYLE 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALALE 72 " --> pdb=" O GLULE 9 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LF' and resid 30 through 36 removed outlier: 7.553A pdb=" N VALLF 45 " --> pdb=" O ILELF 32 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYRLF 34 " --> pdb=" O THRLF 43 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THRLF 43 " --> pdb=" O TYRLF 34 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYSLF 36 " --> pdb=" O TYRLF 41 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYRLF 41 " --> pdb=" O LYSLF 36 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALALF 72 " --> pdb=" O GLULF 9 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARGLF 11 " --> pdb=" O VALLF 70 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VALLF 70 " --> pdb=" O ARGLF 11 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 47 through 54 removed outlier: 6.443A pdb=" N MET G 62 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER G 51 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU G 60 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS G 58 " --> pdb=" O PRO G 53 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 146 through 152 removed outlier: 5.937A pdb=" N LEU G 147 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR G 165 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP G 149 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 47 through 54 removed outlier: 5.236A pdb=" N LEU H 48 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG H 64 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY H 65 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 146 through 152 removed outlier: 6.727A pdb=" N THR H 163 " --> pdb=" O ARG H 148 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N MET H 150 " --> pdb=" O PHE H 161 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE H 161 " --> pdb=" O MET H 150 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL H 121 " --> pdb=" O CYS H 191 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N CYS H 191 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE H 123 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU H 189 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU H 125 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 47 through 54 removed outlier: 6.503A pdb=" N MET I 62 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER I 51 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU I 60 " --> pdb=" O SER I 51 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS I 58 " --> pdb=" O PRO I 53 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY I 65 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 146 through 152 removed outlier: 3.773A pdb=" N VAL I 146 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 163 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET I 150 " --> pdb=" O PHE I 161 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE I 161 " --> pdb=" O MET I 150 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL I 121 " --> pdb=" O CYS I 191 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N CYS I 191 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE I 123 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU I 189 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU I 125 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 48 through 54 Processing sheet with id=AG3, first strand: chain 'M' and resid 146 through 152 removed outlier: 3.665A pdb=" N VAL M 146 " --> pdb=" O THR M 165 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR M 163 " --> pdb=" O ARG M 148 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET M 150 " --> pdb=" O PHE M 161 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE M 161 " --> pdb=" O MET M 150 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL M 121 " --> pdb=" O CYS M 191 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N CYS M 191 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE M 123 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU M 189 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU M 125 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 47 through 54 removed outlier: 6.519A pdb=" N MET N 62 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER N 51 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU N 60 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS N 58 " --> pdb=" O PRO N 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 146 through 152 removed outlier: 6.888A pdb=" N THR N 163 " --> pdb=" O ARG N 148 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET N 150 " --> pdb=" O PHE N 161 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE N 161 " --> pdb=" O MET N 150 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL N 121 " --> pdb=" O CYS N 191 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N CYS N 191 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE N 123 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU N 189 " --> pdb=" O ILE N 123 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU N 125 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 47 through 54 removed outlier: 5.000A pdb=" N LEU O 48 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG O 64 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 146 through 152 removed outlier: 6.733A pdb=" N THR O 163 " --> pdb=" O ARG O 148 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET O 150 " --> pdb=" O PHE O 161 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE O 161 " --> pdb=" O MET O 150 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL O 121 " --> pdb=" O ILE O 192 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU O 125 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 188 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 47 through 54 removed outlier: 5.326A pdb=" N LEU S 48 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG S 64 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 146 through 152 removed outlier: 5.871A pdb=" N LEU S 147 " --> pdb=" O THR S 165 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR S 165 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP S 149 " --> pdb=" O THR S 163 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL S 121 " --> pdb=" O CYS S 191 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N CYS S 191 " --> pdb=" O VAL S 121 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE S 123 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU S 189 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU S 125 " --> pdb=" O LEU S 187 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'T' and resid 47 through 54 removed outlier: 6.686A pdb=" N MET T 62 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER T 51 " --> pdb=" O LEU T 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU T 60 " --> pdb=" O SER T 51 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS T 58 " --> pdb=" O PRO T 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY T 65 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 146 through 152 removed outlier: 6.200A pdb=" N LEU T 147 " --> pdb=" O THR T 165 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR T 165 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP T 149 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL T 121 " --> pdb=" O CYS T 191 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N CYS T 191 " --> pdb=" O VAL T 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE T 123 " --> pdb=" O LEU T 189 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU T 189 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU T 125 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 47 through 54 removed outlier: 5.069A pdb=" N LEU U 48 " --> pdb=" O ARG U 64 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG U 64 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 146 through 151 removed outlier: 6.819A pdb=" N THR U 163 " --> pdb=" O ARG U 148 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET U 150 " --> pdb=" O PHE U 161 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE U 161 " --> pdb=" O MET U 150 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL U 121 " --> pdb=" O CYS U 191 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS U 191 " --> pdb=" O VAL U 121 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE U 123 " --> pdb=" O LEU U 189 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU U 189 " --> pdb=" O ILE U 123 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU U 125 " --> pdb=" O LEU U 187 " (cutoff:3.500A) 2489 hydrogen bonds defined for protein. 7071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.82 Time building geometry restraints manager: 19.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15640 1.34 - 1.46: 6216 1.46 - 1.57: 24635 1.57 - 1.69: 0 1.69 - 1.81: 369 Bond restraints: 46860 Sorted by residual: bond pdb=" C ALALC 86 " pdb=" N LEULC 87 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.07e-02 2.33e+03 1.46e+01 bond pdb=" CA PRO O 144 " pdb=" CB PRO O 144 " ideal model delta sigma weight residual 1.531 1.512 0.019 6.20e-03 2.60e+04 9.80e+00 bond pdb=" C ALAKB 86 " pdb=" N LEUKB 87 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.48e+00 bond pdb=" CG LEUKC 89 " pdb=" CD1 LEUKC 89 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.94e+00 bond pdb=" C PHE A 29 " pdb=" N LEU A 30 " ideal model delta sigma weight residual 1.340 1.230 0.110 5.87e-02 2.90e+02 3.50e+00 ... (remaining 46855 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.27: 856 104.27 - 111.71: 21931 111.71 - 119.15: 17095 119.15 - 126.58: 23346 126.58 - 134.02: 417 Bond angle restraints: 63645 Sorted by residual: angle pdb=" C GLU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 120.82 128.36 -7.54 1.50e+00 4.44e-01 2.53e+01 angle pdb=" CA GLYIF 48 " pdb=" C GLYIF 48 " pdb=" N ASPIF 49 " ideal model delta sigma weight residual 115.22 119.43 -4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" C ASPKD 49 " pdb=" N VALKD 50 " pdb=" CA VALKD 50 " ideal model delta sigma weight residual 120.46 125.41 -4.95 1.37e+00 5.33e-01 1.31e+01 angle pdb=" C ILE B 114 " pdb=" N ARG B 115 " pdb=" CA ARG B 115 " ideal model delta sigma weight residual 121.56 127.11 -5.55 1.56e+00 4.11e-01 1.26e+01 angle pdb=" N GLYKF 33 " pdb=" CA GLYKF 33 " pdb=" C GLYKF 33 " ideal model delta sigma weight residual 111.56 115.13 -3.57 1.01e+00 9.80e-01 1.25e+01 ... (remaining 63640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 27232 15.18 - 30.36: 917 30.36 - 45.55: 241 45.55 - 60.73: 20 60.73 - 75.91: 12 Dihedral angle restraints: 28422 sinusoidal: 10638 harmonic: 17784 Sorted by residual: dihedral pdb=" CA ASPJF 49 " pdb=" C ASPJF 49 " pdb=" N VALJF 50 " pdb=" CA VALJF 50 " ideal model delta harmonic sigma weight residual -180.00 -148.36 -31.64 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA ASPHD 49 " pdb=" C ASPHD 49 " pdb=" N VALHD 50 " pdb=" CA VALHD 50 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASPID 49 " pdb=" C ASPID 49 " pdb=" N VALID 50 " pdb=" CA VALID 50 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 28419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 6055 0.064 - 0.127: 1364 0.127 - 0.191: 178 0.191 - 0.255: 35 0.255 - 0.319: 6 Chirality restraints: 7638 Sorted by residual: chirality pdb=" CB ILE U 122 " pdb=" CA ILE U 122 " pdb=" CG1 ILE U 122 " pdb=" CG2 ILE U 122 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE G 122 " pdb=" CA ILE G 122 " pdb=" CG1 ILE G 122 " pdb=" CG2 ILE G 122 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE N 122 " pdb=" CA ILE N 122 " pdb=" CG1 ILE N 122 " pdb=" CG2 ILE N 122 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 7635 not shown) Planarity restraints: 8340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 122 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C THR E 122 " -0.048 2.00e-02 2.50e+03 pdb=" O THR E 122 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN E 123 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 114 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C ILE B 114 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE B 114 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 115 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 52 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO I 53 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 53 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 53 " 0.032 5.00e-02 4.00e+02 ... (remaining 8337 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8335 2.77 - 3.30: 41257 3.30 - 3.83: 77093 3.83 - 4.37: 87350 4.37 - 4.90: 156250 Nonbonded interactions: 370285 Sorted by model distance: nonbonded pdb=" OE1 GLUKE 9 " pdb=" OG1 THRKE 43 " model vdw 2.235 2.440 nonbonded pdb=" OD1 ASP T 149 " pdb=" OG1 THR T 163 " model vdw 2.254 2.440 nonbonded pdb=" OE1 GLUGE 9 " pdb=" OG1 THRGE 43 " model vdw 2.255 2.440 nonbonded pdb=" OG SER O 120 " pdb=" O ILE O 192 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASP U 149 " pdb=" OG1 THR U 163 " model vdw 2.256 2.440 ... (remaining 370280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 204) selection = (chain 'B' and resid 4 through 204) selection = (chain 'C' and resid 4 through 204) selection = (chain 'D' and resid 4 through 204) selection = (chain 'E' and resid 4 through 204) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'I' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'M' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'N' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'O' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'S' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'T' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'U' and (resid 5 through 83 or resid 88 through 205)) } ncs_group { reference = chain 'GA' selection = chain 'GB' selection = chain 'GC' selection = chain 'GD' selection = chain 'GE' selection = chain 'GF' selection = chain 'HA' selection = chain 'HB' selection = chain 'HC' selection = chain 'HD' selection = chain 'HE' selection = chain 'HF' selection = chain 'IA' selection = chain 'IB' selection = chain 'IC' selection = chain 'ID' selection = chain 'IE' selection = chain 'IF' selection = chain 'JA' selection = chain 'JB' selection = chain 'JC' selection = chain 'JD' selection = chain 'JE' selection = chain 'JF' selection = chain 'KA' selection = chain 'KB' selection = chain 'KC' selection = chain 'KD' selection = chain 'KE' selection = chain 'KF' selection = chain 'LA' selection = chain 'LB' selection = chain 'LC' selection = chain 'LD' selection = chain 'LE' selection = chain 'LF' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 28.710 Check model and map are aligned: 0.920 Set scattering table: 0.500 Process input model: 121.660 Find NCS groups from input model: 3.760 Set up NCS constraints: 0.710 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 46860 Z= 0.507 Angle : 0.860 8.849 63645 Z= 0.478 Chirality : 0.055 0.319 7638 Planarity : 0.007 0.058 8340 Dihedral : 9.184 75.910 16998 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.31 % Allowed : 3.42 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.09), residues: 6183 helix: -3.15 (0.07), residues: 2372 sheet: -1.18 (0.13), residues: 1509 loop : -2.85 (0.11), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 39 HIS 0.010 0.002 HISGB 74 PHE 0.030 0.004 PHE G 162 TYR 0.033 0.003 TYR F 72 ARG 0.011 0.001 ARGIE 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1803 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1789 time to evaluate : 4.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8884 (m) cc_final: 0.8392 (m) REVERT: A 115 ARG cc_start: 0.8450 (mmt180) cc_final: 0.8040 (mmt180) REVERT: A 156 ASN cc_start: 0.8605 (t0) cc_final: 0.8284 (t0) REVERT: A 175 PHE cc_start: 0.7755 (m-80) cc_final: 0.7518 (m-80) REVERT: B 7 THR cc_start: 0.7908 (m) cc_final: 0.7259 (p) REVERT: B 8 TYR cc_start: 0.8420 (t80) cc_final: 0.7843 (t80) REVERT: B 20 THR cc_start: 0.8711 (m) cc_final: 0.8285 (m) REVERT: B 29 PHE cc_start: 0.8700 (m-80) cc_final: 0.8495 (m-80) REVERT: B 67 VAL cc_start: 0.8964 (t) cc_final: 0.8650 (p) REVERT: B 121 GLN cc_start: 0.8536 (tt0) cc_final: 0.8038 (tt0) REVERT: B 128 ASN cc_start: 0.8546 (t0) cc_final: 0.8185 (t0) REVERT: B 163 ASN cc_start: 0.7836 (t0) cc_final: 0.7630 (t0) REVERT: B 188 ASP cc_start: 0.8506 (t0) cc_final: 0.8202 (t70) REVERT: C 128 ASN cc_start: 0.8725 (t0) cc_final: 0.8332 (t0) REVERT: D 8 TYR cc_start: 0.8905 (t80) cc_final: 0.8689 (t80) REVERT: D 27 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7313 (mtp-110) REVERT: D 42 ILE cc_start: 0.9215 (pt) cc_final: 0.8936 (pt) REVERT: D 67 VAL cc_start: 0.9243 (t) cc_final: 0.8860 (m) REVERT: D 72 TYR cc_start: 0.6690 (m-80) cc_final: 0.6310 (m-80) REVERT: D 95 LYS cc_start: 0.8745 (tppt) cc_final: 0.8107 (tppt) REVERT: D 113 ILE cc_start: 0.9369 (mt) cc_final: 0.9067 (pt) REVERT: D 152 VAL cc_start: 0.8998 (m) cc_final: 0.8789 (p) REVERT: E 7 THR cc_start: 0.8707 (m) cc_final: 0.8476 (p) REVERT: E 39 TRP cc_start: 0.7716 (m100) cc_final: 0.6218 (m100) REVERT: E 66 GLN cc_start: 0.9219 (tm130) cc_final: 0.8591 (tm-30) REVERT: E 80 PHE cc_start: 0.9032 (m-80) cc_final: 0.8770 (m-80) REVERT: E 95 LYS cc_start: 0.9251 (tppt) cc_final: 0.8675 (tptp) REVERT: E 109 MET cc_start: 0.8081 (mpm) cc_final: 0.7871 (mpp) REVERT: E 128 ASN cc_start: 0.8534 (t0) cc_final: 0.8142 (t0) REVERT: E 152 VAL cc_start: 0.8607 (m) cc_final: 0.8295 (p) REVERT: F 95 LYS cc_start: 0.9121 (tptp) cc_final: 0.8467 (tptp) REVERT: F 113 ILE cc_start: 0.9193 (mt) cc_final: 0.8932 (pt) REVERT: F 133 MET cc_start: 0.8253 (mtm) cc_final: 0.7962 (mtm) REVERT: F 145 THR cc_start: 0.9541 (p) cc_final: 0.9170 (p) REVERT: GA 16 MET cc_start: 0.9277 (tmm) cc_final: 0.8685 (tmm) REVERT: GA 32 ILE cc_start: 0.8890 (pp) cc_final: 0.8620 (pp) REVERT: GA 43 THR cc_start: 0.9239 (m) cc_final: 0.9029 (p) REVERT: GB 18 GLU cc_start: 0.8947 (tp30) cc_final: 0.8410 (tp30) REVERT: GB 21 ASP cc_start: 0.9042 (t70) cc_final: 0.8509 (t0) REVERT: GB 28 LYS cc_start: 0.8377 (tmmt) cc_final: 0.7569 (mptt) REVERT: GB 73 VAL cc_start: 0.8706 (t) cc_final: 0.7997 (t) REVERT: GB 84 ASP cc_start: 0.8758 (m-30) cc_final: 0.8467 (m-30) REVERT: GC 28 LYS cc_start: 0.8633 (ttpp) cc_final: 0.7906 (mmtt) REVERT: GC 43 THR cc_start: 0.9113 (m) cc_final: 0.8913 (p) REVERT: GC 82 ASN cc_start: 0.8823 (t160) cc_final: 0.8360 (t0) REVERT: GD 62 ARG cc_start: 0.9006 (ttp-110) cc_final: 0.8539 (mtm110) REVERT: GE 32 ILE cc_start: 0.9312 (pp) cc_final: 0.8015 (pp) REVERT: GF 18 GLU cc_start: 0.8822 (tp30) cc_final: 0.8477 (tp30) REVERT: GF 54 LYS cc_start: 0.8564 (tttp) cc_final: 0.8107 (ttpp) REVERT: GF 73 VAL cc_start: 0.9457 (t) cc_final: 0.9247 (m) REVERT: GF 92 THR cc_start: 0.8569 (m) cc_final: 0.8314 (p) REVERT: HA 43 THR cc_start: 0.9273 (m) cc_final: 0.8723 (p) REVERT: HA 61 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8153 (tp40) REVERT: HB 21 ASP cc_start: 0.8534 (t70) cc_final: 0.8281 (t0) REVERT: HB 28 LYS cc_start: 0.8925 (ttpp) cc_final: 0.8567 (ttmm) REVERT: HB 78 ARG cc_start: 0.9078 (ttt90) cc_final: 0.8761 (tpp80) REVERT: HB 92 THR cc_start: 0.8667 (m) cc_final: 0.8246 (p) REVERT: HC 8 ILE cc_start: 0.9032 (mm) cc_final: 0.8763 (tp) REVERT: HC 16 MET cc_start: 0.7994 (tmm) cc_final: 0.7758 (tmm) REVERT: HC 21 ASP cc_start: 0.8819 (t70) cc_final: 0.8447 (t0) REVERT: HC 28 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7540 (mmtt) REVERT: HC 34 TYR cc_start: 0.8429 (p90) cc_final: 0.8217 (p90) REVERT: HD 3 ASP cc_start: 0.8011 (m-30) cc_final: 0.7723 (m-30) REVERT: HD 43 THR cc_start: 0.9593 (m) cc_final: 0.9346 (p) REVERT: HD 78 ARG cc_start: 0.8791 (tmt90) cc_final: 0.7469 (ptp-170) REVERT: HE 16 MET cc_start: 0.8378 (tmm) cc_final: 0.8046 (tmm) REVERT: HE 28 LYS cc_start: 0.9210 (tmmt) cc_final: 0.8899 (tttp) REVERT: HE 30 GLU cc_start: 0.8487 (tt0) cc_final: 0.8154 (tt0) REVERT: HE 43 THR cc_start: 0.9494 (m) cc_final: 0.9229 (p) REVERT: HE 78 ARG cc_start: 0.8248 (tpt170) cc_final: 0.7290 (ptt90) REVERT: HE 84 ASP cc_start: 0.8650 (m-30) cc_final: 0.8328 (p0) REVERT: HF 32 ILE cc_start: 0.9218 (pp) cc_final: 0.8937 (pp) REVERT: HF 43 THR cc_start: 0.8967 (m) cc_final: 0.8520 (p) REVERT: HF 61 GLN cc_start: 0.8975 (tt0) cc_final: 0.8400 (tt0) REVERT: HF 65 GLU cc_start: 0.8737 (mp0) cc_final: 0.8318 (mp0) REVERT: IA 43 THR cc_start: 0.9178 (m) cc_final: 0.8700 (p) REVERT: IB 21 ASP cc_start: 0.8663 (t70) cc_final: 0.8134 (t0) REVERT: IB 78 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.7899 (ttp80) REVERT: IC 5 LEU cc_start: 0.8727 (tp) cc_final: 0.8365 (tp) REVERT: IC 16 MET cc_start: 0.8730 (tmm) cc_final: 0.8479 (tmm) REVERT: IC 35 GLU cc_start: 0.8306 (tp30) cc_final: 0.7999 (tp30) REVERT: IC 43 THR cc_start: 0.9176 (m) cc_final: 0.8894 (p) REVERT: IC 62 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8114 (mtp-110) REVERT: ID 16 MET cc_start: 0.8886 (tmm) cc_final: 0.8606 (tmm) REVERT: ID 31 LEU cc_start: 0.8957 (tp) cc_final: 0.8756 (tt) REVERT: ID 43 THR cc_start: 0.9492 (m) cc_final: 0.9287 (p) REVERT: IF 9 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8257 (tm-30) REVERT: IF 34 TYR cc_start: 0.8257 (p90) cc_final: 0.8049 (p90) REVERT: IF 80 HIS cc_start: 0.8599 (t-90) cc_final: 0.8398 (t-90) REVERT: JA 16 MET cc_start: 0.9069 (tmm) cc_final: 0.8762 (tmm) REVERT: JB 11 ARG cc_start: 0.8442 (ttt180) cc_final: 0.8181 (ttp-170) REVERT: JB 61 GLN cc_start: 0.9127 (tt0) cc_final: 0.8674 (tt0) REVERT: JC 16 MET cc_start: 0.8107 (tmm) cc_final: 0.7818 (tmm) REVERT: JC 28 LYS cc_start: 0.7883 (tmmt) cc_final: 0.7407 (mmtt) REVERT: JD 23 MET cc_start: 0.8393 (mtm) cc_final: 0.8135 (mtm) REVERT: JD 43 THR cc_start: 0.9376 (m) cc_final: 0.8858 (m) REVERT: JD 62 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7967 (ptm160) REVERT: JE 16 MET cc_start: 0.8121 (tmm) cc_final: 0.7723 (tmm) REVERT: JE 28 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8349 (ttmm) REVERT: JF 3 ASP cc_start: 0.8473 (m-30) cc_final: 0.8229 (m-30) REVERT: JF 18 GLU cc_start: 0.8158 (tp30) cc_final: 0.7594 (tp30) REVERT: JF 32 ILE cc_start: 0.9139 (pp) cc_final: 0.8565 (pp) REVERT: JF 61 GLN cc_start: 0.8587 (tt0) cc_final: 0.8030 (tt0) REVERT: JF 62 ARG cc_start: 0.8210 (tmm-80) cc_final: 0.7834 (ttm-80) REVERT: KA 3 ASP cc_start: 0.8342 (m-30) cc_final: 0.7855 (m-30) REVERT: KA 9 GLU cc_start: 0.8176 (tp30) cc_final: 0.7631 (tp30) REVERT: KA 16 MET cc_start: 0.9212 (tmm) cc_final: 0.8832 (tmm) REVERT: KA 18 GLU cc_start: 0.8568 (tp30) cc_final: 0.8315 (tp30) REVERT: KA 25 LYS cc_start: 0.8235 (mttt) cc_final: 0.8003 (mmtt) REVERT: KA 30 GLU cc_start: 0.8741 (tt0) cc_final: 0.8208 (tm-30) REVERT: KA 31 LEU cc_start: 0.9400 (tp) cc_final: 0.8994 (tt) REVERT: KA 41 TYR cc_start: 0.8300 (m-10) cc_final: 0.7910 (m-10) REVERT: KA 43 THR cc_start: 0.9193 (m) cc_final: 0.8871 (m) REVERT: KB 21 ASP cc_start: 0.9004 (t70) cc_final: 0.8656 (t0) REVERT: KB 23 MET cc_start: 0.8777 (mtm) cc_final: 0.8506 (mtt) REVERT: KB 28 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7335 (mttt) REVERT: KB 31 LEU cc_start: 0.9126 (tp) cc_final: 0.8877 (tt) REVERT: KB 43 THR cc_start: 0.9193 (m) cc_final: 0.8924 (p) REVERT: KB 78 ARG cc_start: 0.8734 (mtp85) cc_final: 0.7935 (mtm-85) REVERT: KC 28 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8092 (mptt) REVERT: KC 43 THR cc_start: 0.9255 (m) cc_final: 0.8826 (p) REVERT: KD 23 MET cc_start: 0.8687 (mtm) cc_final: 0.8287 (mtp) REVERT: KD 31 LEU cc_start: 0.8866 (tp) cc_final: 0.8417 (tt) REVERT: KD 62 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8126 (ttp-110) REVERT: KD 78 ARG cc_start: 0.8447 (ttt90) cc_final: 0.7336 (mtm180) REVERT: KE 11 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8102 (ttt90) REVERT: KF 28 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7423 (ptpp) REVERT: KF 41 TYR cc_start: 0.8115 (m-10) cc_final: 0.7834 (m-10) REVERT: KF 92 THR cc_start: 0.8840 (m) cc_final: 0.8589 (p) REVERT: LA 18 GLU cc_start: 0.8399 (tp30) cc_final: 0.7896 (tm-30) REVERT: LA 28 LYS cc_start: 0.8480 (ttpm) cc_final: 0.8269 (ttmm) REVERT: LA 61 GLN cc_start: 0.8912 (tt0) cc_final: 0.8625 (tt0) REVERT: LB 21 ASP cc_start: 0.8791 (t70) cc_final: 0.8574 (t0) REVERT: LB 36 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7391 (mtpt) REVERT: LB 84 ASP cc_start: 0.9240 (m-30) cc_final: 0.8956 (m-30) REVERT: LC 8 ILE cc_start: 0.8624 (mm) cc_final: 0.8115 (tp) REVERT: LC 21 ASP cc_start: 0.8939 (t70) cc_final: 0.8611 (t0) REVERT: LC 66 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7811 (ttp-170) REVERT: LD 16 MET cc_start: 0.8823 (tmm) cc_final: 0.8548 (tmm) REVERT: LD 18 GLU cc_start: 0.8786 (tp30) cc_final: 0.8405 (tp30) REVERT: LD 28 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7947 (tppt) REVERT: LD 30 GLU cc_start: 0.8473 (tt0) cc_final: 0.7968 (tt0) REVERT: LD 62 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7737 (mtp180) REVERT: LE 16 MET cc_start: 0.7975 (tmm) cc_final: 0.7576 (tmm) REVERT: LE 32 ILE cc_start: 0.8705 (pp) cc_final: 0.8483 (pp) REVERT: LF 3 ASP cc_start: 0.7910 (m-30) cc_final: 0.7620 (m-30) REVERT: LF 31 LEU cc_start: 0.8365 (tp) cc_final: 0.7897 (tt) REVERT: G 38 ASP cc_start: 0.7999 (t70) cc_final: 0.7630 (t70) REVERT: G 100 GLN cc_start: 0.8954 (mt0) cc_final: 0.8751 (mt0) REVERT: G 112 ASP cc_start: 0.7037 (p0) cc_final: 0.6364 (m-30) REVERT: H 26 GLU cc_start: 0.7051 (tt0) cc_final: 0.6797 (tt0) REVERT: H 74 MET cc_start: 0.8990 (mmm) cc_final: 0.8501 (mmt) REVERT: H 137 ASP cc_start: 0.8215 (t70) cc_final: 0.7702 (t0) REVERT: I 50 MET cc_start: 0.8533 (ptm) cc_final: 0.8157 (ptt) REVERT: I 62 MET cc_start: 0.9046 (mtt) cc_final: 0.8342 (mtt) REVERT: I 75 ILE cc_start: 0.9121 (tp) cc_final: 0.8876 (pt) REVERT: I 90 ASP cc_start: 0.8155 (t0) cc_final: 0.7731 (t70) REVERT: I 117 ASP cc_start: 0.7383 (p0) cc_final: 0.7143 (p0) REVERT: I 185 ARG cc_start: 0.9123 (mpp80) cc_final: 0.8792 (mtm-85) REVERT: I 187 LEU cc_start: 0.8815 (mt) cc_final: 0.8377 (mp) REVERT: M 19 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8382 (mtt90) REVERT: N 93 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8000 (pt0) REVERT: N 196 VAL cc_start: 0.8963 (t) cc_final: 0.8690 (p) REVERT: O 55 SER cc_start: 0.8577 (m) cc_final: 0.8167 (p) REVERT: O 74 MET cc_start: 0.8805 (mmm) cc_final: 0.8514 (tpp) REVERT: O 90 ASP cc_start: 0.8372 (t0) cc_final: 0.7960 (t0) REVERT: O 118 THR cc_start: 0.8863 (m) cc_final: 0.8340 (p) REVERT: O 119 GLU cc_start: 0.7943 (tt0) cc_final: 0.7681 (tt0) REVERT: O 159 LYS cc_start: 0.9546 (mtmt) cc_final: 0.9128 (mtmm) REVERT: O 176 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8068 (mm-30) REVERT: S 74 MET cc_start: 0.9111 (mmm) cc_final: 0.8879 (mmm) REVERT: S 137 ASP cc_start: 0.8312 (t70) cc_final: 0.7605 (t0) REVERT: S 170 ASP cc_start: 0.8439 (m-30) cc_final: 0.7821 (t0) REVERT: T 71 GLU cc_start: 0.8054 (tp30) cc_final: 0.7806 (tt0) REVERT: T 74 MET cc_start: 0.8758 (mmm) cc_final: 0.8485 (tpp) REVERT: T 90 ASP cc_start: 0.7874 (t0) cc_final: 0.7112 (t70) REVERT: T 96 TYR cc_start: 0.8263 (t80) cc_final: 0.7849 (t80) REVERT: T 106 ASP cc_start: 0.7190 (t0) cc_final: 0.6912 (t0) REVERT: U 75 ILE cc_start: 0.8456 (tp) cc_final: 0.8134 (tp) REVERT: U 100 GLN cc_start: 0.9362 (mt0) cc_final: 0.9125 (mt0) outliers start: 14 outliers final: 4 residues processed: 1800 average time/residue: 0.6337 time to fit residues: 1793.3974 Evaluate side-chains 1170 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1166 time to evaluate : 5.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain S residue 124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 519 optimal weight: 1.9990 chunk 466 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 314 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 482 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 293 optimal weight: 0.9980 chunk 358 optimal weight: 0.8980 chunk 558 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 78 HIS A 79 HIS ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS B 79 HIS B 112 GLN B 123 GLN B 165 HIS B 168 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 123 GLN D 15 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 123 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN E 15 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 15 GLN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS GA 82 ASN GB 82 ASN IA 82 ASN IB 82 ASN IE 74 HIS ** IE 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IF 82 ASN JA 82 ASN JB 82 ASN JD 74 HIS JF 82 ASN KB 82 ASN ** KC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KF 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 82 ASN LB 82 ASN LE 61 GLN LE 82 ASN LF 80 HIS G 98 HIS S 98 HIS S 100 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46860 Z= 0.230 Angle : 0.613 9.655 63645 Z= 0.322 Chirality : 0.044 0.235 7638 Planarity : 0.005 0.049 8340 Dihedral : 4.854 29.322 6784 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.57 % Allowed : 13.03 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.10), residues: 6183 helix: -1.35 (0.10), residues: 2477 sheet: -0.58 (0.13), residues: 1480 loop : -2.40 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 39 HIS 0.007 0.001 HISKD 74 PHE 0.022 0.002 PHE E 10 TYR 0.015 0.001 TYRGB 34 ARG 0.007 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1312 time to evaluate : 5.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8794 (m) cc_final: 0.8561 (m) REVERT: A 35 GLN cc_start: 0.7625 (mt0) cc_final: 0.7413 (mt0) REVERT: A 39 TRP cc_start: 0.8737 (m100) cc_final: 0.8244 (m100) REVERT: A 115 ARG cc_start: 0.8466 (mmt180) cc_final: 0.8174 (mmt180) REVERT: A 156 ASN cc_start: 0.8936 (t0) cc_final: 0.8718 (t0) REVERT: A 199 ARG cc_start: 0.7890 (ptp90) cc_final: 0.7476 (ptp90) REVERT: B 7 THR cc_start: 0.7849 (m) cc_final: 0.7278 (p) REVERT: B 8 TYR cc_start: 0.8332 (t80) cc_final: 0.7927 (t80) REVERT: B 24 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7742 (tttt) REVERT: B 67 VAL cc_start: 0.8810 (t) cc_final: 0.8598 (p) REVERT: B 114 ILE cc_start: 0.8989 (mt) cc_final: 0.8710 (mt) REVERT: B 128 ASN cc_start: 0.8582 (t0) cc_final: 0.8140 (t0) REVERT: B 188 ASP cc_start: 0.8551 (t0) cc_final: 0.8187 (t0) REVERT: C 60 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8733 (ttmt) REVERT: C 128 ASN cc_start: 0.8723 (t0) cc_final: 0.8294 (t0) REVERT: D 70 ARG cc_start: 0.7913 (ptm160) cc_final: 0.7244 (ttt180) REVERT: E 76 GLU cc_start: 0.8342 (tt0) cc_final: 0.8091 (mt-10) REVERT: E 80 PHE cc_start: 0.9002 (m-80) cc_final: 0.8792 (m-80) REVERT: E 109 MET cc_start: 0.8160 (mpm) cc_final: 0.7746 (mpm) REVERT: E 128 ASN cc_start: 0.8346 (t0) cc_final: 0.8014 (t0) REVERT: E 145 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.8805 (t) REVERT: F 105 LYS cc_start: 0.8965 (tptp) cc_final: 0.8241 (tppt) REVERT: F 133 MET cc_start: 0.8255 (mtm) cc_final: 0.7920 (mtm) REVERT: F 184 GLU cc_start: 0.7892 (tm-30) cc_final: 0.6998 (tm-30) REVERT: GA 7 MET cc_start: 0.8473 (mtt) cc_final: 0.8191 (mtm) REVERT: GA 10 VAL cc_start: 0.9720 (t) cc_final: 0.9425 (p) REVERT: GA 16 MET cc_start: 0.9292 (tmm) cc_final: 0.8744 (tmm) REVERT: GA 42 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8696 (p) REVERT: GA 43 THR cc_start: 0.9184 (m) cc_final: 0.8918 (p) REVERT: GB 18 GLU cc_start: 0.8824 (tp30) cc_final: 0.8319 (tp30) REVERT: GB 21 ASP cc_start: 0.8734 (t70) cc_final: 0.8458 (t0) REVERT: GB 28 LYS cc_start: 0.8465 (tmmt) cc_final: 0.7580 (mttt) REVERT: GB 61 GLN cc_start: 0.8701 (tt0) cc_final: 0.8341 (tt0) REVERT: GB 73 VAL cc_start: 0.8888 (t) cc_final: 0.8680 (t) REVERT: GC 28 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8005 (mptt) REVERT: GC 43 THR cc_start: 0.9085 (m) cc_final: 0.8874 (p) REVERT: GC 82 ASN cc_start: 0.8850 (t160) cc_final: 0.8603 (t0) REVERT: GD 16 MET cc_start: 0.8888 (tmm) cc_final: 0.8462 (tmm) REVERT: GD 62 ARG cc_start: 0.9071 (ttp-110) cc_final: 0.8651 (mtm110) REVERT: GE 32 ILE cc_start: 0.9046 (pp) cc_final: 0.8832 (pp) REVERT: GE 58 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7735 (tm-30) REVERT: GF 18 GLU cc_start: 0.8856 (tp30) cc_final: 0.8470 (tp30) REVERT: GF 65 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8267 (pp20) REVERT: GF 73 VAL cc_start: 0.9492 (t) cc_final: 0.9240 (m) REVERT: GF 92 THR cc_start: 0.8454 (m) cc_final: 0.8241 (p) REVERT: HA 18 GLU cc_start: 0.8480 (tp30) cc_final: 0.7996 (tm-30) REVERT: HA 43 THR cc_start: 0.9228 (m) cc_final: 0.8260 (m) REVERT: HA 54 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8291 (ttmt) REVERT: HA 61 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7971 (tp40) REVERT: HB 28 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8131 (ttmm) REVERT: HB 78 ARG cc_start: 0.9045 (ttt90) cc_final: 0.8823 (tpp80) REVERT: HB 92 THR cc_start: 0.8655 (m) cc_final: 0.8218 (p) REVERT: HC 21 ASP cc_start: 0.8857 (t70) cc_final: 0.8507 (t0) REVERT: HC 28 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7559 (mmtm) REVERT: HC 84 ASP cc_start: 0.7900 (m-30) cc_final: 0.7662 (t0) REVERT: HD 3 ASP cc_start: 0.8184 (m-30) cc_final: 0.7793 (m-30) REVERT: HD 16 MET cc_start: 0.8882 (tmm) cc_final: 0.8626 (tmm) REVERT: HD 78 ARG cc_start: 0.8746 (tmt90) cc_final: 0.7424 (ptp-170) REVERT: HE 10 VAL cc_start: 0.9161 (t) cc_final: 0.8800 (p) REVERT: HE 23 MET cc_start: 0.8519 (mtm) cc_final: 0.7757 (mtm) REVERT: HE 30 GLU cc_start: 0.8431 (tt0) cc_final: 0.8181 (tt0) REVERT: HE 43 THR cc_start: 0.9396 (m) cc_final: 0.9171 (t) REVERT: HE 78 ARG cc_start: 0.8244 (tpt170) cc_final: 0.7413 (ptt90) REVERT: HE 84 ASP cc_start: 0.8624 (m-30) cc_final: 0.8299 (p0) REVERT: HF 43 THR cc_start: 0.8815 (m) cc_final: 0.8420 (p) REVERT: HF 61 GLN cc_start: 0.8825 (tt0) cc_final: 0.8508 (tt0) REVERT: HF 62 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.7842 (mtm-85) REVERT: HF 78 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8124 (ttm170) REVERT: IA 3 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7897 (t0) REVERT: IA 41 TYR cc_start: 0.8638 (m-10) cc_final: 0.8152 (m-80) REVERT: IB 21 ASP cc_start: 0.8510 (t70) cc_final: 0.7920 (t0) REVERT: IC 11 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7674 (ttt90) REVERT: IC 16 MET cc_start: 0.8749 (tmm) cc_final: 0.8058 (tmm) REVERT: IC 18 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7983 (tm-30) REVERT: IC 35 GLU cc_start: 0.8305 (tp30) cc_final: 0.8085 (tp30) REVERT: IC 62 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.8064 (mtp-110) REVERT: ID 3 ASP cc_start: 0.8443 (m-30) cc_final: 0.8076 (m-30) REVERT: ID 11 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8144 (ttt90) REVERT: ID 16 MET cc_start: 0.8945 (tmm) cc_final: 0.8586 (tmm) REVERT: ID 61 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8214 (tm-30) REVERT: ID 62 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.7867 (mtm110) REVERT: IE 7 MET cc_start: 0.9082 (mpp) cc_final: 0.8878 (mpp) REVERT: IF 9 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8268 (tm-30) REVERT: JA 16 MET cc_start: 0.9198 (tmm) cc_final: 0.8910 (tmm) REVERT: JA 30 GLU cc_start: 0.8755 (tp30) cc_final: 0.8502 (tp30) REVERT: JA 58 GLU cc_start: 0.7978 (pp20) cc_final: 0.7655 (pp20) REVERT: JA 65 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7916 (mm-30) REVERT: JB 58 GLU cc_start: 0.8133 (tt0) cc_final: 0.7695 (tt0) REVERT: JB 61 GLN cc_start: 0.8981 (tt0) cc_final: 0.8683 (tt0) REVERT: JC 16 MET cc_start: 0.8252 (tmm) cc_final: 0.7869 (tmm) REVERT: JD 9 GLU cc_start: 0.7995 (tp30) cc_final: 0.7647 (tp30) REVERT: JD 23 MET cc_start: 0.8477 (mtm) cc_final: 0.8218 (mtm) REVERT: JD 43 THR cc_start: 0.9020 (m) cc_final: 0.8748 (m) REVERT: JE 7 MET cc_start: 0.8727 (mtp) cc_final: 0.8508 (mtp) REVERT: JE 16 MET cc_start: 0.8210 (tmm) cc_final: 0.7732 (tmm) REVERT: JE 23 MET cc_start: 0.8102 (mtm) cc_final: 0.7835 (mtm) REVERT: JE 61 GLN cc_start: 0.8982 (tt0) cc_final: 0.8675 (tt0) REVERT: JF 18 GLU cc_start: 0.8065 (tp30) cc_final: 0.7563 (tm-30) REVERT: JF 61 GLN cc_start: 0.8702 (tt0) cc_final: 0.8057 (tt0) REVERT: JF 62 ARG cc_start: 0.8314 (tmm-80) cc_final: 0.7852 (ttm-80) REVERT: KA 9 GLU cc_start: 0.8034 (tp30) cc_final: 0.7410 (tp30) REVERT: KA 16 MET cc_start: 0.9165 (tmm) cc_final: 0.8331 (tmm) REVERT: KA 18 GLU cc_start: 0.8737 (tp30) cc_final: 0.8523 (tp30) REVERT: KA 30 GLU cc_start: 0.8637 (tt0) cc_final: 0.8198 (tm-30) REVERT: KA 31 LEU cc_start: 0.9233 (tp) cc_final: 0.9028 (tt) REVERT: KA 43 THR cc_start: 0.9177 (m) cc_final: 0.8838 (m) REVERT: KB 9 GLU cc_start: 0.7796 (tt0) cc_final: 0.7375 (tt0) REVERT: KB 21 ASP cc_start: 0.8890 (t70) cc_final: 0.8670 (t0) REVERT: KB 28 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7456 (mttt) REVERT: KC 7 MET cc_start: 0.8329 (mtp) cc_final: 0.8023 (mtp) REVERT: KC 28 LYS cc_start: 0.8544 (ttpt) cc_final: 0.7986 (mptt) REVERT: KC 41 TYR cc_start: 0.8570 (m-10) cc_final: 0.8364 (m-10) REVERT: KC 43 THR cc_start: 0.9249 (m) cc_final: 0.8819 (p) REVERT: KD 23 MET cc_start: 0.8708 (mtm) cc_final: 0.8149 (mtp) REVERT: KD 78 ARG cc_start: 0.8473 (ttt90) cc_final: 0.7368 (mtm180) REVERT: KE 11 ARG cc_start: 0.8463 (ttt180) cc_final: 0.8191 (ttt90) REVERT: KE 43 THR cc_start: 0.8760 (m) cc_final: 0.8413 (p) REVERT: KE 78 ARG cc_start: 0.8732 (tpt90) cc_final: 0.8450 (tpt90) REVERT: KE 87 LEU cc_start: 0.8997 (mt) cc_final: 0.8718 (mt) REVERT: KF 5 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8284 (tt) REVERT: KF 28 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7554 (ptpp) REVERT: KF 41 TYR cc_start: 0.8565 (m-10) cc_final: 0.8177 (m-10) REVERT: KF 92 THR cc_start: 0.8800 (m) cc_final: 0.8515 (p) REVERT: LA 18 GLU cc_start: 0.8416 (tp30) cc_final: 0.7945 (tm-30) REVERT: LA 32 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7943 (tp) REVERT: LA 61 GLN cc_start: 0.8728 (tt0) cc_final: 0.7919 (tp40) REVERT: LB 21 ASP cc_start: 0.8858 (t70) cc_final: 0.8658 (t0) REVERT: LC 8 ILE cc_start: 0.8471 (mm) cc_final: 0.8171 (tp) REVERT: LC 21 ASP cc_start: 0.8823 (t70) cc_final: 0.8481 (t0) REVERT: LC 66 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7823 (ttp-170) REVERT: LD 8 ILE cc_start: 0.9249 (mm) cc_final: 0.9032 (tt) REVERT: LD 17 VAL cc_start: 0.8734 (t) cc_final: 0.8325 (t) REVERT: LD 18 GLU cc_start: 0.8815 (tp30) cc_final: 0.8408 (tp30) REVERT: LD 28 LYS cc_start: 0.8269 (ttpp) cc_final: 0.7915 (tppt) REVERT: LD 30 GLU cc_start: 0.8432 (tt0) cc_final: 0.7991 (tt0) REVERT: LE 16 MET cc_start: 0.8066 (tmm) cc_final: 0.7827 (tmm) REVERT: LF 18 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6946 (tm-30) REVERT: LF 32 ILE cc_start: 0.9179 (pp) cc_final: 0.8957 (tp) REVERT: LF 58 GLU cc_start: 0.7227 (pt0) cc_final: 0.6816 (tm-30) REVERT: LF 69 GLU cc_start: 0.7204 (tt0) cc_final: 0.6956 (pt0) REVERT: G 62 MET cc_start: 0.9094 (mtt) cc_final: 0.8497 (mtt) REVERT: G 92 LEU cc_start: 0.8863 (tp) cc_final: 0.8633 (tt) REVERT: G 202 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7178 (mtp-110) REVERT: H 74 MET cc_start: 0.8879 (mmm) cc_final: 0.8673 (mmm) REVERT: H 137 ASP cc_start: 0.7937 (t70) cc_final: 0.7415 (t0) REVERT: I 60 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8898 (mt) REVERT: I 62 MET cc_start: 0.9104 (mtt) cc_final: 0.8483 (mtt) REVERT: I 187 LEU cc_start: 0.8554 (mt) cc_final: 0.8217 (mp) REVERT: N 26 GLU cc_start: 0.7738 (tt0) cc_final: 0.7432 (tt0) REVERT: N 196 VAL cc_start: 0.8947 (t) cc_final: 0.8733 (p) REVERT: O 55 SER cc_start: 0.8483 (m) cc_final: 0.8128 (p) REVERT: O 90 ASP cc_start: 0.8245 (t0) cc_final: 0.7819 (t0) REVERT: O 92 LEU cc_start: 0.8971 (tp) cc_final: 0.8666 (tt) REVERT: O 118 THR cc_start: 0.9112 (m) cc_final: 0.8584 (p) REVERT: O 137 ASP cc_start: 0.8220 (t70) cc_final: 0.7866 (t70) REVERT: O 159 LYS cc_start: 0.9508 (mtmt) cc_final: 0.9222 (mtmm) REVERT: O 176 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8010 (mm-30) REVERT: S 74 MET cc_start: 0.9046 (mmm) cc_final: 0.8828 (mmm) REVERT: S 137 ASP cc_start: 0.8305 (t70) cc_final: 0.7516 (t0) REVERT: S 170 ASP cc_start: 0.8270 (m-30) cc_final: 0.7762 (t0) REVERT: T 50 MET cc_start: 0.7840 (ttp) cc_final: 0.7463 (ptt) REVERT: T 71 GLU cc_start: 0.8035 (tp30) cc_final: 0.7833 (tt0) REVERT: T 90 ASP cc_start: 0.7829 (t0) cc_final: 0.7062 (t70) REVERT: T 151 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7254 (ttt-90) REVERT: U 62 MET cc_start: 0.8658 (mtm) cc_final: 0.7821 (mtm) REVERT: U 90 ASP cc_start: 0.7186 (m-30) cc_final: 0.6751 (m-30) REVERT: U 187 LEU cc_start: 0.8358 (mt) cc_final: 0.7949 (tp) outliers start: 163 outliers final: 85 residues processed: 1415 average time/residue: 0.6154 time to fit residues: 1398.4767 Evaluate side-chains 1220 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1128 time to evaluate : 5.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GB residue 43 THR Chi-restraints excluded: chain GC residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain HA residue 17 VAL Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 71 VAL Chi-restraints excluded: chain HC residue 17 VAL Chi-restraints excluded: chain HE residue 31 LEU Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain ID residue 69 GLU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 30 GLU Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 67 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 310 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 464 optimal weight: 5.9990 chunk 380 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 559 optimal weight: 2.9990 chunk 604 optimal weight: 3.9990 chunk 498 optimal weight: 0.9980 chunk 554 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 448 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN B 15 GLN B 121 GLN B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 168 ASN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS HB 82 ASN HD 80 HIS ** IE 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IF 74 HIS IF 82 ASN JB 82 ASN LE 61 GLN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 46860 Z= 0.373 Angle : 0.660 9.391 63645 Z= 0.344 Chirality : 0.045 0.203 7638 Planarity : 0.005 0.053 8340 Dihedral : 4.734 35.134 6784 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.89 % Allowed : 15.00 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.11), residues: 6183 helix: -0.74 (0.10), residues: 2477 sheet: -0.32 (0.13), residues: 1445 loop : -2.21 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 39 HIS 0.013 0.001 HISKD 74 PHE 0.024 0.002 PHE C 10 TYR 0.017 0.002 TYRGB 34 ARG 0.008 0.001 ARGGB 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1148 time to evaluate : 5.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8154 (mmt180) REVERT: A 128 ASN cc_start: 0.8852 (t0) cc_final: 0.8571 (t0) REVERT: A 156 ASN cc_start: 0.9037 (t0) cc_final: 0.8756 (t0) REVERT: A 199 ARG cc_start: 0.7933 (ptp90) cc_final: 0.7493 (ptp90) REVERT: B 7 THR cc_start: 0.8003 (m) cc_final: 0.7505 (p) REVERT: B 8 TYR cc_start: 0.8431 (t80) cc_final: 0.7998 (t80) REVERT: B 128 ASN cc_start: 0.8611 (t0) cc_final: 0.8292 (t0) REVERT: B 188 ASP cc_start: 0.8628 (t0) cc_final: 0.8230 (t0) REVERT: C 60 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8841 (ttmt) REVERT: C 128 ASN cc_start: 0.8732 (t0) cc_final: 0.8332 (t0) REVERT: E 29 PHE cc_start: 0.7971 (m-10) cc_final: 0.7676 (m-10) REVERT: E 80 PHE cc_start: 0.9070 (m-80) cc_final: 0.8793 (m-80) REVERT: E 109 MET cc_start: 0.8143 (mpm) cc_final: 0.7695 (mpm) REVERT: E 128 ASN cc_start: 0.8388 (t0) cc_final: 0.8071 (t0) REVERT: F 133 MET cc_start: 0.8291 (mtm) cc_final: 0.7933 (mtp) REVERT: GA 10 VAL cc_start: 0.9723 (t) cc_final: 0.9409 (p) REVERT: GA 16 MET cc_start: 0.9292 (tmm) cc_final: 0.8743 (tmm) REVERT: GA 42 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8708 (p) REVERT: GA 43 THR cc_start: 0.9306 (m) cc_final: 0.9041 (p) REVERT: GB 7 MET cc_start: 0.8972 (ptp) cc_final: 0.8598 (ptp) REVERT: GB 21 ASP cc_start: 0.8847 (t70) cc_final: 0.8572 (t0) REVERT: GB 28 LYS cc_start: 0.8459 (tmmt) cc_final: 0.7564 (mttt) REVERT: GB 61 GLN cc_start: 0.8733 (tt0) cc_final: 0.8422 (tt0) REVERT: GB 73 VAL cc_start: 0.8960 (t) cc_final: 0.8600 (t) REVERT: GC 28 LYS cc_start: 0.8652 (ttpp) cc_final: 0.7993 (mptt) REVERT: GC 43 THR cc_start: 0.9156 (m) cc_final: 0.8874 (p) REVERT: GC 82 ASN cc_start: 0.8942 (t160) cc_final: 0.8711 (t0) REVERT: GD 16 MET cc_start: 0.8901 (tmm) cc_final: 0.8539 (tmm) REVERT: GD 62 ARG cc_start: 0.9021 (ttp-110) cc_final: 0.8558 (mtm110) REVERT: GE 32 ILE cc_start: 0.9084 (pp) cc_final: 0.8861 (pp) REVERT: GF 9 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8107 (tm-30) REVERT: GF 11 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.7932 (ttm110) REVERT: GF 18 GLU cc_start: 0.8963 (tp30) cc_final: 0.8543 (tp30) REVERT: GF 92 THR cc_start: 0.8609 (m) cc_final: 0.8359 (p) REVERT: HA 18 GLU cc_start: 0.8604 (tp30) cc_final: 0.8022 (tm-30) REVERT: HA 61 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8011 (tp40) REVERT: HA 69 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7275 (tm-30) REVERT: HB 18 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7944 (tm-30) REVERT: HB 65 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7248 (mt-10) REVERT: HB 78 ARG cc_start: 0.9147 (ttt90) cc_final: 0.8943 (tpp80) REVERT: HB 92 THR cc_start: 0.8727 (m) cc_final: 0.8269 (p) REVERT: HC 9 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: HC 21 ASP cc_start: 0.8789 (t70) cc_final: 0.8465 (t0) REVERT: HC 28 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7558 (mmtt) REVERT: HC 84 ASP cc_start: 0.7833 (m-30) cc_final: 0.7622 (t70) REVERT: HD 3 ASP cc_start: 0.8109 (m-30) cc_final: 0.7698 (m-30) REVERT: HD 78 ARG cc_start: 0.8841 (tmt90) cc_final: 0.7527 (ptp-170) REVERT: HE 30 GLU cc_start: 0.8440 (tt0) cc_final: 0.8236 (tt0) REVERT: HE 43 THR cc_start: 0.9369 (m) cc_final: 0.9148 (t) REVERT: HE 78 ARG cc_start: 0.8244 (tpt170) cc_final: 0.7480 (ptt90) REVERT: HF 16 MET cc_start: 0.9120 (tmm) cc_final: 0.8874 (tmm) REVERT: HF 18 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7510 (tm-30) REVERT: HF 43 THR cc_start: 0.8787 (m) cc_final: 0.8434 (p) REVERT: HF 61 GLN cc_start: 0.8770 (tt0) cc_final: 0.8326 (tt0) REVERT: HF 62 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8036 (mtm-85) REVERT: HF 65 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8465 (mp0) REVERT: HF 78 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.8144 (ttm170) REVERT: IA 3 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7936 (t0) REVERT: IB 21 ASP cc_start: 0.8568 (t70) cc_final: 0.8022 (t0) REVERT: IC 16 MET cc_start: 0.8816 (tmm) cc_final: 0.8490 (tmm) REVERT: IC 18 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8061 (tm-30) REVERT: ID 16 MET cc_start: 0.9044 (tmm) cc_final: 0.8596 (tmm) REVERT: ID 61 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8374 (tm-30) REVERT: ID 62 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.7701 (mtm110) REVERT: IE 7 MET cc_start: 0.9101 (mpp) cc_final: 0.8768 (mpp) REVERT: IE 32 ILE cc_start: 0.9186 (pp) cc_final: 0.8973 (pp) REVERT: IF 9 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8302 (tm-30) REVERT: IF 11 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: JA 65 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8043 (mm-30) REVERT: JB 58 GLU cc_start: 0.8106 (tt0) cc_final: 0.7847 (tt0) REVERT: JB 61 GLN cc_start: 0.8927 (tt0) cc_final: 0.8670 (tt0) REVERT: JC 16 MET cc_start: 0.8301 (tmm) cc_final: 0.7885 (tmm) REVERT: JD 18 GLU cc_start: 0.8806 (tp30) cc_final: 0.8420 (tp30) REVERT: JE 16 MET cc_start: 0.8290 (tmm) cc_final: 0.7941 (tmm) REVERT: JE 43 THR cc_start: 0.9403 (m) cc_final: 0.9174 (m) REVERT: JE 61 GLN cc_start: 0.9022 (tt0) cc_final: 0.8668 (tt0) REVERT: JF 18 GLU cc_start: 0.8179 (tp30) cc_final: 0.7691 (tm-30) REVERT: JF 61 GLN cc_start: 0.8569 (tt0) cc_final: 0.8326 (tt0) REVERT: JF 62 ARG cc_start: 0.8320 (tmm-80) cc_final: 0.7828 (ttm-80) REVERT: KA 9 GLU cc_start: 0.8053 (tp30) cc_final: 0.7418 (tp30) REVERT: KA 16 MET cc_start: 0.9241 (tmm) cc_final: 0.8426 (tmm) REVERT: KB 9 GLU cc_start: 0.7863 (tt0) cc_final: 0.7469 (tt0) REVERT: KB 21 ASP cc_start: 0.8857 (t70) cc_final: 0.8506 (t0) REVERT: KB 28 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7474 (mttt) REVERT: KB 41 TYR cc_start: 0.8908 (m-80) cc_final: 0.8698 (m-80) REVERT: KB 43 THR cc_start: 0.9048 (m) cc_final: 0.8750 (p) REVERT: KC 7 MET cc_start: 0.8338 (mtp) cc_final: 0.8133 (mtp) REVERT: KC 28 LYS cc_start: 0.8611 (ttpt) cc_final: 0.8029 (mptt) REVERT: KC 43 THR cc_start: 0.9314 (m) cc_final: 0.8784 (p) REVERT: KD 21 ASP cc_start: 0.8733 (t70) cc_final: 0.8451 (t0) REVERT: KD 23 MET cc_start: 0.8784 (mtm) cc_final: 0.8293 (mtp) REVERT: KD 30 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8519 (tm-30) REVERT: KD 58 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7304 (tm-30) REVERT: KD 62 ARG cc_start: 0.8544 (ttm110) cc_final: 0.8199 (ttp-110) REVERT: KD 78 ARG cc_start: 0.8501 (ttt90) cc_final: 0.7382 (mtm180) REVERT: KE 11 ARG cc_start: 0.8587 (ttt180) cc_final: 0.8126 (ttt90) REVERT: KE 43 THR cc_start: 0.8751 (m) cc_final: 0.8421 (p) REVERT: KF 9 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8300 (tm-30) REVERT: KF 11 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: KF 28 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7559 (ptpp) REVERT: KF 41 TYR cc_start: 0.8557 (m-10) cc_final: 0.7602 (m-10) REVERT: KF 92 THR cc_start: 0.8875 (m) cc_final: 0.8615 (p) REVERT: LA 18 GLU cc_start: 0.8545 (tp30) cc_final: 0.8009 (tm-30) REVERT: LA 32 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7987 (pp) REVERT: LA 61 GLN cc_start: 0.8552 (tt0) cc_final: 0.7812 (tp40) REVERT: LA 69 GLU cc_start: 0.7556 (tp30) cc_final: 0.7298 (tm-30) REVERT: LC 8 ILE cc_start: 0.8599 (mm) cc_final: 0.8240 (tp) REVERT: LC 21 ASP cc_start: 0.8828 (t70) cc_final: 0.8560 (t0) REVERT: LC 65 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8303 (mm-30) REVERT: LC 66 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7991 (ttp-170) REVERT: LD 18 GLU cc_start: 0.8912 (tp30) cc_final: 0.8527 (tp30) REVERT: LD 28 LYS cc_start: 0.8364 (ttpp) cc_final: 0.7922 (tppt) REVERT: LD 30 GLU cc_start: 0.8394 (tt0) cc_final: 0.7889 (tt0) REVERT: LE 42 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8879 (p) REVERT: LF 18 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7474 (tm-30) REVERT: LF 58 GLU cc_start: 0.7382 (pt0) cc_final: 0.6852 (tm-30) REVERT: G 62 MET cc_start: 0.9075 (mtt) cc_final: 0.8549 (mtt) REVERT: G 92 LEU cc_start: 0.9055 (tp) cc_final: 0.8817 (tt) REVERT: H 26 GLU cc_start: 0.7030 (tt0) cc_final: 0.6737 (tt0) REVERT: H 137 ASP cc_start: 0.8112 (t70) cc_final: 0.7613 (t0) REVERT: M 62 MET cc_start: 0.8506 (mtt) cc_final: 0.8177 (mtp) REVERT: N 130 CYS cc_start: 0.8852 (m) cc_final: 0.8447 (m) REVERT: O 11 THR cc_start: 0.9002 (t) cc_final: 0.8663 (p) REVERT: O 55 SER cc_start: 0.8348 (m) cc_final: 0.8039 (p) REVERT: O 90 ASP cc_start: 0.8298 (t0) cc_final: 0.7852 (t0) REVERT: O 118 THR cc_start: 0.9122 (m) cc_final: 0.8590 (p) REVERT: O 119 GLU cc_start: 0.7955 (tt0) cc_final: 0.7744 (tt0) REVERT: O 137 ASP cc_start: 0.8387 (t70) cc_final: 0.8053 (t70) REVERT: O 159 LYS cc_start: 0.9468 (mtmt) cc_final: 0.9211 (mtmm) REVERT: S 137 ASP cc_start: 0.8398 (t70) cc_final: 0.7605 (t0) REVERT: S 140 LEU cc_start: 0.9231 (mt) cc_final: 0.8928 (tp) REVERT: S 170 ASP cc_start: 0.8381 (m-30) cc_final: 0.7954 (t0) REVERT: T 71 GLU cc_start: 0.8138 (tp30) cc_final: 0.7883 (tt0) REVERT: T 151 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7289 (ttt-90) REVERT: U 92 LEU cc_start: 0.9125 (tp) cc_final: 0.8838 (tt) REVERT: U 187 LEU cc_start: 0.8458 (mt) cc_final: 0.8011 (tp) outliers start: 223 outliers final: 150 residues processed: 1277 average time/residue: 0.6387 time to fit residues: 1316.2682 Evaluate side-chains 1221 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1065 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 17 VAL Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 71 VAL Chi-restraints excluded: chain HC residue 9 GLU Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 58 GLU Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain ID residue 35 GLU Chi-restraints excluded: chain ID residue 69 GLU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain JA residue 43 THR Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KD residue 61 GLN Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KE residue 34 TYR Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 69 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 134 ASP Chi-restraints excluded: chain O residue 182 CYS Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 46 SER Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 106 ASP Chi-restraints excluded: chain U residue 135 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 552 optimal weight: 3.9990 chunk 420 optimal weight: 0.8980 chunk 290 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 375 optimal weight: 3.9990 chunk 561 optimal weight: 1.9990 chunk 594 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 532 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 123 GLN B 168 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN F 112 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS JB 82 ASN KE 82 ASN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46860 Z= 0.230 Angle : 0.592 10.009 63645 Z= 0.305 Chirality : 0.043 0.203 7638 Planarity : 0.004 0.048 8340 Dihedral : 4.407 35.861 6784 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.39 % Allowed : 16.69 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.11), residues: 6183 helix: -0.37 (0.11), residues: 2516 sheet: -0.09 (0.13), residues: 1435 loop : -2.04 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 39 HIS 0.004 0.001 HISLC 74 PHE 0.022 0.002 PHE E 10 TYR 0.016 0.001 TYRGB 34 ARG 0.009 0.000 ARGHA 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1367 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1167 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8512 (m100) cc_final: 0.8021 (m100) REVERT: A 115 ARG cc_start: 0.8491 (mmt180) cc_final: 0.8147 (mmt180) REVERT: A 128 ASN cc_start: 0.8854 (t0) cc_final: 0.8589 (t0) REVERT: A 156 ASN cc_start: 0.9011 (t0) cc_final: 0.8740 (t0) REVERT: A 157 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 199 ARG cc_start: 0.7895 (ptp90) cc_final: 0.7479 (ptp90) REVERT: B 8 TYR cc_start: 0.8363 (t80) cc_final: 0.8102 (t80) REVERT: B 128 ASN cc_start: 0.8657 (t0) cc_final: 0.8297 (t0) REVERT: B 188 ASP cc_start: 0.8603 (t0) cc_final: 0.8164 (t0) REVERT: C 115 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7319 (mtp85) REVERT: C 128 ASN cc_start: 0.8713 (t0) cc_final: 0.8269 (t0) REVERT: C 187 ILE cc_start: 0.8928 (tp) cc_final: 0.8690 (tp) REVERT: D 76 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7264 (tm-30) REVERT: E 52 THR cc_start: 0.8927 (m) cc_final: 0.8422 (p) REVERT: E 80 PHE cc_start: 0.9066 (m-80) cc_final: 0.8797 (m-80) REVERT: E 109 MET cc_start: 0.8338 (mpm) cc_final: 0.7947 (mpm) REVERT: E 128 ASN cc_start: 0.8345 (t0) cc_final: 0.8011 (t0) REVERT: F 72 TYR cc_start: 0.8827 (m-80) cc_final: 0.8494 (m-80) REVERT: F 105 LYS cc_start: 0.8850 (tptp) cc_final: 0.8048 (tptp) REVERT: F 115 ARG cc_start: 0.7590 (mpt-90) cc_final: 0.6846 (mpt-90) REVERT: F 133 MET cc_start: 0.8227 (mtm) cc_final: 0.7901 (mtp) REVERT: F 184 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7421 (tp30) REVERT: GA 10 VAL cc_start: 0.9727 (t) cc_final: 0.9468 (p) REVERT: GA 16 MET cc_start: 0.9294 (tmm) cc_final: 0.8786 (tmm) REVERT: GA 34 TYR cc_start: 0.8732 (p90) cc_final: 0.8496 (p90) REVERT: GA 42 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8718 (p) REVERT: GA 43 THR cc_start: 0.9239 (m) cc_final: 0.8991 (p) REVERT: GB 7 MET cc_start: 0.8978 (ptp) cc_final: 0.8488 (ptp) REVERT: GB 21 ASP cc_start: 0.8854 (t70) cc_final: 0.8542 (t0) REVERT: GB 28 LYS cc_start: 0.8455 (tmmt) cc_final: 0.7549 (mttt) REVERT: GB 34 TYR cc_start: 0.8033 (p90) cc_final: 0.7639 (p90) REVERT: GB 61 GLN cc_start: 0.8706 (tt0) cc_final: 0.8491 (tt0) REVERT: GB 73 VAL cc_start: 0.8948 (t) cc_final: 0.8538 (t) REVERT: GC 28 LYS cc_start: 0.8599 (ttpp) cc_final: 0.7964 (mptt) REVERT: GC 43 THR cc_start: 0.9149 (m) cc_final: 0.8881 (p) REVERT: GD 16 MET cc_start: 0.8877 (tmm) cc_final: 0.8519 (tmm) REVERT: GD 62 ARG cc_start: 0.8980 (ttp-110) cc_final: 0.8564 (mtm110) REVERT: GF 9 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8070 (tm-30) REVERT: GF 11 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8041 (ttm110) REVERT: GF 18 GLU cc_start: 0.8872 (tp30) cc_final: 0.8494 (tp30) REVERT: GF 92 THR cc_start: 0.8576 (m) cc_final: 0.8335 (p) REVERT: HA 18 GLU cc_start: 0.8600 (tp30) cc_final: 0.7943 (tm-30) REVERT: HA 61 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8110 (tp40) REVERT: HA 69 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7377 (tm-30) REVERT: HB 92 THR cc_start: 0.8737 (m) cc_final: 0.8270 (p) REVERT: HC 7 MET cc_start: 0.8339 (mtp) cc_final: 0.8100 (mtp) REVERT: HC 9 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: HC 21 ASP cc_start: 0.8819 (t70) cc_final: 0.8457 (t0) REVERT: HC 28 LYS cc_start: 0.8000 (ttpt) cc_final: 0.7545 (mmtt) REVERT: HD 3 ASP cc_start: 0.8093 (m-30) cc_final: 0.7692 (m-30) REVERT: HD 32 ILE cc_start: 0.9584 (pp) cc_final: 0.9324 (tp) REVERT: HD 78 ARG cc_start: 0.8726 (tmt90) cc_final: 0.7424 (ptp-170) REVERT: HE 10 VAL cc_start: 0.9140 (t) cc_final: 0.8863 (m) REVERT: HE 30 GLU cc_start: 0.8417 (tt0) cc_final: 0.8217 (tt0) REVERT: HE 78 ARG cc_start: 0.8165 (tpt170) cc_final: 0.7454 (ptt90) REVERT: HF 18 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7440 (tm-30) REVERT: HF 43 THR cc_start: 0.8741 (m) cc_final: 0.8377 (p) REVERT: HF 61 GLN cc_start: 0.8723 (tt0) cc_final: 0.8368 (tt0) REVERT: HF 65 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8399 (mp0) REVERT: HF 78 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8082 (ttm170) REVERT: IA 3 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7856 (t0) REVERT: IA 35 GLU cc_start: 0.8669 (tp30) cc_final: 0.8432 (tp30) REVERT: IB 21 ASP cc_start: 0.8445 (t70) cc_final: 0.7902 (t0) REVERT: IB 58 GLU cc_start: 0.7060 (pt0) cc_final: 0.6849 (pt0) REVERT: IC 16 MET cc_start: 0.8884 (tmm) cc_final: 0.8478 (tmm) REVERT: IC 18 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7929 (tm-30) REVERT: ID 3 ASP cc_start: 0.8460 (m-30) cc_final: 0.8130 (m-30) REVERT: ID 11 ARG cc_start: 0.8708 (mtp180) cc_final: 0.8066 (ttt90) REVERT: ID 16 MET cc_start: 0.9106 (tmm) cc_final: 0.8864 (tmm) REVERT: ID 61 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8385 (tm-30) REVERT: ID 62 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7852 (mtm110) REVERT: IF 9 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8271 (tm-30) REVERT: IF 32 ILE cc_start: 0.8996 (pp) cc_final: 0.8704 (tp) REVERT: JA 16 MET cc_start: 0.8164 (tmm) cc_final: 0.7523 (tmm) REVERT: JA 65 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8183 (mm-30) REVERT: JB 61 GLN cc_start: 0.8839 (tt0) cc_final: 0.8622 (tt0) REVERT: JC 7 MET cc_start: 0.8955 (mtp) cc_final: 0.8753 (mtt) REVERT: JD 69 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7022 (mm-30) REVERT: JE 16 MET cc_start: 0.8296 (tmm) cc_final: 0.8039 (tmm) REVERT: JE 61 GLN cc_start: 0.9008 (tt0) cc_final: 0.8640 (tt0) REVERT: JF 18 GLU cc_start: 0.8134 (tp30) cc_final: 0.7808 (tm-30) REVERT: JF 62 ARG cc_start: 0.8249 (tmm-80) cc_final: 0.7796 (ttm-80) REVERT: JF 91 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.8110 (mmm-85) REVERT: KA 9 GLU cc_start: 0.8027 (tp30) cc_final: 0.7480 (tp30) REVERT: KA 16 MET cc_start: 0.9207 (tmm) cc_final: 0.8624 (tmm) REVERT: KB 9 GLU cc_start: 0.7947 (tt0) cc_final: 0.7608 (tt0) REVERT: KB 21 ASP cc_start: 0.8821 (t70) cc_final: 0.8498 (t0) REVERT: KB 28 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7480 (mttt) REVERT: KC 7 MET cc_start: 0.8217 (mtp) cc_final: 0.7929 (mtm) REVERT: KC 18 GLU cc_start: 0.8906 (tp30) cc_final: 0.8675 (tp30) REVERT: KC 23 MET cc_start: 0.8399 (ptp) cc_final: 0.8199 (mtm) REVERT: KC 28 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8009 (mptt) REVERT: KC 43 THR cc_start: 0.9326 (m) cc_final: 0.8759 (p) REVERT: KD 23 MET cc_start: 0.8690 (mtm) cc_final: 0.8181 (mtp) REVERT: KD 30 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8268 (tm-30) REVERT: KD 78 ARG cc_start: 0.8481 (ttt90) cc_final: 0.7448 (mtm180) REVERT: KE 11 ARG cc_start: 0.8587 (ttt180) cc_final: 0.8144 (ttt90) REVERT: KE 43 THR cc_start: 0.8692 (m) cc_final: 0.8424 (p) REVERT: KF 9 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8295 (tm-30) REVERT: KF 28 LYS cc_start: 0.8314 (ttpp) cc_final: 0.7629 (ptpp) REVERT: KF 41 TYR cc_start: 0.8565 (m-10) cc_final: 0.8079 (m-10) REVERT: KF 80 HIS cc_start: 0.7738 (t-90) cc_final: 0.7367 (t-90) REVERT: KF 92 THR cc_start: 0.8925 (m) cc_final: 0.8670 (p) REVERT: LA 18 GLU cc_start: 0.8421 (tp30) cc_final: 0.7929 (tm-30) REVERT: LA 32 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7889 (pp) REVERT: LA 35 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7183 (mm-30) REVERT: LA 61 GLN cc_start: 0.8447 (tt0) cc_final: 0.7769 (tp40) REVERT: LC 8 ILE cc_start: 0.8585 (mm) cc_final: 0.8276 (tp) REVERT: LC 21 ASP cc_start: 0.8783 (t70) cc_final: 0.8478 (t0) REVERT: LC 65 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8348 (mm-30) REVERT: LC 66 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7960 (ttm170) REVERT: LD 18 GLU cc_start: 0.8868 (tp30) cc_final: 0.8400 (tp30) REVERT: LD 21 ASP cc_start: 0.8816 (m-30) cc_final: 0.8553 (m-30) REVERT: LD 28 LYS cc_start: 0.8332 (ttpp) cc_final: 0.7933 (tppt) REVERT: LD 30 GLU cc_start: 0.8356 (tt0) cc_final: 0.7886 (tt0) REVERT: LF 18 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7446 (tm-30) REVERT: LF 58 GLU cc_start: 0.7347 (pt0) cc_final: 0.6859 (tm-30) REVERT: G 62 MET cc_start: 0.9045 (mtt) cc_final: 0.8723 (mtt) REVERT: G 92 LEU cc_start: 0.8959 (tp) cc_final: 0.8751 (tt) REVERT: H 74 MET cc_start: 0.8991 (mmm) cc_final: 0.8526 (mmm) REVERT: H 90 ASP cc_start: 0.8095 (t70) cc_final: 0.7852 (t0) REVERT: H 92 LEU cc_start: 0.9282 (tp) cc_final: 0.9080 (tt) REVERT: H 137 ASP cc_start: 0.7860 (t70) cc_final: 0.7396 (t0) REVERT: M 62 MET cc_start: 0.8459 (mtt) cc_final: 0.8130 (mtp) REVERT: O 11 THR cc_start: 0.8980 (t) cc_final: 0.8634 (p) REVERT: O 55 SER cc_start: 0.8175 (m) cc_final: 0.7860 (p) REVERT: O 90 ASP cc_start: 0.8155 (t0) cc_final: 0.7680 (t0) REVERT: O 118 THR cc_start: 0.9068 (m) cc_final: 0.8544 (p) REVERT: O 137 ASP cc_start: 0.8284 (t70) cc_final: 0.7929 (t70) REVERT: O 159 LYS cc_start: 0.9424 (mtmt) cc_final: 0.9150 (mtmm) REVERT: S 137 ASP cc_start: 0.8294 (t70) cc_final: 0.7524 (t0) REVERT: S 140 LEU cc_start: 0.9186 (mt) cc_final: 0.8866 (tp) REVERT: S 170 ASP cc_start: 0.8280 (m-30) cc_final: 0.7786 (t0) REVERT: T 50 MET cc_start: 0.8279 (ttp) cc_final: 0.7832 (ptt) REVERT: U 7 ARG cc_start: 0.7532 (mtm110) cc_final: 0.6838 (ptt-90) REVERT: U 58 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7519 (ptmt) REVERT: U 90 ASP cc_start: 0.7676 (m-30) cc_final: 0.7141 (m-30) REVERT: U 187 LEU cc_start: 0.8400 (mt) cc_final: 0.8036 (tp) outliers start: 200 outliers final: 131 residues processed: 1288 average time/residue: 0.6612 time to fit residues: 1378.6139 Evaluate side-chains 1217 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1081 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HC residue 9 GLU Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 3 ASP Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 69 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 495 optimal weight: 4.9990 chunk 337 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 442 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 507 optimal weight: 3.9990 chunk 410 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 533 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS GB 82 ASN JB 82 ASN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46860 Z= 0.236 Angle : 0.591 10.068 63645 Z= 0.304 Chirality : 0.044 0.210 7638 Planarity : 0.004 0.047 8340 Dihedral : 4.308 36.335 6784 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.65 % Allowed : 17.72 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 6183 helix: -0.17 (0.11), residues: 2514 sheet: 0.03 (0.13), residues: 1444 loop : -1.90 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 39 HIS 0.004 0.001 HISLC 74 PHE 0.024 0.002 PHE C 10 TYR 0.018 0.001 TYR C 8 ARG 0.011 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1115 time to evaluate : 5.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8521 (m100) cc_final: 0.8062 (m100) REVERT: A 115 ARG cc_start: 0.8500 (mmt180) cc_final: 0.8123 (mmt180) REVERT: A 128 ASN cc_start: 0.8788 (t0) cc_final: 0.8546 (t0) REVERT: A 156 ASN cc_start: 0.9012 (t0) cc_final: 0.8735 (t0) REVERT: B 8 TYR cc_start: 0.8435 (t80) cc_final: 0.8143 (t80) REVERT: B 128 ASN cc_start: 0.8634 (t0) cc_final: 0.8391 (t0) REVERT: B 188 ASP cc_start: 0.8601 (t0) cc_final: 0.8160 (t0) REVERT: C 128 ASN cc_start: 0.8708 (t0) cc_final: 0.8246 (t0) REVERT: C 187 ILE cc_start: 0.8934 (tp) cc_final: 0.8704 (tp) REVERT: E 50 ARG cc_start: 0.8581 (ttm110) cc_final: 0.8276 (ttm110) REVERT: E 80 PHE cc_start: 0.9063 (m-80) cc_final: 0.8825 (m-80) REVERT: E 109 MET cc_start: 0.8330 (mpm) cc_final: 0.8013 (mpm) REVERT: E 128 ASN cc_start: 0.8373 (t0) cc_final: 0.8016 (t0) REVERT: F 72 TYR cc_start: 0.8901 (m-80) cc_final: 0.8557 (m-80) REVERT: F 105 LYS cc_start: 0.8852 (tptp) cc_final: 0.8083 (tptp) REVERT: F 133 MET cc_start: 0.8249 (mtm) cc_final: 0.7933 (mtp) REVERT: F 184 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7500 (tm-30) REVERT: F 188 ASP cc_start: 0.8300 (m-30) cc_final: 0.7830 (m-30) REVERT: GA 10 VAL cc_start: 0.9727 (t) cc_final: 0.9486 (p) REVERT: GA 16 MET cc_start: 0.9284 (tmm) cc_final: 0.8782 (tmm) REVERT: GA 34 TYR cc_start: 0.8710 (p90) cc_final: 0.8466 (p90) REVERT: GA 42 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8693 (p) REVERT: GA 43 THR cc_start: 0.9207 (m) cc_final: 0.8993 (p) REVERT: GB 7 MET cc_start: 0.8967 (ptp) cc_final: 0.8189 (ptp) REVERT: GB 21 ASP cc_start: 0.8854 (t70) cc_final: 0.8540 (t0) REVERT: GB 28 LYS cc_start: 0.8487 (tmmt) cc_final: 0.7496 (mttt) REVERT: GB 73 VAL cc_start: 0.8997 (t) cc_final: 0.8607 (t) REVERT: GC 8 ILE cc_start: 0.9112 (mm) cc_final: 0.8797 (mm) REVERT: GC 28 LYS cc_start: 0.8615 (ttpp) cc_final: 0.7950 (mptt) REVERT: GC 34 TYR cc_start: 0.8988 (p90) cc_final: 0.8773 (p90) REVERT: GC 43 THR cc_start: 0.9116 (m) cc_final: 0.8824 (p) REVERT: GD 16 MET cc_start: 0.8880 (tmm) cc_final: 0.8621 (tmm) REVERT: GD 23 MET cc_start: 0.8815 (ptm) cc_final: 0.8470 (ptm) REVERT: GD 62 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8550 (mtm110) REVERT: GF 9 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7926 (tm-30) REVERT: GF 18 GLU cc_start: 0.8949 (tp30) cc_final: 0.8532 (tp30) REVERT: GF 71 VAL cc_start: 0.9146 (t) cc_final: 0.8928 (t) REVERT: GF 92 THR cc_start: 0.8535 (m) cc_final: 0.8297 (p) REVERT: HA 18 GLU cc_start: 0.8598 (tp30) cc_final: 0.7934 (tm-30) REVERT: HA 61 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8115 (tp40) REVERT: HA 69 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7354 (tm-30) REVERT: HB 16 MET cc_start: 0.8908 (tmm) cc_final: 0.8210 (tmm) REVERT: HB 65 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7363 (mt-10) REVERT: HB 92 THR cc_start: 0.8745 (m) cc_final: 0.8268 (p) REVERT: HC 21 ASP cc_start: 0.8772 (t70) cc_final: 0.8477 (t0) REVERT: HC 28 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7548 (mmtt) REVERT: HC 84 ASP cc_start: 0.7817 (t70) cc_final: 0.7542 (t0) REVERT: HD 3 ASP cc_start: 0.8099 (m-30) cc_final: 0.7681 (m-30) REVERT: HD 32 ILE cc_start: 0.9570 (pp) cc_final: 0.9310 (tp) REVERT: HD 78 ARG cc_start: 0.8742 (tmt90) cc_final: 0.7450 (ptp-170) REVERT: HE 10 VAL cc_start: 0.9100 (t) cc_final: 0.8859 (m) REVERT: HE 21 ASP cc_start: 0.8058 (t70) cc_final: 0.7796 (t70) REVERT: HE 65 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8166 (pt0) REVERT: HE 78 ARG cc_start: 0.8178 (tpt170) cc_final: 0.7491 (ptt90) REVERT: HF 18 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7260 (tm-30) REVERT: HF 43 THR cc_start: 0.8717 (m) cc_final: 0.8365 (p) REVERT: HF 61 GLN cc_start: 0.8755 (tt0) cc_final: 0.8427 (tt0) REVERT: HF 65 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8346 (mp0) REVERT: HF 78 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8008 (ttm170) REVERT: IA 3 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7860 (t0) REVERT: IA 35 GLU cc_start: 0.8602 (tp30) cc_final: 0.8401 (tp30) REVERT: IA 41 TYR cc_start: 0.8693 (m-10) cc_final: 0.8487 (m-80) REVERT: IB 16 MET cc_start: 0.8594 (tmm) cc_final: 0.8360 (tmm) REVERT: IB 21 ASP cc_start: 0.8431 (t70) cc_final: 0.7915 (t0) REVERT: IB 58 GLU cc_start: 0.7098 (pt0) cc_final: 0.6879 (pt0) REVERT: IC 5 LEU cc_start: 0.8808 (tp) cc_final: 0.8294 (tp) REVERT: IC 16 MET cc_start: 0.8798 (tmm) cc_final: 0.8446 (tmm) REVERT: IC 18 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7930 (tm-30) REVERT: ID 61 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8393 (tm-30) REVERT: ID 62 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.8142 (ttp80) REVERT: IF 9 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8362 (tm-30) REVERT: IF 11 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: IF 32 ILE cc_start: 0.8946 (pp) cc_final: 0.8655 (tp) REVERT: JA 16 MET cc_start: 0.8344 (tmm) cc_final: 0.7717 (tmm) REVERT: JA 65 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8241 (mm-30) REVERT: JD 23 MET cc_start: 0.8489 (mtm) cc_final: 0.8252 (mtm) REVERT: JE 16 MET cc_start: 0.8184 (tmm) cc_final: 0.7838 (tmm) REVERT: JE 23 MET cc_start: 0.8099 (mtm) cc_final: 0.7777 (mtm) REVERT: JE 61 GLN cc_start: 0.8999 (tt0) cc_final: 0.8481 (tt0) REVERT: JE 73 VAL cc_start: 0.9463 (t) cc_final: 0.8758 (t) REVERT: JF 18 GLU cc_start: 0.8205 (tp30) cc_final: 0.7909 (tm-30) REVERT: JF 62 ARG cc_start: 0.8247 (tmm-80) cc_final: 0.7745 (ttm-80) REVERT: KA 9 GLU cc_start: 0.8028 (tp30) cc_final: 0.7463 (tp30) REVERT: KA 16 MET cc_start: 0.9112 (tmm) cc_final: 0.8540 (tmm) REVERT: KB 9 GLU cc_start: 0.7877 (tt0) cc_final: 0.7609 (tt0) REVERT: KB 21 ASP cc_start: 0.8765 (t70) cc_final: 0.8415 (t0) REVERT: KB 28 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7453 (mttt) REVERT: KC 28 LYS cc_start: 0.8591 (ttpt) cc_final: 0.7969 (mptt) REVERT: KC 35 GLU cc_start: 0.7924 (mp0) cc_final: 0.7525 (mp0) REVERT: KC 43 THR cc_start: 0.9212 (m) cc_final: 0.8759 (p) REVERT: KD 23 MET cc_start: 0.8621 (mtm) cc_final: 0.8095 (mtp) REVERT: KD 30 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8173 (tm-30) REVERT: KD 78 ARG cc_start: 0.8481 (ttt90) cc_final: 0.7457 (mtm180) REVERT: KE 8 ILE cc_start: 0.9105 (mt) cc_final: 0.8717 (tt) REVERT: KE 11 ARG cc_start: 0.8626 (ttt180) cc_final: 0.8141 (ttt90) REVERT: KE 43 THR cc_start: 0.8691 (m) cc_final: 0.8450 (p) REVERT: KF 9 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8250 (tm-30) REVERT: KF 28 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7628 (ptpp) REVERT: KF 41 TYR cc_start: 0.8433 (m-10) cc_final: 0.8229 (m-10) REVERT: KF 80 HIS cc_start: 0.7790 (t-90) cc_final: 0.7371 (t-90) REVERT: KF 89 LEU cc_start: 0.8762 (mp) cc_final: 0.8560 (mp) REVERT: KF 92 THR cc_start: 0.8945 (m) cc_final: 0.8701 (p) REVERT: LA 32 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7829 (pp) REVERT: LA 61 GLN cc_start: 0.8442 (tt0) cc_final: 0.7780 (tp40) REVERT: LC 8 ILE cc_start: 0.8565 (mm) cc_final: 0.8274 (tp) REVERT: LC 21 ASP cc_start: 0.8717 (t70) cc_final: 0.8423 (t0) REVERT: LC 65 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8337 (mm-30) REVERT: LD 18 GLU cc_start: 0.8904 (tp30) cc_final: 0.8417 (tp30) REVERT: LD 21 ASP cc_start: 0.8854 (m-30) cc_final: 0.8584 (m-30) REVERT: LD 28 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7937 (tppt) REVERT: LD 30 GLU cc_start: 0.8356 (tt0) cc_final: 0.7894 (tt0) REVERT: LF 18 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7439 (tm-30) REVERT: LF 58 GLU cc_start: 0.7343 (pt0) cc_final: 0.6885 (tm-30) REVERT: G 62 MET cc_start: 0.9028 (mtt) cc_final: 0.8739 (mtt) REVERT: G 92 LEU cc_start: 0.8946 (tp) cc_final: 0.8711 (tt) REVERT: H 74 MET cc_start: 0.9023 (mmm) cc_final: 0.8571 (mmm) REVERT: H 100 GLN cc_start: 0.8069 (mt0) cc_final: 0.7787 (mp10) REVERT: H 137 ASP cc_start: 0.7843 (t70) cc_final: 0.7397 (t0) REVERT: M 62 MET cc_start: 0.8493 (mtt) cc_final: 0.8116 (mtp) REVERT: M 156 ILE cc_start: 0.8701 (pt) cc_final: 0.8346 (tp) REVERT: N 26 GLU cc_start: 0.7472 (tt0) cc_final: 0.7064 (tt0) REVERT: O 11 THR cc_start: 0.8953 (t) cc_final: 0.8615 (p) REVERT: O 55 SER cc_start: 0.8139 (m) cc_final: 0.7857 (p) REVERT: O 90 ASP cc_start: 0.8069 (t0) cc_final: 0.7590 (t0) REVERT: O 118 THR cc_start: 0.9045 (m) cc_final: 0.8497 (p) REVERT: O 159 LYS cc_start: 0.9399 (mtmt) cc_final: 0.9123 (mtmm) REVERT: S 137 ASP cc_start: 0.8292 (t70) cc_final: 0.7521 (t0) REVERT: S 140 LEU cc_start: 0.9197 (mt) cc_final: 0.8903 (tp) REVERT: S 170 ASP cc_start: 0.8274 (m-30) cc_final: 0.7816 (t0) REVERT: T 50 MET cc_start: 0.8305 (ttp) cc_final: 0.7884 (ptt) REVERT: T 60 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8644 (mt) REVERT: T 71 GLU cc_start: 0.8153 (tp30) cc_final: 0.7885 (tt0) REVERT: T 130 CYS cc_start: 0.8324 (m) cc_final: 0.7762 (m) REVERT: U 7 ARG cc_start: 0.7435 (mtm110) cc_final: 0.6859 (ptt-90) REVERT: U 58 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7589 (ptmt) REVERT: U 90 ASP cc_start: 0.7678 (m-30) cc_final: 0.7113 (m-30) REVERT: U 187 LEU cc_start: 0.8412 (mt) cc_final: 0.8040 (tp) outliers start: 212 outliers final: 159 residues processed: 1244 average time/residue: 0.5950 time to fit residues: 1191.7601 Evaluate side-chains 1235 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1070 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 65 GLU Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 65 GLU Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain ID residue 35 GLU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 3 ASP Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 5 LEU Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 7 MET Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LC residue 69 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 135 SER Chi-restraints excluded: chain U residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 200 optimal weight: 0.8980 chunk 535 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 349 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 595 optimal weight: 2.9990 chunk 493 optimal weight: 0.7980 chunk 275 optimal weight: 0.4980 chunk 49 optimal weight: 0.0030 chunk 196 optimal weight: 0.7980 chunk 312 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS ** GC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 82 ASN LE 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 46860 Z= 0.194 Angle : 0.581 11.777 63645 Z= 0.296 Chirality : 0.043 0.204 7638 Planarity : 0.004 0.050 8340 Dihedral : 4.156 35.793 6783 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.50 % Allowed : 18.95 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.11), residues: 6183 helix: 0.06 (0.11), residues: 2512 sheet: 0.19 (0.14), residues: 1438 loop : -1.76 (0.14), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 39 HIS 0.005 0.001 HISID 74 PHE 0.022 0.002 PHE C 10 TYR 0.019 0.001 TYR C 8 ARG 0.011 0.000 ARGHA 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1147 time to evaluate : 5.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8463 (m100) cc_final: 0.8043 (m100) REVERT: A 115 ARG cc_start: 0.8406 (mmt180) cc_final: 0.8042 (mmt180) REVERT: A 128 ASN cc_start: 0.8768 (t0) cc_final: 0.8552 (t0) REVERT: A 156 ASN cc_start: 0.9043 (t0) cc_final: 0.8708 (t0) REVERT: A 168 ASN cc_start: 0.8841 (t0) cc_final: 0.8622 (t0) REVERT: B 8 TYR cc_start: 0.8424 (t80) cc_final: 0.8193 (t80) REVERT: B 128 ASN cc_start: 0.8628 (t0) cc_final: 0.8379 (t0) REVERT: B 188 ASP cc_start: 0.8563 (t0) cc_final: 0.8108 (t0) REVERT: C 128 ASN cc_start: 0.8718 (t0) cc_final: 0.8293 (t0) REVERT: C 187 ILE cc_start: 0.8890 (tp) cc_final: 0.8579 (tp) REVERT: E 109 MET cc_start: 0.8313 (mpm) cc_final: 0.7991 (mpm) REVERT: E 128 ASN cc_start: 0.8295 (t0) cc_final: 0.7920 (t0) REVERT: F 72 TYR cc_start: 0.8925 (m-80) cc_final: 0.8653 (m-80) REVERT: F 96 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8799 (mm) REVERT: F 105 LYS cc_start: 0.8812 (tptp) cc_final: 0.8187 (tptp) REVERT: F 133 MET cc_start: 0.8230 (mtm) cc_final: 0.7818 (mtp) REVERT: GA 16 MET cc_start: 0.9314 (tmm) cc_final: 0.8829 (tmm) REVERT: GA 34 TYR cc_start: 0.8721 (p90) cc_final: 0.8481 (p90) REVERT: GA 42 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8772 (p) REVERT: GA 43 THR cc_start: 0.9174 (m) cc_final: 0.8956 (p) REVERT: GB 7 MET cc_start: 0.8923 (ptp) cc_final: 0.8202 (ptp) REVERT: GB 21 ASP cc_start: 0.8870 (t70) cc_final: 0.8567 (t0) REVERT: GB 28 LYS cc_start: 0.8491 (tmmt) cc_final: 0.7422 (mttt) REVERT: GB 61 GLN cc_start: 0.8733 (tt0) cc_final: 0.8342 (tt0) REVERT: GC 28 LYS cc_start: 0.8606 (ttpp) cc_final: 0.7949 (mptt) REVERT: GC 43 THR cc_start: 0.9113 (m) cc_final: 0.8804 (p) REVERT: GD 16 MET cc_start: 0.8873 (tmm) cc_final: 0.8586 (tmm) REVERT: GD 62 ARG cc_start: 0.8965 (ttp-110) cc_final: 0.8539 (mtm110) REVERT: GF 9 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7910 (tm-30) REVERT: GF 18 GLU cc_start: 0.8906 (tp30) cc_final: 0.8476 (tp30) REVERT: GF 71 VAL cc_start: 0.9228 (t) cc_final: 0.8939 (t) REVERT: GF 92 THR cc_start: 0.8531 (m) cc_final: 0.8318 (p) REVERT: HA 18 GLU cc_start: 0.8596 (tp30) cc_final: 0.7974 (tm-30) REVERT: HA 61 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8103 (tp40) REVERT: HA 69 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7339 (tm-30) REVERT: HB 65 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7339 (mt-10) REVERT: HB 92 THR cc_start: 0.8745 (m) cc_final: 0.8265 (p) REVERT: HC 9 GLU cc_start: 0.7903 (tt0) cc_final: 0.7651 (tt0) REVERT: HC 21 ASP cc_start: 0.8751 (t70) cc_final: 0.8430 (t0) REVERT: HC 28 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7567 (mmtm) REVERT: HD 3 ASP cc_start: 0.8016 (m-30) cc_final: 0.7601 (m-30) REVERT: HD 78 ARG cc_start: 0.8722 (tmt90) cc_final: 0.7438 (ptp-170) REVERT: HE 10 VAL cc_start: 0.9062 (t) cc_final: 0.8794 (m) REVERT: HE 78 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7516 (ptt90) REVERT: HF 18 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7194 (tm-30) REVERT: HF 43 THR cc_start: 0.8633 (m) cc_final: 0.8295 (p) REVERT: HF 61 GLN cc_start: 0.8742 (tt0) cc_final: 0.8377 (tt0) REVERT: HF 65 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8317 (mp0) REVERT: HF 78 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8225 (ttm170) REVERT: IA 3 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7860 (t0) REVERT: IA 41 TYR cc_start: 0.8632 (m-10) cc_final: 0.8260 (m-80) REVERT: IA 42 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8623 (p) REVERT: IA 62 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.8046 (ttp-110) REVERT: IB 21 ASP cc_start: 0.8420 (t70) cc_final: 0.7919 (t0) REVERT: IB 58 GLU cc_start: 0.7091 (pt0) cc_final: 0.6864 (pt0) REVERT: IC 5 LEU cc_start: 0.8870 (tp) cc_final: 0.8420 (tp) REVERT: IC 16 MET cc_start: 0.8834 (tmm) cc_final: 0.8370 (tmm) REVERT: IC 18 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7848 (tm-30) REVERT: IC 47 ARG cc_start: 0.8910 (mmm160) cc_final: 0.7522 (mmm160) REVERT: ID 3 ASP cc_start: 0.8263 (m-30) cc_final: 0.7963 (m-30) REVERT: IF 9 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8409 (tm-30) REVERT: IF 11 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7945 (ttm-80) REVERT: IF 32 ILE cc_start: 0.8896 (pp) cc_final: 0.8551 (tp) REVERT: JA 16 MET cc_start: 0.8369 (tmm) cc_final: 0.7724 (tmm) REVERT: JA 32 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8184 (pp) REVERT: JA 65 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8232 (mm-30) REVERT: JE 16 MET cc_start: 0.8170 (tmm) cc_final: 0.7821 (tmm) REVERT: JE 43 THR cc_start: 0.9294 (m) cc_final: 0.9039 (m) REVERT: JE 61 GLN cc_start: 0.8990 (tt0) cc_final: 0.8478 (tt0) REVERT: JF 18 GLU cc_start: 0.8182 (tp30) cc_final: 0.7849 (tm-30) REVERT: JF 23 MET cc_start: 0.8546 (mtp) cc_final: 0.8309 (mmt) REVERT: JF 62 ARG cc_start: 0.8219 (tmm-80) cc_final: 0.7915 (ttm-80) REVERT: KA 9 GLU cc_start: 0.8048 (tp30) cc_final: 0.7561 (tp30) REVERT: KA 16 MET cc_start: 0.9105 (tmm) cc_final: 0.8484 (tmm) REVERT: KB 21 ASP cc_start: 0.8679 (t70) cc_final: 0.8352 (t0) REVERT: KB 28 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7502 (mttt) REVERT: KC 10 VAL cc_start: 0.8953 (t) cc_final: 0.8679 (m) REVERT: KC 18 GLU cc_start: 0.8920 (tp30) cc_final: 0.8637 (tp30) REVERT: KC 28 LYS cc_start: 0.8495 (ttpt) cc_final: 0.7874 (mptt) REVERT: KC 35 GLU cc_start: 0.7941 (mp0) cc_final: 0.7548 (mp0) REVERT: KC 43 THR cc_start: 0.9174 (m) cc_final: 0.8741 (p) REVERT: KD 23 MET cc_start: 0.8529 (mtm) cc_final: 0.8139 (mtp) REVERT: KD 30 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8153 (tm-30) REVERT: KD 78 ARG cc_start: 0.8441 (ttt90) cc_final: 0.7439 (mtm180) REVERT: KE 7 MET cc_start: 0.7602 (mtp) cc_final: 0.7384 (ptp) REVERT: KE 8 ILE cc_start: 0.9074 (mt) cc_final: 0.8790 (tt) REVERT: KE 11 ARG cc_start: 0.8614 (ttt180) cc_final: 0.8135 (ttt90) REVERT: KE 43 THR cc_start: 0.8642 (m) cc_final: 0.8429 (p) REVERT: KF 9 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8258 (tm-30) REVERT: KF 28 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7649 (ptpp) REVERT: KF 80 HIS cc_start: 0.7726 (t-90) cc_final: 0.7310 (t-90) REVERT: LA 61 GLN cc_start: 0.8446 (tt0) cc_final: 0.7798 (tp40) REVERT: LC 21 ASP cc_start: 0.8653 (t70) cc_final: 0.8357 (t0) REVERT: LD 18 GLU cc_start: 0.8795 (tp30) cc_final: 0.8289 (tp30) REVERT: LD 21 ASP cc_start: 0.8938 (m-30) cc_final: 0.8697 (m-30) REVERT: LD 28 LYS cc_start: 0.8302 (ttpp) cc_final: 0.7940 (tppt) REVERT: LD 30 GLU cc_start: 0.8307 (tt0) cc_final: 0.7897 (tt0) REVERT: LF 18 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7367 (tm-30) REVERT: LF 58 GLU cc_start: 0.7231 (pt0) cc_final: 0.6929 (tm-30) REVERT: H 74 MET cc_start: 0.8960 (mmm) cc_final: 0.8447 (mmm) REVERT: H 100 GLN cc_start: 0.8066 (mt0) cc_final: 0.7817 (mp10) REVERT: H 137 ASP cc_start: 0.7624 (t70) cc_final: 0.7247 (t0) REVERT: M 62 MET cc_start: 0.8487 (mtt) cc_final: 0.8166 (mtp) REVERT: M 156 ILE cc_start: 0.8617 (pt) cc_final: 0.8333 (tp) REVERT: O 11 THR cc_start: 0.8880 (t) cc_final: 0.8550 (p) REVERT: O 55 SER cc_start: 0.8124 (m) cc_final: 0.7818 (p) REVERT: O 90 ASP cc_start: 0.8038 (t0) cc_final: 0.7759 (t70) REVERT: O 118 THR cc_start: 0.8968 (m) cc_final: 0.8305 (p) REVERT: O 137 ASP cc_start: 0.8051 (t70) cc_final: 0.7764 (t70) REVERT: O 159 LYS cc_start: 0.9373 (mtmt) cc_final: 0.9153 (mtmm) REVERT: S 137 ASP cc_start: 0.8222 (t70) cc_final: 0.7471 (t0) REVERT: S 170 ASP cc_start: 0.8230 (m-30) cc_final: 0.7720 (t0) REVERT: T 50 MET cc_start: 0.8252 (ttp) cc_final: 0.7938 (ptt) REVERT: T 71 GLU cc_start: 0.8111 (tp30) cc_final: 0.7864 (tt0) REVERT: T 151 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7368 (mtp-110) REVERT: U 7 ARG cc_start: 0.7379 (mtm110) cc_final: 0.6942 (ptt-90) REVERT: U 58 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7544 (ptmt) REVERT: U 62 MET cc_start: 0.8900 (mtp) cc_final: 0.8323 (mtm) REVERT: U 90 ASP cc_start: 0.7757 (m-30) cc_final: 0.7236 (m-30) outliers start: 205 outliers final: 147 residues processed: 1270 average time/residue: 0.6379 time to fit residues: 1313.4440 Evaluate side-chains 1232 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1079 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JA residue 32 ILE Chi-restraints excluded: chain JB residue 71 VAL Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 8 ILE Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 5 LEU Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 69 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 135 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 573 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 339 optimal weight: 4.9990 chunk 434 optimal weight: 0.7980 chunk 336 optimal weight: 4.9990 chunk 500 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 592 optimal weight: 1.9990 chunk 370 optimal weight: 0.8980 chunk 361 optimal weight: 0.4980 chunk 273 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS JB 82 ASN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 46860 Z= 0.238 Angle : 0.600 11.596 63645 Z= 0.307 Chirality : 0.044 0.216 7638 Planarity : 0.004 0.059 8340 Dihedral : 4.153 40.136 6783 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.19 % Allowed : 19.98 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.11), residues: 6183 helix: 0.14 (0.11), residues: 2508 sheet: 0.17 (0.13), residues: 1460 loop : -1.68 (0.14), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 39 HIS 0.005 0.001 HISKF 74 PHE 0.024 0.002 PHE D 10 TYR 0.022 0.001 TYR C 8 ARG 0.011 0.000 ARGHA 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1077 time to evaluate : 5.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8467 (m100) cc_final: 0.8082 (m100) REVERT: A 75 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8257 (pp) REVERT: A 115 ARG cc_start: 0.8462 (mmt180) cc_final: 0.8059 (mmt180) REVERT: A 133 MET cc_start: 0.7902 (ttp) cc_final: 0.7620 (ttm) REVERT: A 156 ASN cc_start: 0.8951 (t0) cc_final: 0.8669 (t0) REVERT: A 168 ASN cc_start: 0.8866 (t0) cc_final: 0.8638 (t0) REVERT: B 128 ASN cc_start: 0.8552 (t0) cc_final: 0.8306 (t0) REVERT: B 188 ASP cc_start: 0.8581 (t0) cc_final: 0.8133 (t0) REVERT: C 39 TRP cc_start: 0.7592 (m100) cc_final: 0.7355 (m100) REVERT: C 115 ARG cc_start: 0.8138 (mmt-90) cc_final: 0.7366 (mmt180) REVERT: C 128 ASN cc_start: 0.8704 (t0) cc_final: 0.8240 (t0) REVERT: D 120 TYR cc_start: 0.8371 (m-80) cc_final: 0.7901 (m-80) REVERT: E 50 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8365 (ttm110) REVERT: E 109 MET cc_start: 0.8324 (mpm) cc_final: 0.8022 (mpm) REVERT: E 115 ARG cc_start: 0.8291 (mmt180) cc_final: 0.7417 (mmt-90) REVERT: E 128 ASN cc_start: 0.8294 (t0) cc_final: 0.7925 (t0) REVERT: F 72 TYR cc_start: 0.8961 (m-80) cc_final: 0.8608 (m-80) REVERT: F 96 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8898 (mm) REVERT: F 133 MET cc_start: 0.8259 (mtm) cc_final: 0.7818 (mtp) REVERT: GA 16 MET cc_start: 0.9305 (tmm) cc_final: 0.8861 (tmm) REVERT: GA 34 TYR cc_start: 0.8712 (p90) cc_final: 0.8483 (p90) REVERT: GA 42 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8844 (p) REVERT: GA 43 THR cc_start: 0.9216 (m) cc_final: 0.9004 (p) REVERT: GB 21 ASP cc_start: 0.9021 (t70) cc_final: 0.8656 (t0) REVERT: GB 28 LYS cc_start: 0.8465 (tmmt) cc_final: 0.7439 (mttt) REVERT: GB 61 GLN cc_start: 0.8757 (tt0) cc_final: 0.8356 (tt0) REVERT: GC 28 LYS cc_start: 0.8613 (ttpp) cc_final: 0.7949 (mptt) REVERT: GC 43 THR cc_start: 0.9094 (m) cc_final: 0.8824 (p) REVERT: GD 16 MET cc_start: 0.8870 (tmm) cc_final: 0.8622 (tmm) REVERT: GD 62 ARG cc_start: 0.8968 (ttp-110) cc_final: 0.8539 (mtm110) REVERT: GF 9 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8040 (tm-30) REVERT: GF 18 GLU cc_start: 0.8941 (tp30) cc_final: 0.8544 (tp30) REVERT: GF 92 THR cc_start: 0.8555 (m) cc_final: 0.8332 (p) REVERT: HA 18 GLU cc_start: 0.8669 (tp30) cc_final: 0.8002 (tm-30) REVERT: HA 61 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8091 (tp40) REVERT: HA 69 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7332 (tm-30) REVERT: HB 65 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7332 (mt-10) REVERT: HB 92 THR cc_start: 0.8759 (m) cc_final: 0.8278 (p) REVERT: HC 7 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: HC 21 ASP cc_start: 0.8674 (t70) cc_final: 0.8363 (t0) REVERT: HC 28 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7555 (mmtm) REVERT: HD 3 ASP cc_start: 0.8039 (m-30) cc_final: 0.7654 (m-30) REVERT: HE 78 ARG cc_start: 0.8208 (tpt170) cc_final: 0.7637 (ptt90) REVERT: HF 18 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7231 (tm-30) REVERT: HF 43 THR cc_start: 0.8626 (m) cc_final: 0.8273 (p) REVERT: HF 61 GLN cc_start: 0.8731 (tt0) cc_final: 0.8376 (tt0) REVERT: HF 65 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8361 (mp0) REVERT: IA 3 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7822 (t0) REVERT: IA 41 TYR cc_start: 0.8596 (m-10) cc_final: 0.8294 (m-80) REVERT: IA 62 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8033 (ttp-110) REVERT: IB 16 MET cc_start: 0.8546 (tmm) cc_final: 0.8332 (tmm) REVERT: IB 21 ASP cc_start: 0.8458 (t70) cc_final: 0.7968 (t0) REVERT: IB 58 GLU cc_start: 0.7129 (pt0) cc_final: 0.6907 (pt0) REVERT: IC 5 LEU cc_start: 0.8925 (tp) cc_final: 0.8418 (tp) REVERT: IC 16 MET cc_start: 0.8841 (tmm) cc_final: 0.8614 (tmm) REVERT: IC 18 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7846 (tm-30) REVERT: ID 16 MET cc_start: 0.8956 (tmm) cc_final: 0.8694 (tmm) REVERT: ID 58 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7869 (tm-30) REVERT: IE 7 MET cc_start: 0.8983 (mpp) cc_final: 0.8699 (mpp) REVERT: IF 9 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8358 (tm-30) REVERT: IF 11 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: IF 32 ILE cc_start: 0.8901 (pp) cc_final: 0.8572 (tp) REVERT: JA 16 MET cc_start: 0.8469 (tmm) cc_final: 0.7838 (tmm) REVERT: JA 65 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8273 (mm-30) REVERT: JB 18 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8047 (tm-30) REVERT: JB 62 ARG cc_start: 0.8548 (ttm110) cc_final: 0.8264 (mtp-110) REVERT: JE 16 MET cc_start: 0.8182 (tmm) cc_final: 0.7845 (tmm) REVERT: JE 23 MET cc_start: 0.7924 (mtm) cc_final: 0.7624 (mtm) REVERT: JE 43 THR cc_start: 0.9287 (m) cc_final: 0.9036 (m) REVERT: JE 61 GLN cc_start: 0.8941 (tt0) cc_final: 0.8663 (tt0) REVERT: JF 18 GLU cc_start: 0.8275 (tp30) cc_final: 0.7855 (tm-30) REVERT: JF 23 MET cc_start: 0.8623 (mtp) cc_final: 0.8359 (mmt) REVERT: JF 62 ARG cc_start: 0.8308 (tmm-80) cc_final: 0.7962 (ttm-80) REVERT: KA 9 GLU cc_start: 0.8085 (tp30) cc_final: 0.7597 (tp30) REVERT: KA 16 MET cc_start: 0.9193 (tmm) cc_final: 0.8578 (tmm) REVERT: KB 21 ASP cc_start: 0.8655 (t70) cc_final: 0.8307 (t0) REVERT: KB 28 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7528 (mttt) REVERT: KC 18 GLU cc_start: 0.8947 (tp30) cc_final: 0.8637 (tp30) REVERT: KC 28 LYS cc_start: 0.8475 (ttpt) cc_final: 0.7877 (mptt) REVERT: KC 35 GLU cc_start: 0.7967 (mp0) cc_final: 0.7525 (mp0) REVERT: KC 43 THR cc_start: 0.9227 (m) cc_final: 0.8796 (p) REVERT: KD 23 MET cc_start: 0.8536 (mtm) cc_final: 0.8094 (mtp) REVERT: KD 30 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8107 (tm-30) REVERT: KD 78 ARG cc_start: 0.8470 (ttt90) cc_final: 0.7443 (mtm180) REVERT: KE 8 ILE cc_start: 0.9115 (mt) cc_final: 0.8796 (tt) REVERT: KE 43 THR cc_start: 0.8689 (m) cc_final: 0.8457 (p) REVERT: KE 78 ARG cc_start: 0.8502 (tpt170) cc_final: 0.8183 (tpt90) REVERT: KF 28 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7733 (ptpp) REVERT: KF 80 HIS cc_start: 0.7881 (t-90) cc_final: 0.7419 (t-90) REVERT: LA 32 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7772 (pp) REVERT: LA 61 GLN cc_start: 0.8501 (tt0) cc_final: 0.7854 (tp40) REVERT: LC 21 ASP cc_start: 0.8640 (t70) cc_final: 0.8351 (t0) REVERT: LD 18 GLU cc_start: 0.8794 (tp30) cc_final: 0.8400 (tp30) REVERT: LD 21 ASP cc_start: 0.8989 (m-30) cc_final: 0.8774 (m-30) REVERT: LD 28 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7924 (tppt) REVERT: LD 30 GLU cc_start: 0.8339 (tt0) cc_final: 0.7938 (tt0) REVERT: LF 18 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7374 (tm-30) REVERT: LF 58 GLU cc_start: 0.7382 (pt0) cc_final: 0.6929 (tm-30) REVERT: G 63 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: H 74 MET cc_start: 0.8990 (mmm) cc_final: 0.8495 (mmm) REVERT: H 137 ASP cc_start: 0.7696 (t70) cc_final: 0.7316 (t0) REVERT: I 74 MET cc_start: 0.8921 (tpp) cc_final: 0.8558 (mmm) REVERT: M 62 MET cc_start: 0.8545 (mtt) cc_final: 0.8334 (mtm) REVERT: M 156 ILE cc_start: 0.8655 (pt) cc_final: 0.8385 (tp) REVERT: O 11 THR cc_start: 0.8859 (t) cc_final: 0.8541 (p) REVERT: O 55 SER cc_start: 0.8190 (m) cc_final: 0.7873 (p) REVERT: O 90 ASP cc_start: 0.8078 (t0) cc_final: 0.7658 (t0) REVERT: O 118 THR cc_start: 0.8998 (m) cc_final: 0.8423 (p) REVERT: O 137 ASP cc_start: 0.8045 (t70) cc_final: 0.7756 (t70) REVERT: O 159 LYS cc_start: 0.9407 (mtmt) cc_final: 0.9178 (mtmm) REVERT: S 49 LEU cc_start: 0.9075 (mt) cc_final: 0.8826 (tp) REVERT: S 137 ASP cc_start: 0.8314 (t70) cc_final: 0.7554 (t0) REVERT: S 170 ASP cc_start: 0.8248 (m-30) cc_final: 0.7734 (t0) REVERT: T 50 MET cc_start: 0.8170 (ttp) cc_final: 0.7799 (ptt) REVERT: T 71 GLU cc_start: 0.8134 (tp30) cc_final: 0.7908 (tt0) REVERT: U 7 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7060 (ptt-90) REVERT: U 90 ASP cc_start: 0.7736 (m-30) cc_final: 0.7180 (m-30) outliers start: 191 outliers final: 154 residues processed: 1199 average time/residue: 0.6073 time to fit residues: 1177.2609 Evaluate side-chains 1200 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1039 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 49 ASP Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HC residue 7 MET Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 43 THR Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain ID residue 61 GLN Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JB residue 71 VAL Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 8 ILE Chi-restraints excluded: chain KA residue 31 LEU Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 5 LEU Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 135 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 366 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 354 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 116 optimal weight: 0.0970 chunk 114 optimal weight: 0.7980 chunk 376 optimal weight: 1.9990 chunk 403 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 465 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 HIS ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 GLN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS HE 61 GLN JB 82 ASN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 46860 Z= 0.216 Angle : 0.605 11.142 63645 Z= 0.308 Chirality : 0.044 0.238 7638 Planarity : 0.004 0.055 8340 Dihedral : 4.108 38.305 6783 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.21 % Allowed : 20.61 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 6183 helix: 0.33 (0.11), residues: 2470 sheet: 0.24 (0.14), residues: 1450 loop : -1.69 (0.14), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 39 HIS 0.004 0.001 HIS I 98 PHE 0.025 0.002 PHE D 10 TYR 0.022 0.001 TYR A 8 ARG 0.012 0.000 ARGHA 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1084 time to evaluate : 4.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8427 (m100) cc_final: 0.8193 (m100) REVERT: A 75 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8272 (pp) REVERT: A 115 ARG cc_start: 0.8433 (mmt180) cc_final: 0.8031 (mmt180) REVERT: A 156 ASN cc_start: 0.8963 (t0) cc_final: 0.8679 (t0) REVERT: A 168 ASN cc_start: 0.8877 (t0) cc_final: 0.8657 (t0) REVERT: B 115 ARG cc_start: 0.8512 (mtp85) cc_final: 0.7896 (mtp85) REVERT: B 128 ASN cc_start: 0.8542 (t0) cc_final: 0.8299 (t0) REVERT: B 188 ASP cc_start: 0.8566 (t0) cc_final: 0.8118 (t0) REVERT: C 39 TRP cc_start: 0.7639 (m100) cc_final: 0.7369 (m100) REVERT: C 115 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7336 (mmt180) REVERT: C 128 ASN cc_start: 0.8695 (t0) cc_final: 0.8205 (t0) REVERT: D 8 TYR cc_start: 0.8934 (t80) cc_final: 0.8694 (t80) REVERT: E 50 ARG cc_start: 0.8662 (ttm110) cc_final: 0.8420 (ttm110) REVERT: E 109 MET cc_start: 0.8307 (mpm) cc_final: 0.8023 (mpm) REVERT: E 115 ARG cc_start: 0.7918 (mmt180) cc_final: 0.7603 (mmt-90) REVERT: E 128 ASN cc_start: 0.8266 (t0) cc_final: 0.7909 (t0) REVERT: F 39 TRP cc_start: 0.7770 (m100) cc_final: 0.7426 (m100) REVERT: F 72 TYR cc_start: 0.8949 (m-80) cc_final: 0.8651 (m-80) REVERT: F 133 MET cc_start: 0.8219 (mtm) cc_final: 0.7929 (mtp) REVERT: GA 16 MET cc_start: 0.9296 (tmm) cc_final: 0.8887 (tmm) REVERT: GA 34 TYR cc_start: 0.8692 (p90) cc_final: 0.8455 (p90) REVERT: GA 42 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8839 (p) REVERT: GA 43 THR cc_start: 0.9221 (m) cc_final: 0.8989 (p) REVERT: GB 7 MET cc_start: 0.8919 (ptp) cc_final: 0.8172 (ptp) REVERT: GB 16 MET cc_start: 0.8691 (tmm) cc_final: 0.8461 (tmm) REVERT: GB 21 ASP cc_start: 0.9025 (t70) cc_final: 0.8643 (t0) REVERT: GB 28 LYS cc_start: 0.8459 (tmmt) cc_final: 0.7481 (mttt) REVERT: GB 61 GLN cc_start: 0.8789 (tt0) cc_final: 0.8364 (tt0) REVERT: GC 28 LYS cc_start: 0.8606 (ttpp) cc_final: 0.7934 (mptt) REVERT: GC 43 THR cc_start: 0.9101 (m) cc_final: 0.8788 (p) REVERT: GD 13 PHE cc_start: 0.8589 (t80) cc_final: 0.8275 (t80) REVERT: GD 16 MET cc_start: 0.8873 (tmm) cc_final: 0.8597 (tmm) REVERT: GD 62 ARG cc_start: 0.8945 (ttp-110) cc_final: 0.8516 (mtm110) REVERT: GD 78 ARG cc_start: 0.8350 (tmt90) cc_final: 0.7447 (mtm180) REVERT: GE 16 MET cc_start: 0.8993 (tmm) cc_final: 0.8607 (tmt) REVERT: GF 18 GLU cc_start: 0.8907 (tp30) cc_final: 0.8469 (tp30) REVERT: GF 92 THR cc_start: 0.8556 (m) cc_final: 0.8356 (p) REVERT: HA 18 GLU cc_start: 0.8680 (tp30) cc_final: 0.8013 (tm-30) REVERT: HA 61 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8075 (tp40) REVERT: HA 69 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7309 (tm-30) REVERT: HB 92 THR cc_start: 0.8760 (m) cc_final: 0.8255 (p) REVERT: HC 9 GLU cc_start: 0.7973 (tt0) cc_final: 0.7531 (tp30) REVERT: HC 21 ASP cc_start: 0.8684 (t70) cc_final: 0.8359 (t0) REVERT: HC 28 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7542 (mmtm) REVERT: HD 3 ASP cc_start: 0.7995 (m-30) cc_final: 0.7614 (m-30) REVERT: HE 78 ARG cc_start: 0.8201 (tpt170) cc_final: 0.7652 (ptt90) REVERT: HF 18 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7283 (tm-30) REVERT: HF 61 GLN cc_start: 0.8713 (tt0) cc_final: 0.8366 (tt0) REVERT: HF 65 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8336 (mp0) REVERT: IA 3 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7825 (t0) REVERT: IA 42 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8672 (p) REVERT: IA 62 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8027 (ttp-110) REVERT: IB 16 MET cc_start: 0.8485 (tmm) cc_final: 0.8252 (tmm) REVERT: IB 21 ASP cc_start: 0.8451 (t70) cc_final: 0.7962 (t0) REVERT: IB 58 GLU cc_start: 0.7129 (pt0) cc_final: 0.6898 (pt0) REVERT: IC 5 LEU cc_start: 0.8944 (tp) cc_final: 0.8454 (tp) REVERT: IC 16 MET cc_start: 0.8841 (tmm) cc_final: 0.8377 (tmm) REVERT: IC 18 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7823 (tm-30) REVERT: ID 11 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8267 (ttt90) REVERT: ID 16 MET cc_start: 0.8973 (tmm) cc_final: 0.8700 (tmm) REVERT: ID 25 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8746 (mttp) REVERT: ID 58 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7894 (tm-30) REVERT: IF 9 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8355 (tm-30) REVERT: IF 32 ILE cc_start: 0.8881 (pp) cc_final: 0.8536 (tp) REVERT: JA 16 MET cc_start: 0.8500 (tmm) cc_final: 0.7855 (tmm) REVERT: JA 32 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8174 (pp) REVERT: JA 65 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8266 (mm-30) REVERT: JB 18 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8065 (tm-30) REVERT: JB 61 GLN cc_start: 0.8609 (tt0) cc_final: 0.8254 (mt0) REVERT: JB 62 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8261 (mtp-110) REVERT: JD 80 HIS cc_start: 0.8156 (t-90) cc_final: 0.7933 (t-170) REVERT: JE 16 MET cc_start: 0.8202 (tmm) cc_final: 0.7836 (tmm) REVERT: JE 23 MET cc_start: 0.7922 (mtm) cc_final: 0.7596 (mtm) REVERT: JE 61 GLN cc_start: 0.8923 (tt0) cc_final: 0.8668 (tt0) REVERT: JF 18 GLU cc_start: 0.8301 (tp30) cc_final: 0.7899 (tm-30) REVERT: JF 23 MET cc_start: 0.8626 (mtp) cc_final: 0.8364 (mmt) REVERT: JF 62 ARG cc_start: 0.8221 (tmm-80) cc_final: 0.7726 (ttm-80) REVERT: JF 65 GLU cc_start: 0.8547 (mp0) cc_final: 0.8128 (mp0) REVERT: KA 9 GLU cc_start: 0.8134 (tp30) cc_final: 0.7685 (tp30) REVERT: KA 16 MET cc_start: 0.9121 (tmm) cc_final: 0.8493 (tmm) REVERT: KA 76 ILE cc_start: 0.9094 (mt) cc_final: 0.8866 (mm) REVERT: KB 21 ASP cc_start: 0.8653 (t70) cc_final: 0.8295 (t0) REVERT: KB 28 LYS cc_start: 0.7905 (ttpt) cc_final: 0.7513 (mttt) REVERT: KC 18 GLU cc_start: 0.8921 (tp30) cc_final: 0.8651 (tp30) REVERT: KC 28 LYS cc_start: 0.8470 (ttpt) cc_final: 0.7863 (mptt) REVERT: KC 35 GLU cc_start: 0.8055 (mp0) cc_final: 0.7521 (mp0) REVERT: KC 43 THR cc_start: 0.9245 (m) cc_final: 0.8796 (p) REVERT: KD 23 MET cc_start: 0.8475 (mtm) cc_final: 0.8026 (mtp) REVERT: KD 30 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8062 (tm-30) REVERT: KD 78 ARG cc_start: 0.8478 (ttt90) cc_final: 0.7468 (mtm180) REVERT: KE 8 ILE cc_start: 0.9121 (mt) cc_final: 0.8902 (tt) REVERT: KE 43 THR cc_start: 0.8654 (m) cc_final: 0.8444 (p) REVERT: KE 78 ARG cc_start: 0.8492 (tpt170) cc_final: 0.7690 (ttp80) REVERT: KF 28 LYS cc_start: 0.8343 (ttpp) cc_final: 0.7789 (ptpp) REVERT: KF 80 HIS cc_start: 0.7940 (t-90) cc_final: 0.7451 (t-90) REVERT: LA 32 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7755 (pp) REVERT: LA 61 GLN cc_start: 0.8434 (tt0) cc_final: 0.7837 (tp40) REVERT: LC 21 ASP cc_start: 0.8653 (t70) cc_final: 0.8377 (t0) REVERT: LD 28 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7886 (tppt) REVERT: LD 30 GLU cc_start: 0.8354 (tt0) cc_final: 0.7884 (tt0) REVERT: LF 18 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7353 (tm-30) REVERT: LF 58 GLU cc_start: 0.7364 (pt0) cc_final: 0.6929 (tm-30) REVERT: H 74 MET cc_start: 0.8997 (mmm) cc_final: 0.8497 (mmm) REVERT: I 74 MET cc_start: 0.8927 (tpp) cc_final: 0.8595 (mmm) REVERT: M 62 MET cc_start: 0.8569 (mtt) cc_final: 0.8214 (mmm) REVERT: M 156 ILE cc_start: 0.8650 (pt) cc_final: 0.8374 (tp) REVERT: N 26 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: O 11 THR cc_start: 0.8907 (t) cc_final: 0.8587 (p) REVERT: O 55 SER cc_start: 0.8220 (m) cc_final: 0.7869 (p) REVERT: O 90 ASP cc_start: 0.8091 (t0) cc_final: 0.7639 (t0) REVERT: O 118 THR cc_start: 0.8812 (m) cc_final: 0.8141 (p) REVERT: O 159 LYS cc_start: 0.9389 (mtmt) cc_final: 0.9187 (mtmm) REVERT: S 49 LEU cc_start: 0.9038 (mt) cc_final: 0.8745 (tp) REVERT: S 50 MET cc_start: 0.8572 (ttp) cc_final: 0.8214 (ptm) REVERT: S 137 ASP cc_start: 0.8336 (t70) cc_final: 0.7585 (t0) REVERT: S 170 ASP cc_start: 0.8241 (m-30) cc_final: 0.7713 (t0) REVERT: T 50 MET cc_start: 0.8109 (ttp) cc_final: 0.7841 (ptt) REVERT: T 71 GLU cc_start: 0.8138 (tp30) cc_final: 0.7905 (tt0) REVERT: U 7 ARG cc_start: 0.7279 (mtm110) cc_final: 0.7059 (ptt-90) REVERT: U 90 ASP cc_start: 0.7744 (m-30) cc_final: 0.7196 (m-30) outliers start: 192 outliers final: 158 residues processed: 1205 average time/residue: 0.5996 time to fit residues: 1163.7273 Evaluate side-chains 1212 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1047 time to evaluate : 5.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 49 ASP Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GC residue 82 ASN Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 25 LYS Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain HA residue 17 VAL Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain HA residue 84 ASP Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JA residue 32 ILE Chi-restraints excluded: chain JB residue 7 MET Chi-restraints excluded: chain JB residue 71 VAL Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 8 ILE Chi-restraints excluded: chain KA residue 31 LEU Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 3 ASP Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 135 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 539 optimal weight: 5.9990 chunk 567 optimal weight: 3.9990 chunk 518 optimal weight: 0.9980 chunk 552 optimal weight: 0.3980 chunk 332 optimal weight: 0.6980 chunk 240 optimal weight: 0.9980 chunk 433 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 499 optimal weight: 0.0670 chunk 522 optimal weight: 0.8980 chunk 550 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 165 HIS ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS IF 82 ASN LE 82 ASN LF 61 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 46860 Z= 0.209 Angle : 0.615 10.900 63645 Z= 0.313 Chirality : 0.044 0.293 7638 Planarity : 0.004 0.053 8340 Dihedral : 4.096 37.755 6783 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.97 % Allowed : 20.94 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 6183 helix: 0.34 (0.11), residues: 2496 sheet: 0.27 (0.13), residues: 1454 loop : -1.85 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 39 HIS 0.005 0.001 HIS E 111 PHE 0.024 0.002 PHE D 10 TYR 0.024 0.001 TYR C 8 ARG 0.012 0.000 ARGHA 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1073 time to evaluate : 5.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8418 (m100) cc_final: 0.8191 (m100) REVERT: A 75 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 115 ARG cc_start: 0.8392 (mmt180) cc_final: 0.7990 (mmt180) REVERT: A 156 ASN cc_start: 0.8963 (t0) cc_final: 0.8737 (t0) REVERT: B 115 ARG cc_start: 0.8507 (mtp85) cc_final: 0.7878 (mtp85) REVERT: B 128 ASN cc_start: 0.8534 (t0) cc_final: 0.8230 (t0) REVERT: B 168 ASN cc_start: 0.9033 (t0) cc_final: 0.8589 (t0) REVERT: B 188 ASP cc_start: 0.8546 (t0) cc_final: 0.8079 (t0) REVERT: C 39 TRP cc_start: 0.7630 (m100) cc_final: 0.7359 (m100) REVERT: C 115 ARG cc_start: 0.8149 (mmt-90) cc_final: 0.7336 (mmt180) REVERT: C 128 ASN cc_start: 0.8711 (t0) cc_final: 0.8218 (t0) REVERT: D 8 TYR cc_start: 0.8948 (t80) cc_final: 0.8698 (t80) REVERT: E 128 ASN cc_start: 0.8216 (t0) cc_final: 0.7907 (t0) REVERT: F 39 TRP cc_start: 0.7856 (m100) cc_final: 0.7479 (m100) REVERT: F 72 TYR cc_start: 0.8957 (m-80) cc_final: 0.8663 (m-80) REVERT: F 128 ASN cc_start: 0.8860 (p0) cc_final: 0.8625 (p0) REVERT: F 184 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7528 (tm-30) REVERT: F 188 ASP cc_start: 0.8447 (m-30) cc_final: 0.7980 (m-30) REVERT: GA 16 MET cc_start: 0.9265 (tmm) cc_final: 0.8825 (tmm) REVERT: GA 34 TYR cc_start: 0.8672 (p90) cc_final: 0.8435 (p90) REVERT: GA 42 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8891 (p) REVERT: GA 43 THR cc_start: 0.9236 (m) cc_final: 0.8978 (p) REVERT: GB 7 MET cc_start: 0.8902 (ptp) cc_final: 0.8226 (ptp) REVERT: GB 21 ASP cc_start: 0.8943 (t70) cc_final: 0.8537 (t0) REVERT: GB 28 LYS cc_start: 0.8454 (tmmt) cc_final: 0.7468 (mttt) REVERT: GB 61 GLN cc_start: 0.8770 (tt0) cc_final: 0.8362 (tt0) REVERT: GC 43 THR cc_start: 0.9091 (m) cc_final: 0.8738 (p) REVERT: GD 13 PHE cc_start: 0.8546 (t80) cc_final: 0.8246 (t80) REVERT: GD 16 MET cc_start: 0.8858 (tmm) cc_final: 0.8593 (tmm) REVERT: GD 62 ARG cc_start: 0.8939 (ttp-110) cc_final: 0.8525 (mtm110) REVERT: GD 78 ARG cc_start: 0.8341 (tmt90) cc_final: 0.7443 (mtm180) REVERT: GE 16 MET cc_start: 0.8987 (tmm) cc_final: 0.8592 (tmm) REVERT: GF 18 GLU cc_start: 0.8878 (tp30) cc_final: 0.8514 (tp30) REVERT: GF 92 THR cc_start: 0.8600 (m) cc_final: 0.8382 (p) REVERT: HA 18 GLU cc_start: 0.8656 (tp30) cc_final: 0.7992 (tm-30) REVERT: HA 30 GLU cc_start: 0.8194 (tt0) cc_final: 0.7984 (tt0) REVERT: HA 61 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8055 (tp40) REVERT: HA 69 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7338 (tm-30) REVERT: HB 65 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7385 (mt-10) REVERT: HB 92 THR cc_start: 0.8717 (m) cc_final: 0.8204 (p) REVERT: HC 9 GLU cc_start: 0.7934 (tt0) cc_final: 0.7711 (tt0) REVERT: HC 21 ASP cc_start: 0.8669 (t70) cc_final: 0.8330 (t0) REVERT: HC 28 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7546 (mmtm) REVERT: HC 65 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8251 (mm-30) REVERT: HD 3 ASP cc_start: 0.8022 (m-30) cc_final: 0.7596 (m-30) REVERT: HD 78 ARG cc_start: 0.8558 (tmt90) cc_final: 0.7447 (ptp-170) REVERT: HE 78 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7654 (ptt90) REVERT: HF 18 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7175 (tm-30) REVERT: HF 61 GLN cc_start: 0.8699 (tt0) cc_final: 0.8388 (tt0) REVERT: HF 65 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8289 (mp0) REVERT: HF 69 GLU cc_start: 0.8132 (pm20) cc_final: 0.7891 (pm20) REVERT: IA 3 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7805 (t0) REVERT: IA 41 TYR cc_start: 0.8669 (m-80) cc_final: 0.8189 (m-80) REVERT: IA 42 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8715 (p) REVERT: IB 16 MET cc_start: 0.8482 (tmm) cc_final: 0.8262 (tmm) REVERT: IB 21 ASP cc_start: 0.8443 (t70) cc_final: 0.7965 (t0) REVERT: IB 58 GLU cc_start: 0.7115 (pt0) cc_final: 0.6892 (pt0) REVERT: IC 5 LEU cc_start: 0.8936 (tp) cc_final: 0.8440 (tp) REVERT: IC 16 MET cc_start: 0.8841 (tmm) cc_final: 0.8377 (tmm) REVERT: IC 18 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7823 (tm-30) REVERT: ID 11 ARG cc_start: 0.8605 (mtp180) cc_final: 0.8248 (ttt90) REVERT: ID 16 MET cc_start: 0.8970 (tmm) cc_final: 0.8696 (tmm) REVERT: ID 25 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8668 (mttp) REVERT: IF 9 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8361 (tm-30) REVERT: IF 32 ILE cc_start: 0.8857 (pp) cc_final: 0.8512 (tp) REVERT: JA 16 MET cc_start: 0.8486 (tmm) cc_final: 0.7860 (tmm) REVERT: JA 32 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8192 (pp) REVERT: JA 35 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6271 (mp0) REVERT: JA 65 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8307 (mm-30) REVERT: JB 18 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8005 (tm-30) REVERT: JB 61 GLN cc_start: 0.8615 (tt0) cc_final: 0.8273 (mt0) REVERT: JB 62 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8267 (mtp-110) REVERT: JD 80 HIS cc_start: 0.8143 (t-90) cc_final: 0.7922 (t-170) REVERT: JE 16 MET cc_start: 0.8193 (tmm) cc_final: 0.7836 (tmm) REVERT: JE 23 MET cc_start: 0.7866 (mtm) cc_final: 0.7501 (mtm) REVERT: JE 43 THR cc_start: 0.9270 (m) cc_final: 0.9016 (m) REVERT: JE 61 GLN cc_start: 0.8851 (tt0) cc_final: 0.8630 (tt0) REVERT: JF 18 GLU cc_start: 0.8294 (tp30) cc_final: 0.7929 (tm-30) REVERT: JF 23 MET cc_start: 0.8633 (mtp) cc_final: 0.8375 (mmt) REVERT: JF 62 ARG cc_start: 0.8247 (tmm-80) cc_final: 0.7739 (ttm-80) REVERT: JF 65 GLU cc_start: 0.8586 (mp0) cc_final: 0.8192 (mp0) REVERT: KA 9 GLU cc_start: 0.8067 (tp30) cc_final: 0.7683 (tp30) REVERT: KA 16 MET cc_start: 0.9149 (tmm) cc_final: 0.8504 (tmm) REVERT: KB 21 ASP cc_start: 0.8606 (t70) cc_final: 0.8263 (t0) REVERT: KB 28 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7625 (mttt) REVERT: KC 18 GLU cc_start: 0.8893 (tp30) cc_final: 0.8640 (tp30) REVERT: KC 28 LYS cc_start: 0.8461 (ttpt) cc_final: 0.7852 (mptt) REVERT: KC 35 GLU cc_start: 0.8072 (mp0) cc_final: 0.7498 (mp0) REVERT: KC 43 THR cc_start: 0.9221 (m) cc_final: 0.8792 (p) REVERT: KD 23 MET cc_start: 0.8361 (mtm) cc_final: 0.8017 (mtp) REVERT: KD 30 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8044 (tm-30) REVERT: KD 78 ARG cc_start: 0.8424 (ttt90) cc_final: 0.7404 (mtm180) REVERT: KE 8 ILE cc_start: 0.9077 (mt) cc_final: 0.8755 (tt) REVERT: KE 11 ARG cc_start: 0.8557 (ttt180) cc_final: 0.8109 (ttt90) REVERT: KE 43 THR cc_start: 0.8709 (m) cc_final: 0.8431 (p) REVERT: KE 78 ARG cc_start: 0.8567 (tpt170) cc_final: 0.7861 (ttp80) REVERT: KF 28 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7788 (ptpp) REVERT: KF 80 HIS cc_start: 0.7929 (t-90) cc_final: 0.7452 (t-90) REVERT: LA 32 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7729 (pp) REVERT: LA 61 GLN cc_start: 0.8438 (tt0) cc_final: 0.8022 (pt0) REVERT: LC 21 ASP cc_start: 0.8642 (t70) cc_final: 0.8362 (t0) REVERT: LD 18 GLU cc_start: 0.8728 (tp30) cc_final: 0.8363 (tp30) REVERT: LD 21 ASP cc_start: 0.8698 (m-30) cc_final: 0.8425 (m-30) REVERT: LD 28 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7873 (tppt) REVERT: LD 30 GLU cc_start: 0.8352 (tt0) cc_final: 0.7889 (tt0) REVERT: LE 43 THR cc_start: 0.8993 (m) cc_final: 0.8632 (p) REVERT: LF 18 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7341 (tm-30) REVERT: LF 58 GLU cc_start: 0.7330 (pt0) cc_final: 0.6916 (tm-30) REVERT: H 74 MET cc_start: 0.8941 (mmm) cc_final: 0.8451 (mmm) REVERT: H 100 GLN cc_start: 0.8176 (mt0) cc_final: 0.7849 (mp10) REVERT: H 137 ASP cc_start: 0.8103 (t70) cc_final: 0.7766 (t0) REVERT: I 74 MET cc_start: 0.8951 (tpp) cc_final: 0.8621 (mmm) REVERT: M 62 MET cc_start: 0.8583 (mtt) cc_final: 0.8266 (mmm) REVERT: M 156 ILE cc_start: 0.8642 (pt) cc_final: 0.8389 (tp) REVERT: N 202 ARG cc_start: 0.7480 (ttp80) cc_final: 0.6742 (ttp80) REVERT: O 55 SER cc_start: 0.8243 (m) cc_final: 0.7898 (p) REVERT: O 90 ASP cc_start: 0.8056 (t0) cc_final: 0.7594 (t0) REVERT: O 118 THR cc_start: 0.8780 (m) cc_final: 0.8082 (p) REVERT: O 137 ASP cc_start: 0.8176 (t70) cc_final: 0.7588 (t70) REVERT: S 49 LEU cc_start: 0.8994 (mt) cc_final: 0.8758 (tp) REVERT: S 137 ASP cc_start: 0.8315 (t70) cc_final: 0.7574 (t0) REVERT: S 170 ASP cc_start: 0.8237 (m-30) cc_final: 0.7706 (t0) REVERT: T 50 MET cc_start: 0.8194 (ttp) cc_final: 0.7889 (ptt) REVERT: T 71 GLU cc_start: 0.8141 (tp30) cc_final: 0.7911 (tt0) REVERT: U 90 ASP cc_start: 0.7749 (m-30) cc_final: 0.7263 (m-30) outliers start: 181 outliers final: 151 residues processed: 1184 average time/residue: 0.6202 time to fit residues: 1180.3884 Evaluate side-chains 1187 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1030 time to evaluate : 5.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 49 ASP Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GC residue 82 ASN Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 25 LYS Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain HA residue 17 VAL Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JA residue 32 ILE Chi-restraints excluded: chain JB residue 7 MET Chi-restraints excluded: chain JB residue 71 VAL Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 7 MET Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 3 ASP Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 362 optimal weight: 0.0050 chunk 584 optimal weight: 0.9980 chunk 356 optimal weight: 0.6980 chunk 277 optimal weight: 0.7980 chunk 406 optimal weight: 1.9990 chunk 612 optimal weight: 0.7980 chunk 563 optimal weight: 2.9990 chunk 487 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 376 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 HIS ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HD 80 HIS JB 82 ASN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 46860 Z= 0.222 Angle : 0.629 11.733 63645 Z= 0.321 Chirality : 0.044 0.453 7638 Planarity : 0.004 0.055 8340 Dihedral : 4.135 37.762 6783 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.88 % Allowed : 21.18 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 6183 helix: 0.34 (0.11), residues: 2500 sheet: 0.21 (0.13), residues: 1465 loop : -1.84 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 39 HIS 0.004 0.001 HISID 74 PHE 0.026 0.002 PHE D 10 TYR 0.025 0.001 TYR A 8 ARG 0.013 0.000 ARGHA 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1050 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8398 (m100) cc_final: 0.8193 (m100) REVERT: A 75 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8308 (pp) REVERT: A 115 ARG cc_start: 0.8361 (mmt180) cc_final: 0.7959 (mmt180) REVERT: A 156 ASN cc_start: 0.9085 (t0) cc_final: 0.8668 (t0) REVERT: A 159 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7413 (mt-10) REVERT: B 115 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7832 (mtp85) REVERT: B 128 ASN cc_start: 0.8516 (t0) cc_final: 0.8209 (t0) REVERT: B 168 ASN cc_start: 0.9040 (t0) cc_final: 0.8582 (t0) REVERT: B 188 ASP cc_start: 0.8551 (t0) cc_final: 0.8077 (t0) REVERT: C 39 TRP cc_start: 0.7627 (m100) cc_final: 0.7376 (m100) REVERT: C 115 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7383 (mmt180) REVERT: C 128 ASN cc_start: 0.8730 (t0) cc_final: 0.8222 (t0) REVERT: D 8 TYR cc_start: 0.8961 (t80) cc_final: 0.8715 (t80) REVERT: E 50 ARG cc_start: 0.8529 (ttm110) cc_final: 0.8317 (ttm110) REVERT: E 128 ASN cc_start: 0.8219 (t0) cc_final: 0.7912 (t0) REVERT: F 72 TYR cc_start: 0.8942 (m-80) cc_final: 0.8644 (m-80) REVERT: F 128 ASN cc_start: 0.8842 (p0) cc_final: 0.8589 (p0) REVERT: F 132 MET cc_start: 0.7712 (mmm) cc_final: 0.7458 (mmm) REVERT: F 184 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7523 (tm-30) REVERT: F 188 ASP cc_start: 0.8471 (m-30) cc_final: 0.7970 (m-30) REVERT: GA 16 MET cc_start: 0.9259 (tmm) cc_final: 0.8806 (tmm) REVERT: GA 18 GLU cc_start: 0.8744 (tp30) cc_final: 0.8501 (tp30) REVERT: GA 34 TYR cc_start: 0.8661 (p90) cc_final: 0.8427 (p90) REVERT: GA 42 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8901 (p) REVERT: GA 43 THR cc_start: 0.9255 (m) cc_final: 0.9008 (p) REVERT: GB 7 MET cc_start: 0.8873 (ptp) cc_final: 0.8141 (ptp) REVERT: GB 21 ASP cc_start: 0.8914 (t70) cc_final: 0.8489 (t0) REVERT: GB 28 LYS cc_start: 0.8473 (tmmt) cc_final: 0.7508 (mttt) REVERT: GB 61 GLN cc_start: 0.8761 (tt0) cc_final: 0.8326 (tt0) REVERT: GC 43 THR cc_start: 0.8952 (m) cc_final: 0.8530 (p) REVERT: GD 13 PHE cc_start: 0.8538 (t80) cc_final: 0.8267 (t80) REVERT: GD 16 MET cc_start: 0.8854 (tmm) cc_final: 0.8557 (tmm) REVERT: GD 62 ARG cc_start: 0.8939 (ttp-110) cc_final: 0.8512 (mtm110) REVERT: GD 78 ARG cc_start: 0.8349 (tmt90) cc_final: 0.7456 (mtm180) REVERT: GF 18 GLU cc_start: 0.8880 (tp30) cc_final: 0.8494 (tp30) REVERT: HA 7 MET cc_start: 0.8377 (mtp) cc_final: 0.8156 (mtp) REVERT: HA 18 GLU cc_start: 0.8645 (tp30) cc_final: 0.7949 (tm-30) REVERT: HA 58 GLU cc_start: 0.8236 (pm20) cc_final: 0.7571 (pm20) REVERT: HA 61 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8126 (tp40) REVERT: HB 65 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7359 (mt-10) REVERT: HB 92 THR cc_start: 0.8759 (m) cc_final: 0.8307 (p) REVERT: HC 21 ASP cc_start: 0.8642 (t70) cc_final: 0.8323 (t0) REVERT: HC 28 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7550 (mmtm) REVERT: HD 3 ASP cc_start: 0.7968 (m-30) cc_final: 0.7582 (m-30) REVERT: HD 78 ARG cc_start: 0.8570 (tmt90) cc_final: 0.7456 (ptp-170) REVERT: HE 61 GLN cc_start: 0.8851 (tt0) cc_final: 0.8568 (tt0) REVERT: HE 78 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7661 (ptt90) REVERT: HF 18 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7161 (tm-30) REVERT: HF 61 GLN cc_start: 0.8690 (tt0) cc_final: 0.8357 (tt0) REVERT: HF 65 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8273 (mp0) REVERT: IA 3 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7784 (t0) REVERT: IA 41 TYR cc_start: 0.8612 (m-80) cc_final: 0.8177 (m-80) REVERT: IA 42 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8722 (p) REVERT: IB 16 MET cc_start: 0.8473 (tmm) cc_final: 0.8250 (tmm) REVERT: IB 21 ASP cc_start: 0.8438 (t70) cc_final: 0.7964 (t0) REVERT: IB 58 GLU cc_start: 0.7102 (pt0) cc_final: 0.6889 (pt0) REVERT: IC 5 LEU cc_start: 0.8965 (tp) cc_final: 0.8459 (tp) REVERT: IC 16 MET cc_start: 0.8842 (tmm) cc_final: 0.8614 (tmm) REVERT: IC 18 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7826 (tm-30) REVERT: ID 16 MET cc_start: 0.8990 (tmm) cc_final: 0.8707 (tmm) REVERT: ID 25 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8639 (mttp) REVERT: IF 9 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8413 (tm-30) REVERT: IF 32 ILE cc_start: 0.8878 (pp) cc_final: 0.8540 (tp) REVERT: JA 16 MET cc_start: 0.8491 (tmm) cc_final: 0.7849 (tmm) REVERT: JA 35 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6308 (mp0) REVERT: JA 65 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8303 (mm-30) REVERT: JB 35 GLU cc_start: 0.8250 (tp30) cc_final: 0.7740 (mm-30) REVERT: JB 61 GLN cc_start: 0.8615 (tt0) cc_final: 0.8262 (mt0) REVERT: JB 62 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8250 (mtp-110) REVERT: JC 7 MET cc_start: 0.8959 (ptm) cc_final: 0.8726 (ptm) REVERT: JE 16 MET cc_start: 0.8179 (tmm) cc_final: 0.7815 (tmm) REVERT: JE 23 MET cc_start: 0.7883 (mtm) cc_final: 0.7505 (mtm) REVERT: JE 61 GLN cc_start: 0.8889 (tt0) cc_final: 0.8659 (tt0) REVERT: JF 18 GLU cc_start: 0.8280 (tp30) cc_final: 0.8041 (tm-30) REVERT: JF 23 MET cc_start: 0.8617 (mtp) cc_final: 0.8348 (mmt) REVERT: JF 62 ARG cc_start: 0.8245 (tmm-80) cc_final: 0.7728 (ttm-80) REVERT: JF 65 GLU cc_start: 0.8591 (mp0) cc_final: 0.8196 (mp0) REVERT: KA 16 MET cc_start: 0.9131 (tmm) cc_final: 0.8463 (tmm) REVERT: KB 21 ASP cc_start: 0.8638 (t70) cc_final: 0.8322 (t0) REVERT: KB 28 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7612 (mttt) REVERT: KC 18 GLU cc_start: 0.8939 (tp30) cc_final: 0.8697 (tp30) REVERT: KC 28 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7862 (mptt) REVERT: KC 35 GLU cc_start: 0.8063 (mp0) cc_final: 0.7494 (mp0) REVERT: KC 43 THR cc_start: 0.9210 (m) cc_final: 0.8789 (p) REVERT: KD 23 MET cc_start: 0.8322 (mtm) cc_final: 0.7993 (mtp) REVERT: KD 30 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8025 (tm-30) REVERT: KD 78 ARG cc_start: 0.8427 (ttt90) cc_final: 0.7406 (mtm180) REVERT: KE 8 ILE cc_start: 0.9169 (mt) cc_final: 0.8939 (tt) REVERT: KE 78 ARG cc_start: 0.8575 (tpt170) cc_final: 0.7850 (ttp80) REVERT: KF 28 LYS cc_start: 0.8340 (ttpp) cc_final: 0.7842 (ptpp) REVERT: KF 80 HIS cc_start: 0.7989 (t-90) cc_final: 0.7491 (t-90) REVERT: LA 32 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7741 (pp) REVERT: LA 61 GLN cc_start: 0.8422 (tt0) cc_final: 0.7991 (pt0) REVERT: LC 21 ASP cc_start: 0.8661 (t70) cc_final: 0.8374 (t0) REVERT: LD 18 GLU cc_start: 0.8714 (tp30) cc_final: 0.8241 (tp30) REVERT: LD 21 ASP cc_start: 0.8685 (m-30) cc_final: 0.8469 (m-30) REVERT: LD 28 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7878 (tppt) REVERT: LD 30 GLU cc_start: 0.8341 (tt0) cc_final: 0.7882 (tt0) REVERT: LF 18 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7336 (tm-30) REVERT: LF 58 GLU cc_start: 0.7388 (pt0) cc_final: 0.6914 (tm-30) REVERT: LF 65 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8397 (mp0) REVERT: H 74 MET cc_start: 0.8931 (mmm) cc_final: 0.8457 (mmm) REVERT: I 74 MET cc_start: 0.8948 (tpp) cc_final: 0.8632 (mmm) REVERT: M 62 MET cc_start: 0.8594 (mtt) cc_final: 0.8291 (mmm) REVERT: M 156 ILE cc_start: 0.8652 (pt) cc_final: 0.8428 (tp) REVERT: N 202 ARG cc_start: 0.7494 (ttp80) cc_final: 0.6735 (ttp80) REVERT: O 11 THR cc_start: 0.8883 (t) cc_final: 0.8548 (p) REVERT: O 55 SER cc_start: 0.8264 (m) cc_final: 0.7912 (p) REVERT: O 90 ASP cc_start: 0.8024 (t0) cc_final: 0.7686 (t70) REVERT: O 118 THR cc_start: 0.8791 (m) cc_final: 0.8208 (p) REVERT: O 137 ASP cc_start: 0.8171 (t70) cc_final: 0.7663 (t70) REVERT: S 137 ASP cc_start: 0.8324 (t70) cc_final: 0.7587 (t0) REVERT: S 170 ASP cc_start: 0.8273 (m-30) cc_final: 0.7767 (t0) REVERT: T 50 MET cc_start: 0.8186 (ttp) cc_final: 0.7882 (ptt) REVERT: T 71 GLU cc_start: 0.8147 (tp30) cc_final: 0.7914 (tt0) REVERT: U 50 MET cc_start: 0.8387 (ptt) cc_final: 0.8111 (ppp) REVERT: U 90 ASP cc_start: 0.7747 (m-30) cc_final: 0.7269 (m-30) outliers start: 177 outliers final: 157 residues processed: 1161 average time/residue: 0.6201 time to fit residues: 1157.6431 Evaluate side-chains 1192 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1030 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 49 ASP Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GC residue 82 ASN Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 25 LYS Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain HA residue 17 VAL Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JB residue 7 MET Chi-restraints excluded: chain JB residue 71 VAL Chi-restraints excluded: chain JB residue 82 ASN Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain JF residue 92 THR Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 7 MET Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 3 ASP Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 130 CYS Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 387 optimal weight: 4.9990 chunk 519 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 449 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 135 optimal weight: 0.7980 chunk 488 optimal weight: 0.5980 chunk 204 optimal weight: 0.0370 chunk 501 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 168 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085127 restraints weight = 112050.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.087339 restraints weight = 57326.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088813 restraints weight = 34314.575| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 46860 Z= 0.309 Angle : 0.785 59.199 63645 Z= 0.438 Chirality : 0.053 1.974 7638 Planarity : 0.005 0.206 8340 Dihedral : 4.193 42.740 6783 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.90 % Allowed : 21.60 % Favored : 74.50 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.11), residues: 6183 helix: 0.31 (0.11), residues: 2515 sheet: 0.21 (0.13), residues: 1465 loop : -1.84 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 39 HIS 0.349 0.002 HIS E 111 PHE 0.026 0.002 PHE D 10 TYR 0.053 0.001 TYR C 72 ARG 0.057 0.001 ARG G 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17389.59 seconds wall clock time: 309 minutes 25.31 seconds (18565.31 seconds total)