Starting phenix.real_space_refine on Thu Feb 22 04:18:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n07_9312/02_2024/6n07_9312_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n07_9312/02_2024/6n07_9312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n07_9312/02_2024/6n07_9312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n07_9312/02_2024/6n07_9312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n07_9312/02_2024/6n07_9312_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n07_9312/02_2024/6n07_9312_neut.pdb" } resolution = 3.6 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= 0.002 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 126 5.16 5 C 20691 2.51 5 N 5909 2.21 5 O 6107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 70": "NH1" <-> "NH2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "JB ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32833 Number of models: 1 Model: "" Number of chains: 42 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} Time building chain proxies: 16.70, per 1000 atoms: 0.51 Number of scatterers: 32833 At special positions: 0 Unit cell: (123.6, 215.27, 192.61, 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 126 16.00 O 6107 8.00 N 5909 7.00 C 20691 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: 12.17 Conformation dependent library (CDL) restraints added in 6.5 seconds 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8074 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 48 sheets defined 43.7% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 47 through 59 removed outlier: 4.009A pdb=" N ASP A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.513A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.684A pdb=" N ILE A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) 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 162 Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.544A 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 47 through 59 removed outlier: 4.024A pdb=" N ASP B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.689A pdb=" N ILE B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.527A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 47 through 59 removed outlier: 3.964A pdb=" N ASP C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.521A pdb=" N GLY C 102 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 103 " --> pdb=" O GLU C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.647A pdb=" N GLN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.571A pdb=" N ALA C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.531A 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: 3.678A pdb=" N ASP D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.905A pdb=" N ILE D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN D 126 " --> pdb=" O THR D 122 " (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 161 removed outlier: 4.002A pdb=" N ALA D 158 " --> pdb=" O ALA D 154 " (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: 3.809A pdb=" N ASP E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 96 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.914A pdb=" N GLY E 102 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG E 103 " --> pdb=" O GLU E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 103' Processing helix chain 'E' and resid 118 through 126 removed outlier: 4.016A 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 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.835A 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 57 removed outlier: 3.760A pdb=" N ASP F 53 " --> pdb=" O ASN F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 118 through 128 removed outlier: 4.257A pdb=" N ILE F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 161 removed outlier: 4.026A pdb=" N ALA F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.535A pdb=" N METGA 16 " --> pdb=" O GLYGA 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALAGA 27 " --> pdb=" O METGA 23 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 3.840A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.627A pdb=" N VALGB 24 " --> pdb=" O ALAGB 20 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 4.155A pdb=" N ALAGB 55 " --> pdb=" O ALAGB 51 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLUGB 65 " --> pdb=" O GLNGB 61 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 87 Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.504A pdb=" N METGC 16 " --> pdb=" O GLYGC 12 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.878A pdb=" N LYSGC 54 " --> pdb=" O VALGC 50 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALAGC 55 " --> pdb=" O ALAGC 51 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 removed outlier: 3.520A pdb=" N ALAGC 86 " --> pdb=" O ASNGC 82 " (cutoff:3.500A) Processing helix chain 'GD' and resid 12 through 27 removed outlier: 3.624A pdb=" N VALGD 24 " --> pdb=" O ALAGD 20 " (cutoff:3.500A) Processing helix chain 'GD' and resid 49 through 65 removed outlier: 4.003A pdb=" N ARGGD 62 " --> pdb=" O GLUGD 58 " (cutoff:3.500A) Processing helix chain 'GD' and resid 80 through 87 Processing helix chain 'GE' and resid 12 through 27 removed outlier: 3.614A pdb=" N METGE 16 " --> pdb=" O GLYGE 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VALGE 24 " --> pdb=" O ALAGE 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALAGE 27 " --> pdb=" O METGE 23 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 3.713A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALAGE 59 " --> pdb=" O ALAGE 55 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 Processing helix chain 'GF' and resid 12 through 27 removed outlier: 3.561A pdb=" N LYSGF 25 " --> pdb=" O ASPGF 21 " (cutoff:3.500A) Processing helix chain 'GF' and resid 49 through 65 removed outlier: 4.057A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALAGF 59 " --> pdb=" O ALAGF 55 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 27 removed outlier: 3.565A pdb=" N METHA 16 " --> pdb=" O GLYHA 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 3.761A pdb=" N ALAHA 55 " --> pdb=" O ALAHA 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 87 Processing helix chain 'HB' and resid 12 through 27 removed outlier: 3.589A pdb=" N METHB 16 " --> pdb=" O GLYHB 12 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALAHB 27 " --> pdb=" O METHB 23 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 65 removed outlier: 3.510A pdb=" N LYSHB 54 " --> pdb=" O VALHB 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALAHB 59 " --> pdb=" O ALAHB 55 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 87 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.613A pdb=" N METHC 16 " --> pdb=" O GLYHC 12 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.862A pdb=" N ALAHC 55 " --> pdb=" O ALAHC 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLUHC 58 " --> pdb=" O LYSHC 54 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.745A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 4.017A pdb=" N ALAHD 55 " --> pdb=" O ALAHD 51 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.508A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 Processing helix chain 'HE' and resid 80 through 87 removed outlier: 3.538A pdb=" N ALAHE 86 " --> pdb=" O ASNHE 82 " (cutoff:3.500A) Processing helix chain 'HF' and resid 12 through 26 removed outlier: 3.722A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 65 removed outlier: 3.945A pdb=" N ARGHF 62 " --> pdb=" O GLUHF 58 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.518A pdb=" N METIA 16 " --> pdb=" O GLYIA 12 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 65 removed outlier: 3.886A pdb=" N ALAIA 55 " --> pdb=" O ALAIA 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLUIA 58 " --> pdb=" O LYSIA 54 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.638A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSIB 25 " --> pdb=" O ASPIB 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAIB 27 " --> pdb=" O METIB 23 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 65 removed outlier: 4.239A pdb=" N ALAIB 55 " --> pdb=" O ALAIB 51 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.520A pdb=" N VALIC 24 " --> pdb=" O ALAIC 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAIC 27 " --> pdb=" O METIC 23 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 3.767A pdb=" N ALAIC 55 " --> pdb=" O ALAIC 51 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.633A pdb=" N VALID 24 " --> pdb=" O ALAID 20 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 4.183A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 87 Processing helix chain 'IE' and resid 12 through 27 removed outlier: 3.545A pdb=" N METIE 16 " --> pdb=" O GLYIE 12 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 65 removed outlier: 3.778A pdb=" N ALAIE 55 " --> pdb=" O ALAIE 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALAIE 59 " --> pdb=" O ALAIE 55 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 removed outlier: 3.548A pdb=" N ALAIF 27 " --> pdb=" O METIF 23 " (cutoff:3.500A) Processing helix chain 'IF' and resid 49 through 65 removed outlier: 3.704A pdb=" N GLUIF 65 " --> pdb=" O GLNIF 61 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.591A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYSJA 25 " --> pdb=" O ASPJA 21 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 65 removed outlier: 3.655A pdb=" N ALAJA 55 " --> pdb=" O ALAJA 51 " (cutoff:3.500A) removed outlier: 3.909A 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: 3.543A pdb=" N METJB 16 " --> pdb=" O GLYJB 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALAJB 27 " --> pdb=" O METJB 23 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 65 removed outlier: 4.135A pdb=" N GLUJB 58 " --> pdb=" O LYSJB 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALAJB 59 " --> pdb=" O ALAJB 55 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 87 removed outlier: 3.562A pdb=" N ASPJB 84 " --> pdb=" O HISJB 80 " (cutoff:3.500A) Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.675A pdb=" N METJC 16 " --> pdb=" O GLYJC 12 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 65 removed outlier: 3.750A pdb=" N ALAJC 55 " --> pdb=" O ALAJC 51 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUJC 58 " --> pdb=" O LYSJC 54 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.555A pdb=" N VALJD 24 " --> pdb=" O ALAJD 20 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 65 removed outlier: 4.037A pdb=" N ALAJD 55 " --> pdb=" O ALAJD 51 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 87 Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.647A pdb=" N ALAJE 27 " --> pdb=" O METJE 23 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 Processing helix chain 'JE' and resid 80 through 87 Processing helix chain 'JF' and resid 12 through 25 removed outlier: 3.693A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 65 removed outlier: 3.973A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 removed outlier: 3.694A pdb=" N ASPJF 84 " --> pdb=" O HISJF 80 " (cutoff:3.500A) Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.520A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 65 removed outlier: 3.778A pdb=" N ALAKA 55 " --> pdb=" O ALAKA 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.653A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALAKB 27 " --> pdb=" O METKB 23 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 4.168A pdb=" N ALAKB 55 " --> pdb=" O ALAKB 51 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLUKB 58 " --> pdb=" O LYSKB 54 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 87 Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.547A pdb=" N METKC 16 " --> pdb=" O GLYKC 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYSKC 25 " --> pdb=" O ASPKC 21 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.867A pdb=" N ALAKC 55 " --> pdb=" O ALAKC 51 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 removed outlier: 3.589A pdb=" N ALAKC 86 " --> pdb=" O ASNKC 82 " (cutoff:3.500A) Processing helix chain 'KD' and resid 12 through 27 removed outlier: 3.683A pdb=" N VALKD 24 " --> pdb=" O ALAKD 20 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 65 removed outlier: 3.595A pdb=" N GLUKD 58 " --> pdb=" O LYSKD 54 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 Processing helix chain 'KE' and resid 12 through 27 removed outlier: 3.556A pdb=" N METKE 16 " --> pdb=" O GLYKE 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALAKE 27 " --> pdb=" O METKE 23 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 3.776A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALAKE 59 " --> pdb=" O ALAKE 55 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 removed outlier: 3.585A pdb=" N LYSKF 25 " --> pdb=" O ASPKF 21 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.640A pdb=" N LYSKF 54 " --> pdb=" O VALKF 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALAKF 55 " --> pdb=" O ALAKF 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALAKF 59 " --> pdb=" O ALAKF 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLUKF 65 " --> pdb=" O GLNKF 61 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.572A pdb=" N METLA 16 " --> pdb=" O GLYLA 12 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYSLA 25 " --> pdb=" O ASPLA 21 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 65 removed outlier: 3.768A pdb=" N ALALA 55 " --> pdb=" O ALALA 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLULA 58 " --> pdb=" O LYSLA 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALALA 59 " --> pdb=" O ALALA 55 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 87 Processing helix chain 'LB' and resid 12 through 27 removed outlier: 3.576A pdb=" N ALALB 27 " --> pdb=" O METLB 23 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 65 removed outlier: 4.118A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALALB 59 " --> pdb=" O ALALB 55 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 87 Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.577A pdb=" N METLC 16 " --> pdb=" O GLYLC 12 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALALC 27 " --> pdb=" O METLC 23 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 65 removed outlier: 4.023A pdb=" N ALALC 55 " --> pdb=" O ALALC 51 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.755A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 65 removed outlier: 4.027A pdb=" N ALALD 55 " --> pdb=" O ALALD 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLULD 65 " --> pdb=" O GLNLD 61 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.635A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 Processing helix chain 'LE' and resid 80 through 87 removed outlier: 3.576A pdb=" N ALALE 86 " --> pdb=" O ASNLE 82 " (cutoff:3.500A) Processing helix chain 'LF' and resid 12 through 26 removed outlier: 3.802A pdb=" N VALLF 24 " --> pdb=" O ALALF 20 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 65 removed outlier: 3.889A pdb=" N ARGLF 62 " --> pdb=" O GLULF 58 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 87 removed outlier: 3.506A pdb=" N ASPLF 84 " --> pdb=" O HISLF 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 114 removed outlier: 5.671A pdb=" N VAL A 108 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 146 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 181 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU A 166 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 11 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 113 removed outlier: 5.809A pdb=" N VAL B 108 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN B 146 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 110 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 182 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 177 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 169 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.535A 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: 4.014A pdb=" N VAL C 65 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 6.188A 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: 5.820A pdb=" N VAL C 108 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 146 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 182 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 169 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.639A 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 removed outlier: 4.241A pdb=" N VAL D 65 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS D 78 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 114 removed outlier: 5.639A pdb=" N VAL D 108 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN D 146 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG D 177 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL D 169 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.719A 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: 4.146A pdb=" N VAL E 65 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 6.462A 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: 5.875A pdb=" N VAL E 108 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN E 146 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG E 177 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL E 169 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.477A 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: 4.235A pdb=" N VAL F 65 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.889A 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 114 removed outlier: 5.614A pdb=" N VAL F 108 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN F 146 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 110 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA F 181 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU F 166 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'GA' and resid 30 through 36 removed outlier: 5.749A pdb=" N LEUGA 31 " --> pdb=" O ARGGA 47 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARGGA 47 " --> pdb=" O LEUGA 31 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLYGA 33 " --> pdb=" O VALGA 45 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALGA 45 " --> pdb=" O GLYGA 33 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALAGA 72 " --> pdb=" O GLUGA 9 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARGGA 11 " --> pdb=" O VALGA 70 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VALGA 70 " --> pdb=" O ARGGA 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'GB' and resid 30 through 38 removed outlier: 5.437A pdb=" N LEUGB 31 " --> pdb=" O ARGGB 47 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARGGB 47 " --> pdb=" O LEUGB 31 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALGB 45 " --> pdb=" O GLYGB 33 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYRGB 41 " --> pdb=" O THRGB 37 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'GC' and resid 30 through 38 removed outlier: 7.484A pdb=" N VALGC 45 " --> pdb=" O ILEGC 32 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYRGC 34 " --> pdb=" O THRGC 43 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THRGC 43 " --> pdb=" O TYRGC 34 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYSGC 36 " --> pdb=" O TYRGC 41 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TYRGC 41 " --> pdb=" O LYSGC 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEUGC 5 " --> pdb=" O VALGC 75 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VALGC 75 " --> pdb=" O LEUGC 5 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N METGC 7 " --> pdb=" O VALGC 73 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VALGC 73 " --> pdb=" O METGC 7 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLUGC 9 " --> pdb=" O VALGC 71 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLUGC 69 " --> pdb=" O ARGGC 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'GD' and resid 30 through 38 removed outlier: 5.466A pdb=" N LEUGD 31 " --> pdb=" O ARGGD 47 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARGGD 47 " --> pdb=" O LEUGD 31 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VALGD 45 " --> pdb=" O GLYGD 33 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYRGD 41 " --> pdb=" O THRGD 37 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAGD 72 " --> pdb=" O GLUGD 9 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'GE' and resid 31 through 36 removed outlier: 5.824A pdb=" N LEUGE 31 " --> pdb=" O ARGGE 47 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARGGE 47 " --> pdb=" O LEUGE 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLYGE 33 " --> pdb=" O VALGE 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HISGE 74 " --> pdb=" O METGE 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALAGE 72 " --> pdb=" O GLUGE 9 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARGGE 11 " --> pdb=" O VALGE 70 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VALGE 70 " --> pdb=" O ARGGE 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'GF' and resid 30 through 36 removed outlier: 5.468A pdb=" N LEUGF 31 " --> pdb=" O ARGGF 47 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARGGF 47 " --> pdb=" O LEUGF 31 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLYGF 33 " --> pdb=" O VALGF 45 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VALGF 45 " --> pdb=" O GLYGF 33 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALAGF 72 " --> pdb=" O GLUGF 9 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARGGF 11 " --> pdb=" O VALGF 70 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VALGF 70 " --> pdb=" O ARGGF 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'HA' and resid 31 through 36 removed outlier: 5.854A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VALHA 45 " --> pdb=" O GLYHA 33 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HISHA 74 " --> pdb=" O METHA 7 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALAHA 72 " --> pdb=" O GLUHA 9 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARGHA 11 " --> pdb=" O VALHA 70 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VALHA 70 " --> pdb=" O ARGHA 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 30 through 36 removed outlier: 5.581A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VALHB 45 " --> pdb=" O GLYHB 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALAHB 72 " --> pdb=" O GLUHB 9 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'HC' and resid 30 through 36 removed outlier: 5.653A pdb=" N LEUHC 31 " --> pdb=" O ARGHC 47 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARGHC 47 " --> pdb=" O LEUHC 31 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALHC 45 " --> pdb=" O GLYHC 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALAHC 72 " --> pdb=" O GLUHC 9 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARGHC 11 " --> pdb=" O VALHC 70 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VALHC 70 " --> pdb=" O ARGHC 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'HD' and resid 30 through 36 removed outlier: 5.324A pdb=" N LEUHD 31 " --> pdb=" O ARGHD 47 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARGHD 47 " --> pdb=" O LEUHD 31 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLYHD 33 " --> pdb=" O VALHD 45 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEUHD 5 " --> pdb=" O VALHD 75 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VALHD 75 " --> pdb=" O LEUHD 5 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N METHD 7 " --> pdb=" O VALHD 73 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VALHD 73 " --> pdb=" O METHD 7 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLUHD 9 " --> pdb=" O VALHD 71 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLUHD 69 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'HE' and resid 30 through 36 removed outlier: 7.496A pdb=" N VALHE 45 " --> pdb=" O ILEHE 32 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYRHE 34 " --> pdb=" O THRHE 43 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRHE 43 " --> pdb=" O TYRHE 34 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYSHE 36 " --> pdb=" O TYRHE 41 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYRHE 41 " --> pdb=" O LYSHE 36 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEUHE 5 " --> pdb=" O VALHE 75 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VALHE 75 " --> pdb=" O LEUHE 5 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N METHE 7 " --> pdb=" O VALHE 73 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VALHE 73 " --> pdb=" O METHE 7 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLUHE 9 " --> pdb=" O VALHE 71 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLUHE 69 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'HF' and resid 30 through 36 removed outlier: 5.616A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALHF 45 " --> pdb=" O GLYHF 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'IA' and resid 30 through 36 removed outlier: 5.623A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALAIA 72 " --> pdb=" O GLUIA 9 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARGIA 11 " --> pdb=" O VALIA 70 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VALIA 70 " --> pdb=" O ARGIA 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'IB' and resid 30 through 38 removed outlier: 5.411A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALIB 45 " --> pdb=" O GLYIB 33 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALAIB 72 " --> pdb=" O GLUIB 9 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARGIB 11 " --> pdb=" O VALIB 70 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VALIB 70 " --> pdb=" O ARGIB 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'IC' and resid 30 through 38 removed outlier: 6.813A pdb=" N ILEIC 32 " --> pdb=" O ARGIC 47 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ARGIC 47 " --> pdb=" O ILEIC 32 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYRIC 34 " --> pdb=" O VALIC 45 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VALIC 45 " --> pdb=" O TYRIC 34 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYSIC 36 " --> pdb=" O THRIC 43 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THRIC 43 " --> pdb=" O LYSIC 36 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLYIC 38 " --> pdb=" O TYRIC 41 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEUIC 5 " --> pdb=" O VALIC 75 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VALIC 75 " --> pdb=" O LEUIC 5 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N METIC 7 " --> pdb=" O VALIC 73 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VALIC 73 " --> pdb=" O METIC 7 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLUIC 9 " --> pdb=" O VALIC 71 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLUIC 69 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'ID' and resid 30 through 36 removed outlier: 5.385A pdb=" N LEUID 31 " --> pdb=" O ARGID 47 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARGID 47 " --> pdb=" O LEUID 31 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLYID 33 " --> pdb=" O VALID 45 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VALID 45 " --> pdb=" O GLYID 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEUID 5 " --> pdb=" O VALID 75 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VALID 75 " --> pdb=" O LEUID 5 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N METID 7 " --> pdb=" O VALID 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VALID 73 " --> pdb=" O METID 7 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLUID 9 " --> pdb=" O VALID 71 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUID 69 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'IE' and resid 30 through 38 removed outlier: 7.378A pdb=" N VALIE 45 " --> pdb=" O ILEIE 32 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYRIE 34 " --> pdb=" O THRIE 43 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THRIE 43 " --> pdb=" O TYRIE 34 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYSIE 36 " --> pdb=" O TYRIE 41 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYRIE 41 " --> pdb=" O LYSIE 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALAIE 72 " --> pdb=" O GLUIE 9 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARGIE 11 " --> pdb=" O VALIE 70 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VALIE 70 " --> pdb=" O ARGIE 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'IF' and resid 31 through 36 removed outlier: 4.139A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VALIF 45 " --> pdb=" O GLYIF 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGIF 11 " --> pdb=" O VALIF 70 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VALIF 70 " --> pdb=" O ARGIF 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'JA' and resid 31 through 38 removed outlier: 5.663A pdb=" N LEUJA 31 " --> pdb=" O ARGJA 47 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARGJA 47 " --> pdb=" O LEUJA 31 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYRJA 41 " --> pdb=" O THRJA 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HISJA 74 " --> pdb=" O METJA 7 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALAJA 72 " --> pdb=" O GLUJA 9 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARGJA 11 " --> pdb=" O VALJA 70 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VALJA 70 " --> pdb=" O ARGJA 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'JB' and resid 31 through 36 removed outlier: 5.801A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALJB 45 " --> pdb=" O GLYJB 33 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALAJB 72 " --> pdb=" O GLUJB 9 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARGJB 11 " --> pdb=" O VALJB 70 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VALJB 70 " --> pdb=" O ARGJB 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'JC' and resid 30 through 36 removed outlier: 5.646A pdb=" N LEUJC 31 " --> pdb=" O ARGJC 47 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARGJC 47 " --> pdb=" O LEUJC 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLYJC 33 " --> pdb=" O VALJC 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALJC 45 " --> pdb=" O GLYJC 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALAJC 72 " --> pdb=" O GLUJC 9 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARGJC 11 " --> pdb=" O VALJC 70 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VALJC 70 " --> pdb=" O ARGJC 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'JD' and resid 30 through 36 removed outlier: 5.194A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEUJD 5 " --> pdb=" O VALJD 75 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VALJD 75 " --> pdb=" O LEUJD 5 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N METJD 7 " --> pdb=" O VALJD 73 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VALJD 73 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLUJD 9 " --> pdb=" O VALJD 71 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLUJD 69 " --> pdb=" O ARGJD 11 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'JE' and resid 30 through 36 removed outlier: 5.550A pdb=" N LEUJE 31 " --> pdb=" O ARGJE 47 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARGJE 47 " --> pdb=" O LEUJE 31 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLYJE 33 " --> pdb=" O VALJE 45 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VALJE 45 " --> pdb=" O GLYJE 33 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARGJE 11 " --> pdb=" O VALJE 70 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VALJE 70 " --> pdb=" O ARGJE 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'JF' and resid 33 through 36 removed outlier: 4.214A pdb=" N GLYJF 33 " --> pdb=" O VALJF 45 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VALJF 45 " --> pdb=" O GLYJF 33 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'KA' and resid 30 through 36 removed outlier: 5.775A pdb=" N LEUKA 31 " --> pdb=" O ARGKA 47 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARGKA 47 " --> pdb=" O LEUKA 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLYKA 33 " --> pdb=" O VALKA 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALAKA 72 " --> pdb=" O GLUKA 9 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARGKA 11 " --> pdb=" O VALKA 70 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VALKA 70 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'KB' and resid 30 through 38 removed outlier: 5.260A pdb=" N LEUKB 31 " --> pdb=" O ARGKB 47 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARGKB 47 " --> pdb=" O LEUKB 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLYKB 33 " --> pdb=" O VALKB 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THRKB 37 " --> pdb=" O TYRKB 41 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYRKB 41 " --> pdb=" O THRKB 37 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HISKB 74 " --> pdb=" O METKB 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALAKB 72 " --> pdb=" O GLUKB 9 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'KC' and resid 30 through 36 removed outlier: 5.542A pdb=" N LEUKC 31 " --> pdb=" O ARGKC 47 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARGKC 47 " --> pdb=" O LEUKC 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLYKC 33 " --> pdb=" O VALKC 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VALKC 45 " --> pdb=" O GLYKC 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALAKC 72 " --> pdb=" O GLUKC 9 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARGKC 11 " --> pdb=" O VALKC 70 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VALKC 70 " --> pdb=" O ARGKC 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'KD' and resid 30 through 36 removed outlier: 5.591A pdb=" N LEUKD 31 " --> pdb=" O ARGKD 47 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARGKD 47 " --> pdb=" O LEUKD 31 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VALKD 45 " --> pdb=" O GLYKD 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARGKD 11 " --> pdb=" O VALKD 70 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VALKD 70 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'KE' and resid 31 through 38 removed outlier: 5.735A pdb=" N LEUKE 31 " --> pdb=" O ARGKE 47 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARGKE 47 " --> pdb=" O LEUKE 31 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLYKE 33 " --> pdb=" O VALKE 45 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYRKE 41 " --> pdb=" O THRKE 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HISKE 74 " --> pdb=" O METKE 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALAKE 72 " --> pdb=" O GLUKE 9 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARGKE 11 " --> pdb=" O VALKE 70 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALKE 70 " --> pdb=" O ARGKE 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KF' and resid 30 through 36 removed outlier: 5.494A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VALKF 45 " --> pdb=" O GLYKF 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LA' and resid 33 through 38 removed outlier: 3.996A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYRLA 41 " --> pdb=" O THRLA 37 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEULA 5 " --> pdb=" O VALLA 75 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VALLA 75 " --> pdb=" O LEULA 5 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N METLA 7 " --> pdb=" O VALLA 73 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VALLA 73 " --> pdb=" O METLA 7 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLULA 9 " --> pdb=" O VALLA 71 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLULA 69 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LB' and resid 30 through 36 removed outlier: 5.678A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALALB 72 " --> pdb=" O GLULB 9 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARGLB 11 " --> pdb=" O VALLB 70 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VALLB 70 " --> pdb=" O ARGLB 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LC' and resid 30 through 36 removed outlier: 5.679A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALLC 45 " --> pdb=" O GLYLC 33 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALALC 72 " --> pdb=" O GLULC 9 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARGLC 11 " --> pdb=" O VALLC 70 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VALLC 70 " --> pdb=" O ARGLC 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LD' and resid 30 through 38 removed outlier: 5.542A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALALD 72 " --> pdb=" O GLULD 9 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LE' and resid 30 through 36 removed outlier: 5.584A pdb=" N LEULE 31 " --> pdb=" O ARGLE 47 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARGLE 47 " --> pdb=" O LEULE 31 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLYLE 33 " --> pdb=" O VALLE 45 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VALLE 45 " --> pdb=" O GLYLE 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LF' and resid 30 through 36 removed outlier: 5.616A pdb=" N LEULF 31 " --> pdb=" O ARGLF 47 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARGLF 47 " --> pdb=" O LEULF 31 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLYLF 33 " --> pdb=" O VALLF 45 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VALLF 45 " --> pdb=" O GLYLF 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARGLF 11 " --> pdb=" O VALLF 70 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VALLF 70 " --> pdb=" O ARGLF 11 " (cutoff:3.500A) 1922 hydrogen bonds defined for protein. 5571 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: 11.80 Time building geometry restraints manager: 13.07 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: 11210 1.34 - 1.46: 3908 1.46 - 1.57: 17907 1.57 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 33277 Sorted by residual: bond pdb=" CB THR B 20 " pdb=" CG2 THR B 20 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" C ARGKB 78 " pdb=" O ARGKB 78 " ideal model delta sigma weight residual 1.249 1.235 0.014 8.50e-03 1.38e+04 2.64e+00 bond pdb=" CG LEUHD 89 " pdb=" CD1 LEUHD 89 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.63e+00 bond pdb=" C ILE B 134 " pdb=" N LEU B 135 " ideal model delta sigma weight residual 1.340 1.251 0.090 5.87e-02 2.90e+02 2.34e+00 bond pdb=" CB THR A 20 " pdb=" CG2 THR A 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 ... (remaining 33272 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.15: 784 105.15 - 112.37: 17277 112.37 - 119.58: 11035 119.58 - 126.80: 15858 126.80 - 134.01: 249 Bond angle restraints: 45203 Sorted by residual: angle pdb=" N ALA C 71 " pdb=" CA ALA C 71 " pdb=" C ALA C 71 " ideal model delta sigma weight residual 114.62 108.16 6.46 1.14e+00 7.69e-01 3.22e+01 angle pdb=" C GLU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C GLU B 69 " pdb=" N ARG B 70 " pdb=" CA ARG B 70 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" CA ARG A 70 " pdb=" CB ARG A 70 " pdb=" CG ARG A 70 " ideal model delta sigma weight residual 114.10 123.08 -8.98 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA ARG B 70 " pdb=" CB ARG B 70 " pdb=" CG ARG B 70 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.85e+01 ... (remaining 45198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 19326 15.30 - 30.61: 562 30.61 - 45.91: 122 45.91 - 61.22: 23 61.22 - 76.52: 10 Dihedral angle restraints: 20043 sinusoidal: 7380 harmonic: 12663 Sorted by residual: dihedral pdb=" CA ASPHE 49 " pdb=" C ASPHE 49 " pdb=" N VALHE 50 " pdb=" CA VALHE 50 " ideal model delta harmonic sigma weight residual -180.00 -148.94 -31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASPHF 49 " pdb=" C ASPHF 49 " pdb=" N VALHF 50 " pdb=" CA VALHF 50 " ideal model delta harmonic sigma weight residual -180.00 -150.16 -29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASPJA 49 " pdb=" C ASPJA 49 " pdb=" N VALJA 50 " pdb=" CA VALJA 50 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3602 0.046 - 0.092: 1330 0.092 - 0.138: 406 0.138 - 0.183: 75 0.183 - 0.229: 10 Chirality restraints: 5423 Sorted by residual: chirality pdb=" CB ILE B 114 " pdb=" CA ILE B 114 " pdb=" CG1 ILE B 114 " pdb=" CG2 ILE B 114 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE B 134 " pdb=" CA ILE B 134 " pdb=" CG1 ILE B 134 " pdb=" CG2 ILE B 134 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ARG C 70 " pdb=" N ARG C 70 " pdb=" C ARG C 70 " pdb=" CB ARG C 70 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5420 not shown) Planarity restraints: 5939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 126 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" CG ASN F 126 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN F 126 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 126 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 62 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO E 63 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 55 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C ALA E 55 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA E 55 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU E 56 " -0.013 2.00e-02 2.50e+03 ... (remaining 5936 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10085 2.84 - 3.36: 29017 3.36 - 3.87: 55529 3.87 - 4.39: 61274 4.39 - 4.90: 109855 Nonbonded interactions: 265760 Sorted by model distance: nonbonded pdb=" NZ LYSGD 36 " pdb=" OE2 GLUGE 35 " model vdw 2.330 2.520 nonbonded pdb=" O PRO D 16 " pdb=" OG1 THR D 20 " model vdw 2.337 2.440 nonbonded pdb=" O ALA B 119 " pdb=" OG1 THR B 122 " model vdw 2.338 2.440 nonbonded pdb=" O PRO F 16 " pdb=" OG1 THR F 20 " model vdw 2.348 2.440 nonbonded pdb=" O ALA A 119 " pdb=" OG1 THR A 122 " model vdw 2.359 2.440 ... (remaining 265755 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 '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: 9.830 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: 0.030 Extract box with map and model: 28.420 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 82.880 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.420 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.007 0.090 33277 Z= 0.437 Angle : 0.768 10.314 45203 Z= 0.434 Chirality : 0.052 0.229 5423 Planarity : 0.006 0.058 5939 Dihedral : 9.000 76.524 11969 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -3.72 (0.11), residues: 4439 helix: -3.16 (0.08), residues: 1794 sheet: -0.93 (0.14), residues: 1249 loop : -2.54 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP F 39 HIS 0.010 0.002 HIS A 78 PHE 0.018 0.003 PHEJB 13 TYR 0.027 0.003 TYRGF 34 ARG 0.006 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1286 time to evaluate : 3.694 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: A 163 ASN cc_start: 0.8161 (t0) cc_final: 0.7859 (t0) REVERT: A 170 THR cc_start: 0.8821 (m) cc_final: 0.8269 (p) REVERT: B 90 SER cc_start: 0.8479 (m) cc_final: 0.8097 (p) REVERT: B 138 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7829 (mt-10) REVERT: B 144 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 20 THR cc_start: 0.8846 (m) cc_final: 0.8604 (m) REVERT: C 138 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 168 ASN cc_start: 0.8620 (t0) cc_final: 0.8317 (t0) REVERT: D 6 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7665 (mtp85) REVERT: D 139 SER cc_start: 0.8847 (m) cc_final: 0.8571 (p) REVERT: D 150 TYR cc_start: 0.7889 (m-80) cc_final: 0.7206 (m-80) REVERT: D 188 ASP cc_start: 0.8593 (m-30) cc_final: 0.8118 (m-30) REVERT: F 30 LEU cc_start: 0.8409 (mt) cc_final: 0.8076 (pp) REVERT: F 69 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7485 (tm-30) REVERT: F 133 MET cc_start: 0.8643 (mtm) cc_final: 0.8369 (mtp) REVERT: GA 16 MET cc_start: 0.8664 (tmm) cc_final: 0.8415 (tmm) REVERT: GC 28 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7491 (mmtt) REVERT: GC 43 THR cc_start: 0.9219 (m) cc_final: 0.8811 (p) REVERT: GC 62 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.7583 (ttt180) REVERT: GC 78 ARG cc_start: 0.7566 (mmm160) cc_final: 0.7279 (ptt90) REVERT: GD 78 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7085 (mtm180) REVERT: GE 18 GLU cc_start: 0.8732 (tp30) cc_final: 0.8518 (tp30) REVERT: GF 61 GLN cc_start: 0.8701 (tt0) cc_final: 0.7717 (tt0) REVERT: HA 16 MET cc_start: 0.8397 (tmm) cc_final: 0.8186 (tmm) REVERT: HB 36 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8031 (mttp) REVERT: HB 47 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8586 (mtp180) REVERT: HB 84 ASP cc_start: 0.8317 (m-30) cc_final: 0.8041 (m-30) REVERT: HC 78 ARG cc_start: 0.8372 (mtp180) cc_final: 0.6805 (mtm-85) REVERT: HD 16 MET cc_start: 0.9101 (tmm) cc_final: 0.8900 (tmm) REVERT: HD 28 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8291 (mttt) REVERT: HE 23 MET cc_start: 0.8588 (mtm) cc_final: 0.8360 (mtm) REVERT: HE 32 ILE cc_start: 0.9172 (pp) cc_final: 0.8969 (pt) REVERT: HF 10 VAL cc_start: 0.9419 (t) cc_final: 0.9184 (p) REVERT: IB 16 MET cc_start: 0.8850 (tmm) cc_final: 0.8642 (tmm) REVERT: IB 78 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8298 (ttp80) REVERT: IC 7 MET cc_start: 0.8680 (mtm) cc_final: 0.8444 (mtm) REVERT: IC 28 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7635 (mptt) REVERT: IC 43 THR cc_start: 0.9249 (m) cc_final: 0.8950 (p) REVERT: IC 62 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7464 (ttt180) REVERT: IF 61 GLN cc_start: 0.8215 (tt0) cc_final: 0.7775 (tt0) REVERT: JA 16 MET cc_start: 0.8446 (tmm) cc_final: 0.8155 (tmm) REVERT: JA 21 ASP cc_start: 0.8481 (t70) cc_final: 0.7724 (t0) REVERT: JA 31 LEU cc_start: 0.8919 (tp) cc_final: 0.8698 (tt) REVERT: JB 88 PRO cc_start: 0.7340 (Cg_endo) cc_final: 0.7137 (Cg_exo) REVERT: JC 35 GLU cc_start: 0.8266 (tp30) cc_final: 0.7993 (tp30) REVERT: JC 78 ARG cc_start: 0.7916 (mtp180) cc_final: 0.6488 (mtm-85) REVERT: JC 89 LEU cc_start: 0.9314 (mm) cc_final: 0.9113 (mp) REVERT: JD 28 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8199 (mttt) REVERT: JE 18 GLU cc_start: 0.8128 (tp30) cc_final: 0.7648 (tp30) REVERT: JE 43 THR cc_start: 0.9209 (m) cc_final: 0.8900 (p) REVERT: JE 67 VAL cc_start: 0.8853 (m) cc_final: 0.8520 (p) REVERT: JF 43 THR cc_start: 0.9530 (m) cc_final: 0.9214 (p) REVERT: JF 73 VAL cc_start: 0.9139 (t) cc_final: 0.8782 (m) REVERT: JF 82 ASN cc_start: 0.9090 (t160) cc_final: 0.8815 (m-40) REVERT: KA 18 GLU cc_start: 0.8296 (tp30) cc_final: 0.8064 (tp30) REVERT: KA 23 MET cc_start: 0.8971 (mtm) cc_final: 0.8719 (mtm) REVERT: KB 23 MET cc_start: 0.9464 (mtm) cc_final: 0.9214 (mtp) REVERT: KB 62 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7748 (mtt180) REVERT: KC 21 ASP cc_start: 0.8899 (t70) cc_final: 0.8410 (t0) REVERT: KC 23 MET cc_start: 0.8535 (mtm) cc_final: 0.8242 (mtm) REVERT: KC 28 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7910 (mptt) REVERT: KC 41 TYR cc_start: 0.9087 (m-10) cc_final: 0.8876 (m-80) REVERT: KC 62 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.7300 (ttt180) REVERT: KD 76 ILE cc_start: 0.9369 (mt) cc_final: 0.9169 (mm) REVERT: KD 78 ARG cc_start: 0.7946 (tpt-90) cc_final: 0.7298 (ttp-170) REVERT: KE 32 ILE cc_start: 0.9128 (pp) cc_final: 0.8915 (pt) REVERT: KF 61 GLN cc_start: 0.8487 (tt0) cc_final: 0.8266 (tt0) REVERT: LA 18 GLU cc_start: 0.8362 (tp30) cc_final: 0.7536 (tp30) REVERT: LA 21 ASP cc_start: 0.8634 (t70) cc_final: 0.7992 (t0) REVERT: LB 16 MET cc_start: 0.8746 (tmm) cc_final: 0.8370 (tmm) REVERT: LB 67 VAL cc_start: 0.9265 (m) cc_final: 0.8979 (p) REVERT: LC 41 TYR cc_start: 0.8909 (m-10) cc_final: 0.8219 (m-80) REVERT: LC 78 ARG cc_start: 0.7984 (mtp180) cc_final: 0.6350 (mtm-85) REVERT: LD 28 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8246 (mttt) REVERT: LE 7 MET cc_start: 0.8837 (mtm) cc_final: 0.8577 (mtp) REVERT: LE 41 TYR cc_start: 0.9075 (m-10) cc_final: 0.8839 (m-80) REVERT: LE 43 THR cc_start: 0.9303 (m) cc_final: 0.9046 (t) REVERT: LF 43 THR cc_start: 0.9623 (m) cc_final: 0.9305 (p) outliers start: 2 outliers final: 2 residues processed: 1288 average time/residue: 0.5381 time to fit residues: 1035.9642 Evaluate side-chains 940 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 938 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain B residue 70 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 3.9990 chunk 336 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 211 optimal weight: 0.5980 chunk 259 optimal weight: 0.5980 chunk 403 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 123 GLN A 128 ASN B 17 GLN B 123 GLN B 165 HIS C 17 GLN D 112 GLN E 17 GLN E 66 GLN E 79 HIS E 82 GLN E 112 GLN E 128 ASN F 112 GLN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GD 82 ASN GE 61 GLN GE 82 ASN GF 82 ASN HE 74 HIS HE 82 ASN IB 61 GLN ID 82 ASN IE 82 ASN JB 82 ASN JF 82 ASN KD 82 ASN KE 61 GLN KE 82 ASN KF 82 ASN LA 61 GLN LB 82 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33277 Z= 0.280 Angle : 0.604 9.619 45203 Z= 0.321 Chirality : 0.045 0.181 5423 Planarity : 0.004 0.059 5939 Dihedral : 4.633 25.534 4873 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.47 % Allowed : 10.71 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.01 (0.12), residues: 4439 helix: -1.10 (0.11), residues: 1903 sheet: -0.15 (0.15), residues: 1069 loop : -2.38 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 39 HIS 0.004 0.001 HIS E 79 PHE 0.020 0.002 PHE B 175 TYR 0.018 0.001 TYR F 172 ARG 0.006 0.001 ARGKA 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1017 time to evaluate : 3.597 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 111 HIS cc_start: 0.8509 (p90) cc_final: 0.8191 (p-80) REVERT: A 163 ASN cc_start: 0.8238 (t0) cc_final: 0.7851 (t0) REVERT: A 170 THR cc_start: 0.8848 (m) cc_final: 0.8285 (p) REVERT: B 90 SER cc_start: 0.8357 (m) cc_final: 0.8144 (p) REVERT: B 170 THR cc_start: 0.8848 (m) cc_final: 0.8322 (p) REVERT: C 170 THR cc_start: 0.8941 (m) cc_final: 0.8564 (p) REVERT: D 50 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8482 (ttp80) REVERT: D 139 SER cc_start: 0.8690 (m) cc_final: 0.8192 (p) REVERT: F 30 LEU cc_start: 0.8543 (mt) cc_final: 0.8285 (pp) REVERT: F 69 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7278 (tm-30) REVERT: F 179 TYR cc_start: 0.8684 (m-10) cc_final: 0.8254 (m-80) REVERT: GA 16 MET cc_start: 0.8898 (tmm) cc_final: 0.8436 (tmm) REVERT: GA 18 GLU cc_start: 0.8364 (tp30) cc_final: 0.8117 (tp30) REVERT: GC 21 ASP cc_start: 0.8606 (t70) cc_final: 0.8369 (t0) REVERT: GC 28 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7664 (mptt) REVERT: GC 43 THR cc_start: 0.9178 (m) cc_final: 0.8642 (p) REVERT: GC 62 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8037 (ptm160) REVERT: GD 76 ILE cc_start: 0.9542 (mt) cc_final: 0.9303 (mm) REVERT: GD 78 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7221 (mtm180) REVERT: GE 11 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.7859 (ttt90) REVERT: GF 18 GLU cc_start: 0.8725 (tp30) cc_final: 0.8411 (tp30) REVERT: HC 78 ARG cc_start: 0.8392 (mtp180) cc_final: 0.6781 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8409 (mttt) REVERT: HE 23 MET cc_start: 0.8791 (mtm) cc_final: 0.8582 (mtp) REVERT: HF 61 GLN cc_start: 0.8650 (tt0) cc_final: 0.8443 (tm-30) REVERT: HF 82 ASN cc_start: 0.9100 (t0) cc_final: 0.8781 (t0) REVERT: IA 11 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.8258 (ttm-80) REVERT: IB 16 MET cc_start: 0.8962 (tmm) cc_final: 0.8540 (tmm) REVERT: IC 21 ASP cc_start: 0.8983 (t70) cc_final: 0.8389 (t0) REVERT: IC 28 LYS cc_start: 0.8083 (ttpt) cc_final: 0.7615 (mptt) REVERT: IC 43 THR cc_start: 0.9168 (m) cc_final: 0.8860 (p) REVERT: IC 54 LYS cc_start: 0.8838 (tttm) cc_final: 0.8602 (tttp) REVERT: IC 62 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.7555 (ttt180) REVERT: ID 41 TYR cc_start: 0.8894 (m-80) cc_final: 0.8627 (m-80) REVERT: IE 35 GLU cc_start: 0.7957 (tp30) cc_final: 0.7713 (tp30) REVERT: JA 16 MET cc_start: 0.8549 (tmm) cc_final: 0.8259 (tmm) REVERT: JA 21 ASP cc_start: 0.8619 (t70) cc_final: 0.7995 (t0) REVERT: JB 16 MET cc_start: 0.8646 (tmm) cc_final: 0.8390 (tmm) REVERT: JC 78 ARG cc_start: 0.8205 (mtp180) cc_final: 0.6669 (mtt90) REVERT: JD 28 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8294 (mttt) REVERT: JE 18 GLU cc_start: 0.8368 (tp30) cc_final: 0.8097 (tp30) REVERT: JE 43 THR cc_start: 0.9179 (m) cc_final: 0.8834 (p) REVERT: JE 67 VAL cc_start: 0.8869 (m) cc_final: 0.8598 (p) REVERT: JF 43 THR cc_start: 0.9539 (m) cc_final: 0.9240 (p) REVERT: JF 82 ASN cc_start: 0.9194 (t0) cc_final: 0.8909 (m-40) REVERT: KA 18 GLU cc_start: 0.8357 (tp30) cc_final: 0.8022 (tp30) REVERT: KB 23 MET cc_start: 0.9505 (mtm) cc_final: 0.9233 (mtp) REVERT: KB 62 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7896 (mtt180) REVERT: KC 21 ASP cc_start: 0.8977 (t70) cc_final: 0.8493 (t0) REVERT: KC 28 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7910 (mptt) REVERT: KC 62 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.7410 (ttt180) REVERT: KD 11 ARG cc_start: 0.9041 (ttt90) cc_final: 0.8409 (ttt90) REVERT: KD 78 ARG cc_start: 0.8137 (tpt-90) cc_final: 0.7089 (mtm110) REVERT: LA 11 ARG cc_start: 0.8528 (ttt90) cc_final: 0.8161 (ttt-90) REVERT: LB 7 MET cc_start: 0.8540 (mtm) cc_final: 0.8292 (mtm) REVERT: LB 11 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8050 (ttm-80) REVERT: LB 16 MET cc_start: 0.8822 (tmm) cc_final: 0.8601 (tmm) REVERT: LC 11 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8098 (ttm170) REVERT: LC 16 MET cc_start: 0.8691 (tmm) cc_final: 0.8449 (tmm) REVERT: LC 78 ARG cc_start: 0.8014 (mtp180) cc_final: 0.6422 (mtt90) REVERT: LD 23 MET cc_start: 0.9101 (mtm) cc_final: 0.8646 (mtm) REVERT: LD 28 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8240 (mttt) REVERT: LE 18 GLU cc_start: 0.8499 (tp30) cc_final: 0.8163 (tp30) REVERT: LE 43 THR cc_start: 0.9226 (m) cc_final: 0.8785 (p) REVERT: LE 65 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7658 (mm-30) REVERT: LF 43 THR cc_start: 0.9631 (m) cc_final: 0.9236 (p) outliers start: 79 outliers final: 42 residues processed: 1051 average time/residue: 0.5423 time to fit residues: 860.9479 Evaluate side-chains 967 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 925 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 37 THR Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain JA residue 46 VAL Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 335 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 403 optimal weight: 0.9980 chunk 436 optimal weight: 0.9980 chunk 359 optimal weight: 1.9990 chunk 400 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 128 ASN B 15 GLN B 123 GLN B 128 ASN B 165 HIS C 49 ASN C 123 GLN F 82 GLN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 82 ASN GD 82 ASN HE 82 ASN JB 82 ASN JD 82 ASN KF 61 GLN LA 61 GLN LB 82 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33277 Z= 0.267 Angle : 0.577 9.782 45203 Z= 0.303 Chirality : 0.044 0.201 5423 Planarity : 0.003 0.049 5939 Dihedral : 4.339 34.475 4873 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.32 % Allowed : 12.50 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.21 (0.13), residues: 4439 helix: -0.26 (0.12), residues: 1871 sheet: -0.34 (0.14), residues: 1285 loop : -1.86 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 39 HIS 0.004 0.001 HIS C 165 PHE 0.023 0.002 PHE C 175 TYR 0.018 0.001 TYR E 150 ARG 0.006 0.000 ARGKA 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 982 time to evaluate : 3.692 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 163 ASN cc_start: 0.8282 (t0) cc_final: 0.7932 (t0) REVERT: A 170 THR cc_start: 0.8806 (m) cc_final: 0.8345 (p) REVERT: B 120 TYR cc_start: 0.8728 (m-80) cc_final: 0.8474 (m-10) REVERT: B 170 THR cc_start: 0.8916 (m) cc_final: 0.8415 (p) REVERT: C 170 THR cc_start: 0.8877 (m) cc_final: 0.8605 (p) REVERT: D 6 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8268 (mtp-110) REVERT: D 50 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8324 (ttp80) REVERT: D 99 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7793 (mtp85) REVERT: D 139 SER cc_start: 0.8689 (m) cc_final: 0.8169 (p) REVERT: F 175 PHE cc_start: 0.9027 (m-10) cc_final: 0.8805 (m-10) REVERT: F 179 TYR cc_start: 0.8713 (m-10) cc_final: 0.8360 (m-80) REVERT: GA 16 MET cc_start: 0.8897 (tmm) cc_final: 0.8451 (tmm) REVERT: GA 18 GLU cc_start: 0.8417 (tp30) cc_final: 0.8122 (tp30) REVERT: GB 23 MET cc_start: 0.9318 (mtm) cc_final: 0.9102 (mtp) REVERT: GC 21 ASP cc_start: 0.8620 (t70) cc_final: 0.8363 (t0) REVERT: GC 28 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7509 (mmtm) REVERT: GC 43 THR cc_start: 0.9087 (m) cc_final: 0.8652 (p) REVERT: GD 78 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7103 (mtm180) REVERT: GE 11 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7943 (ttt90) REVERT: GF 8 ILE cc_start: 0.9153 (mt) cc_final: 0.8946 (tt) REVERT: HA 23 MET cc_start: 0.8608 (mtp) cc_final: 0.8331 (mtp) REVERT: HA 32 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8757 (tp) REVERT: HC 78 ARG cc_start: 0.8379 (mtp180) cc_final: 0.6820 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8313 (mttt) REVERT: HE 23 MET cc_start: 0.8827 (mtm) cc_final: 0.8623 (mtp) REVERT: IC 18 GLU cc_start: 0.7686 (tp30) cc_final: 0.7297 (tp30) REVERT: IC 21 ASP cc_start: 0.8997 (t70) cc_final: 0.8639 (t0) REVERT: IC 28 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7632 (mptt) REVERT: IC 43 THR cc_start: 0.9159 (m) cc_final: 0.8883 (p) REVERT: IC 62 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7588 (ttm170) REVERT: IC 82 ASN cc_start: 0.8763 (t0) cc_final: 0.8557 (t0) REVERT: IF 7 MET cc_start: 0.8458 (mtm) cc_final: 0.8188 (mtp) REVERT: IF 61 GLN cc_start: 0.8374 (tt0) cc_final: 0.8142 (tt0) REVERT: JA 16 MET cc_start: 0.8637 (tmm) cc_final: 0.8320 (tmm) REVERT: JA 21 ASP cc_start: 0.8736 (t70) cc_final: 0.8203 (t0) REVERT: JA 58 GLU cc_start: 0.7615 (tp30) cc_final: 0.7404 (tp30) REVERT: JC 78 ARG cc_start: 0.8367 (mtp180) cc_final: 0.6616 (mtt90) REVERT: JD 11 ARG cc_start: 0.8559 (ttt180) cc_final: 0.7969 (ttt180) REVERT: JD 28 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8181 (mttt) REVERT: JE 18 GLU cc_start: 0.8369 (tp30) cc_final: 0.8101 (tp30) REVERT: JE 43 THR cc_start: 0.9121 (m) cc_final: 0.8731 (p) REVERT: JE 67 VAL cc_start: 0.8870 (m) cc_final: 0.8640 (p) REVERT: JF 43 THR cc_start: 0.9590 (m) cc_final: 0.9222 (p) REVERT: JF 82 ASN cc_start: 0.9158 (t0) cc_final: 0.8835 (m-40) REVERT: KA 7 MET cc_start: 0.8814 (mtm) cc_final: 0.8586 (mtm) REVERT: KA 18 GLU cc_start: 0.8395 (tp30) cc_final: 0.8077 (tp30) REVERT: KB 62 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.7974 (mtt90) REVERT: KC 21 ASP cc_start: 0.8949 (t70) cc_final: 0.8485 (t0) REVERT: KC 28 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7934 (mptt) REVERT: KC 62 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.7421 (ttt180) REVERT: KD 11 ARG cc_start: 0.9029 (ttt90) cc_final: 0.8394 (ttt90) REVERT: KD 78 ARG cc_start: 0.8242 (tpt-90) cc_final: 0.7231 (mtm110) REVERT: KF 61 GLN cc_start: 0.8637 (tt0) cc_final: 0.8178 (tt0) REVERT: LA 11 ARG cc_start: 0.8590 (ttt90) cc_final: 0.8288 (ttt-90) REVERT: LB 11 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: LC 11 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: LC 78 ARG cc_start: 0.8050 (mtp180) cc_final: 0.6442 (mtt90) REVERT: LD 23 MET cc_start: 0.9126 (mtm) cc_final: 0.8691 (mtm) REVERT: LD 28 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8232 (mttt) REVERT: LD 89 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8933 (mm) REVERT: LE 18 GLU cc_start: 0.8500 (tp30) cc_final: 0.8210 (tp30) REVERT: LE 34 TYR cc_start: 0.8459 (p90) cc_final: 0.8163 (p90) REVERT: LF 43 THR cc_start: 0.9601 (m) cc_final: 0.9179 (p) outliers start: 106 outliers final: 75 residues processed: 1030 average time/residue: 0.5350 time to fit residues: 829.5725 Evaluate side-chains 989 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 912 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HA residue 32 ILE Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 37 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LC residue 10 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 209 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 429 optimal weight: 0.0970 chunk 211 optimal weight: 1.9990 chunk 384 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 128 ASN C 66 GLN F 15 GLN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GD 82 ASN HD 82 ASN HF 82 ASN JD 82 ASN LD 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33277 Z= 0.261 Angle : 0.567 9.280 45203 Z= 0.296 Chirality : 0.044 0.189 5423 Planarity : 0.003 0.042 5939 Dihedral : 4.179 30.099 4873 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.98 % Allowed : 13.19 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.76 (0.13), residues: 4439 helix: 0.07 (0.12), residues: 1902 sheet: -0.12 (0.15), residues: 1285 loop : -1.56 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 39 HIS 0.005 0.001 HIS A 165 PHE 0.011 0.002 PHE C 175 TYR 0.017 0.001 TYRLC 34 ARG 0.008 0.000 ARGGB 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 962 time to evaluate : 3.885 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: A 95 LYS cc_start: 0.9066 (tppp) cc_final: 0.8765 (tppt) REVERT: A 132 MET cc_start: 0.7373 (mtp) cc_final: 0.6897 (mtp) REVERT: A 163 ASN cc_start: 0.8278 (t0) cc_final: 0.7924 (t0) REVERT: A 165 HIS cc_start: 0.7582 (m170) cc_final: 0.7308 (m-70) REVERT: A 170 THR cc_start: 0.8803 (m) cc_final: 0.8368 (p) REVERT: B 120 TYR cc_start: 0.8744 (m-80) cc_final: 0.8512 (m-10) REVERT: B 170 THR cc_start: 0.8900 (m) cc_final: 0.8431 (p) REVERT: C 170 THR cc_start: 0.8947 (m) cc_final: 0.8702 (p) REVERT: D 99 ARG cc_start: 0.8127 (mtp-110) cc_final: 0.7834 (mtp85) REVERT: D 139 SER cc_start: 0.8688 (m) cc_final: 0.8144 (p) REVERT: F 175 PHE cc_start: 0.9015 (m-10) cc_final: 0.8760 (m-10) REVERT: F 179 TYR cc_start: 0.8695 (m-10) cc_final: 0.8309 (m-80) REVERT: GA 16 MET cc_start: 0.8898 (tmm) cc_final: 0.8434 (tmm) REVERT: GA 18 GLU cc_start: 0.8411 (tp30) cc_final: 0.8144 (tp30) REVERT: GC 21 ASP cc_start: 0.8659 (t70) cc_final: 0.8403 (t0) REVERT: GC 28 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7521 (mmtm) REVERT: GC 43 THR cc_start: 0.9095 (m) cc_final: 0.8676 (p) REVERT: GC 62 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.7530 (ttt180) REVERT: GC 82 ASN cc_start: 0.8870 (t0) cc_final: 0.8400 (t0) REVERT: GE 11 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7965 (ttt90) REVERT: GF 11 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8421 (ttm-80) REVERT: GF 18 GLU cc_start: 0.8781 (tp30) cc_final: 0.8373 (tp30) REVERT: GF 41 TYR cc_start: 0.9160 (m-10) cc_final: 0.8820 (m-10) REVERT: HA 32 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8723 (tp) REVERT: HC 78 ARG cc_start: 0.8434 (mtp180) cc_final: 0.6822 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8334 (mttt) REVERT: HF 61 GLN cc_start: 0.8648 (tt0) cc_final: 0.8418 (tm-30) REVERT: IA 11 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8126 (ttm-80) REVERT: IC 18 GLU cc_start: 0.7709 (tp30) cc_final: 0.7264 (tp30) REVERT: IC 21 ASP cc_start: 0.8989 (t70) cc_final: 0.8633 (t0) REVERT: IC 28 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7641 (mptt) REVERT: IC 43 THR cc_start: 0.9125 (m) cc_final: 0.8826 (p) REVERT: IC 62 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.7584 (ttm170) REVERT: ID 28 LYS cc_start: 0.8867 (tptt) cc_final: 0.8626 (tppt) REVERT: IF 7 MET cc_start: 0.8436 (mtm) cc_final: 0.8171 (mtp) REVERT: IF 36 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8410 (mtpp) REVERT: JA 16 MET cc_start: 0.8668 (tmm) cc_final: 0.8345 (tmm) REVERT: JA 21 ASP cc_start: 0.8727 (t70) cc_final: 0.8248 (t0) REVERT: JA 58 GLU cc_start: 0.7695 (tp30) cc_final: 0.7465 (tp30) REVERT: JC 78 ARG cc_start: 0.8396 (mtp180) cc_final: 0.6658 (mtt90) REVERT: JD 28 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8214 (mttt) REVERT: JE 18 GLU cc_start: 0.8371 (tp30) cc_final: 0.8125 (tp30) REVERT: JE 43 THR cc_start: 0.9110 (m) cc_final: 0.8734 (p) REVERT: JF 82 ASN cc_start: 0.9168 (t0) cc_final: 0.8832 (m-40) REVERT: KA 18 GLU cc_start: 0.8363 (tp30) cc_final: 0.8051 (tp30) REVERT: KA 62 ARG cc_start: 0.8345 (ttm110) cc_final: 0.8070 (ttm110) REVERT: KB 62 ARG cc_start: 0.8335 (mmt-90) cc_final: 0.7587 (mtm-85) REVERT: KB 78 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8374 (ttp-170) REVERT: KC 21 ASP cc_start: 0.8940 (t70) cc_final: 0.8515 (t0) REVERT: KC 28 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7914 (mptt) REVERT: KC 62 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.7467 (ttt180) REVERT: KD 11 ARG cc_start: 0.8993 (ttt90) cc_final: 0.8772 (ttt-90) REVERT: KD 78 ARG cc_start: 0.8263 (tpt-90) cc_final: 0.7193 (mtm110) REVERT: LA 11 ARG cc_start: 0.8598 (ttt90) cc_final: 0.8312 (ttt-90) REVERT: LA 18 GLU cc_start: 0.8455 (tp30) cc_final: 0.7488 (tp30) REVERT: LB 11 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: LB 16 MET cc_start: 0.8940 (tmm) cc_final: 0.8649 (tmm) REVERT: LC 11 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7941 (ttm170) REVERT: LC 78 ARG cc_start: 0.8031 (mtp180) cc_final: 0.6505 (mtm180) REVERT: LD 23 MET cc_start: 0.9130 (mtm) cc_final: 0.8698 (mtm) REVERT: LD 28 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8215 (mttt) REVERT: LD 89 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8998 (mm) REVERT: LE 18 GLU cc_start: 0.8519 (tp30) cc_final: 0.8310 (tp30) REVERT: LE 34 TYR cc_start: 0.8436 (p90) cc_final: 0.8167 (p90) REVERT: LF 43 THR cc_start: 0.9556 (m) cc_final: 0.9120 (p) outliers start: 127 outliers final: 84 residues processed: 1018 average time/residue: 0.5270 time to fit residues: 810.9508 Evaluate side-chains 996 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 909 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HA residue 32 ILE Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 37 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain JB residue 5 LEU Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KB residue 78 ARG Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain LA residue 37 THR Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 49 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 319 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 366 optimal weight: 0.6980 chunk 296 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 385 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN C 165 HIS ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 82 ASN HD 82 ASN JC 82 ASN JD 82 ASN KE 61 GLN LC 82 ASN LD 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33277 Z= 0.276 Angle : 0.581 8.864 45203 Z= 0.303 Chirality : 0.045 0.273 5423 Planarity : 0.003 0.038 5939 Dihedral : 4.112 30.682 4873 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.51 % Allowed : 14.60 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.49 (0.13), residues: 4439 helix: 0.38 (0.13), residues: 1856 sheet: 0.02 (0.15), residues: 1285 loop : -1.55 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 39 HIS 0.005 0.001 HISJB 74 PHE 0.021 0.002 PHE E 21 TYR 0.014 0.001 TYRLC 34 ARG 0.007 0.000 ARGKA 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 933 time to evaluate : 3.612 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: A 95 LYS cc_start: 0.9102 (tppp) cc_final: 0.8795 (tppt) REVERT: A 163 ASN cc_start: 0.8311 (t0) cc_final: 0.7951 (t0) REVERT: A 170 THR cc_start: 0.8814 (m) cc_final: 0.8388 (p) REVERT: A 195 GLU cc_start: 0.7484 (tp30) cc_final: 0.5650 (tp30) REVERT: A 199 ARG cc_start: 0.7062 (ptp-170) cc_final: 0.6593 (ptp-170) REVERT: B 120 TYR cc_start: 0.8757 (m-80) cc_final: 0.8535 (m-10) REVERT: B 170 THR cc_start: 0.8936 (m) cc_final: 0.8494 (p) REVERT: C 170 THR cc_start: 0.8990 (m) cc_final: 0.8748 (p) REVERT: D 50 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8402 (ttp80) REVERT: D 57 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8413 (mmtm) REVERT: D 99 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7914 (mtp85) REVERT: F 175 PHE cc_start: 0.8921 (m-10) cc_final: 0.8713 (m-10) REVERT: F 179 TYR cc_start: 0.8687 (m-10) cc_final: 0.8327 (m-80) REVERT: GA 16 MET cc_start: 0.8908 (tmm) cc_final: 0.8437 (tmm) REVERT: GA 18 GLU cc_start: 0.8453 (tp30) cc_final: 0.8196 (tp30) REVERT: GC 21 ASP cc_start: 0.8586 (t70) cc_final: 0.8312 (t0) REVERT: GC 28 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7627 (mmtm) REVERT: GC 43 THR cc_start: 0.9129 (m) cc_final: 0.8730 (p) REVERT: GC 82 ASN cc_start: 0.8852 (t0) cc_final: 0.8363 (t0) REVERT: GF 8 ILE cc_start: 0.9191 (mt) cc_final: 0.8954 (tt) REVERT: HA 32 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8678 (tp) REVERT: HC 7 MET cc_start: 0.8964 (mtm) cc_final: 0.8685 (mtp) REVERT: HC 78 ARG cc_start: 0.8441 (mtp180) cc_final: 0.6797 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8345 (mttt) REVERT: HE 62 ARG cc_start: 0.8860 (ttp-170) cc_final: 0.8658 (ttp-170) REVERT: IB 18 GLU cc_start: 0.8168 (tp30) cc_final: 0.7935 (tp30) REVERT: IC 18 GLU cc_start: 0.7743 (tp30) cc_final: 0.7322 (tp30) REVERT: IC 21 ASP cc_start: 0.8967 (t70) cc_final: 0.8630 (t0) REVERT: IC 28 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7599 (mptt) REVERT: IC 43 THR cc_start: 0.9137 (m) cc_final: 0.8860 (p) REVERT: IC 62 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.7597 (ttt180) REVERT: IF 62 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7620 (ttm170) REVERT: JA 16 MET cc_start: 0.8639 (tmm) cc_final: 0.8346 (tmm) REVERT: JA 21 ASP cc_start: 0.8708 (t70) cc_final: 0.8250 (t0) REVERT: JA 58 GLU cc_start: 0.7663 (tp30) cc_final: 0.7450 (tp30) REVERT: JC 78 ARG cc_start: 0.8414 (mtp180) cc_final: 0.6681 (mtt90) REVERT: JE 18 GLU cc_start: 0.8412 (tp30) cc_final: 0.7986 (tp30) REVERT: JE 43 THR cc_start: 0.9119 (m) cc_final: 0.8698 (p) REVERT: JF 82 ASN cc_start: 0.9169 (t0) cc_final: 0.8833 (m-40) REVERT: KA 7 MET cc_start: 0.8832 (mtm) cc_final: 0.8597 (mtm) REVERT: KA 18 GLU cc_start: 0.8387 (tp30) cc_final: 0.8080 (tp30) REVERT: KA 66 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7495 (ttp80) REVERT: KB 23 MET cc_start: 0.9467 (mtm) cc_final: 0.9266 (mtp) REVERT: KB 62 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.7625 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8951 (t70) cc_final: 0.8520 (t0) REVERT: KC 28 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7896 (mptt) REVERT: KC 62 ARG cc_start: 0.8695 (ttp-110) cc_final: 0.7454 (ttt180) REVERT: KD 78 ARG cc_start: 0.8264 (tpt-90) cc_final: 0.7210 (mtm110) REVERT: KF 8 ILE cc_start: 0.9165 (mt) cc_final: 0.8897 (tt) REVERT: LA 11 ARG cc_start: 0.8607 (ttt90) cc_final: 0.8351 (ttt-90) REVERT: LB 11 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: LB 16 MET cc_start: 0.8866 (tmm) cc_final: 0.8538 (tmm) REVERT: LC 11 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.7911 (ttm170) REVERT: LC 78 ARG cc_start: 0.8213 (mtp180) cc_final: 0.6612 (mtm-85) REVERT: LD 23 MET cc_start: 0.9132 (mtm) cc_final: 0.8715 (mtm) REVERT: LD 28 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8211 (mttt) REVERT: LD 82 ASN cc_start: 0.8813 (t0) cc_final: 0.8549 (t0) REVERT: LD 89 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8944 (mm) REVERT: LE 18 GLU cc_start: 0.8524 (tp30) cc_final: 0.8301 (tp30) REVERT: LF 43 THR cc_start: 0.9536 (m) cc_final: 0.9106 (p) REVERT: LF 82 ASN cc_start: 0.9110 (t0) cc_final: 0.8862 (t0) outliers start: 112 outliers final: 84 residues processed: 983 average time/residue: 0.5327 time to fit residues: 788.4453 Evaluate side-chains 977 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 891 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HA residue 32 ILE Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 46 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 37 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 49 ASP Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain LA residue 37 THR Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 49 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 1.9990 chunk 386 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 429 optimal weight: 0.5980 chunk 356 optimal weight: 0.2980 chunk 198 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN E 66 GLN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 82 ASN HD 82 ASN IE 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33277 Z= 0.258 Angle : 0.570 11.222 45203 Z= 0.297 Chirality : 0.045 0.231 5423 Planarity : 0.003 0.041 5939 Dihedral : 4.052 31.722 4873 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.60 % Allowed : 15.88 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.32 (0.13), residues: 4439 helix: 0.50 (0.13), residues: 1861 sheet: 0.12 (0.15), residues: 1285 loop : -1.45 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 39 HIS 0.006 0.001 HIS A 165 PHE 0.021 0.002 PHE D 21 TYR 0.014 0.001 TYR E 150 ARG 0.008 0.000 ARGGB 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 929 time to evaluate : 3.601 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: A 95 LYS cc_start: 0.9138 (tppp) cc_final: 0.8828 (tppt) REVERT: A 163 ASN cc_start: 0.8334 (t0) cc_final: 0.7958 (t0) REVERT: A 165 HIS cc_start: 0.7452 (m170) cc_final: 0.6925 (m170) REVERT: A 170 THR cc_start: 0.8774 (m) cc_final: 0.8354 (p) REVERT: A 195 GLU cc_start: 0.7554 (tp30) cc_final: 0.6126 (tp30) REVERT: A 199 ARG cc_start: 0.7253 (ptp-170) cc_final: 0.6903 (ptp-170) REVERT: B 120 TYR cc_start: 0.8762 (m-80) cc_final: 0.8558 (m-10) REVERT: B 163 ASN cc_start: 0.8281 (t0) cc_final: 0.8065 (t0) REVERT: B 170 THR cc_start: 0.8929 (m) cc_final: 0.8512 (p) REVERT: C 170 THR cc_start: 0.9006 (m) cc_final: 0.8758 (p) REVERT: D 57 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8494 (mmtm) REVERT: D 99 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7889 (mtp85) REVERT: F 175 PHE cc_start: 0.8869 (m-10) cc_final: 0.8644 (m-10) REVERT: F 179 TYR cc_start: 0.8689 (m-10) cc_final: 0.8360 (m-80) REVERT: GC 21 ASP cc_start: 0.8552 (t70) cc_final: 0.8198 (t0) REVERT: GC 28 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7525 (mmtm) REVERT: GC 43 THR cc_start: 0.9133 (m) cc_final: 0.8706 (p) REVERT: GC 82 ASN cc_start: 0.8837 (t0) cc_final: 0.8377 (t0) REVERT: GD 11 ARG cc_start: 0.8582 (ttt90) cc_final: 0.8279 (ttt90) REVERT: HA 32 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8597 (tp) REVERT: HC 78 ARG cc_start: 0.8403 (mtp180) cc_final: 0.6857 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8993 (ttpt) cc_final: 0.8336 (mttt) REVERT: IC 18 GLU cc_start: 0.7730 (tp30) cc_final: 0.7345 (tp30) REVERT: IC 21 ASP cc_start: 0.8955 (t70) cc_final: 0.8641 (t0) REVERT: IC 28 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7578 (mptt) REVERT: IC 43 THR cc_start: 0.9117 (m) cc_final: 0.8836 (p) REVERT: IC 62 ARG cc_start: 0.8706 (ttp-110) cc_final: 0.7632 (ttt180) REVERT: JA 16 MET cc_start: 0.8645 (tmm) cc_final: 0.8365 (tmm) REVERT: JA 21 ASP cc_start: 0.8712 (t70) cc_final: 0.8247 (t0) REVERT: JA 58 GLU cc_start: 0.7637 (tp30) cc_final: 0.7418 (tp30) REVERT: JC 78 ARG cc_start: 0.8419 (mtp180) cc_final: 0.6688 (mtt90) REVERT: JE 18 GLU cc_start: 0.8407 (tp30) cc_final: 0.7974 (tp30) REVERT: JE 43 THR cc_start: 0.9140 (m) cc_final: 0.8688 (p) REVERT: JF 82 ASN cc_start: 0.9173 (t0) cc_final: 0.8834 (m-40) REVERT: KA 18 GLU cc_start: 0.8343 (tp30) cc_final: 0.8025 (tp30) REVERT: KB 62 ARG cc_start: 0.8315 (mmt-90) cc_final: 0.7623 (mtm-85) REVERT: KC 7 MET cc_start: 0.8088 (mtm) cc_final: 0.7884 (mtm) REVERT: KC 21 ASP cc_start: 0.8906 (t70) cc_final: 0.8506 (t0) REVERT: KC 28 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7881 (mptt) REVERT: KC 62 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.7476 (ttt180) REVERT: KD 78 ARG cc_start: 0.8282 (tpt-90) cc_final: 0.7227 (mtm110) REVERT: KF 8 ILE cc_start: 0.9115 (mt) cc_final: 0.8903 (tt) REVERT: LA 11 ARG cc_start: 0.8582 (ttt90) cc_final: 0.8334 (ttt-90) REVERT: LB 11 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8088 (ttm-80) REVERT: LB 16 MET cc_start: 0.8901 (tmm) cc_final: 0.8551 (tmm) REVERT: LC 11 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7911 (ttm170) REVERT: LC 78 ARG cc_start: 0.8209 (mtp180) cc_final: 0.6618 (mtm-85) REVERT: LD 28 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8195 (mttt) REVERT: LD 82 ASN cc_start: 0.8879 (t0) cc_final: 0.8648 (t0) REVERT: LD 89 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8929 (mm) REVERT: LE 18 GLU cc_start: 0.8538 (tp30) cc_final: 0.8320 (tp30) REVERT: LF 43 THR cc_start: 0.9511 (m) cc_final: 0.9100 (p) REVERT: LF 82 ASN cc_start: 0.9093 (t0) cc_final: 0.8838 (t0) outliers start: 115 outliers final: 90 residues processed: 983 average time/residue: 0.5493 time to fit residues: 824.8487 Evaluate side-chains 987 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 895 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 5 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HA residue 32 ILE Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 37 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 49 ASP Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain LA residue 37 THR Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 49 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 31 LEU Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 313 optimal weight: 0.9980 chunk 243 optimal weight: 0.7980 chunk 361 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 427 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 260 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 82 ASN HD 82 ASN IE 61 GLN JF 61 GLN KD 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33277 Z= 0.280 Angle : 0.580 10.359 45203 Z= 0.302 Chirality : 0.045 0.196 5423 Planarity : 0.003 0.038 5939 Dihedral : 4.044 32.478 4873 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.63 % Allowed : 16.60 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.20 (0.13), residues: 4439 helix: 0.51 (0.13), residues: 1892 sheet: 0.18 (0.15), residues: 1285 loop : -1.28 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 39 HIS 0.009 0.001 HIS A 165 PHE 0.022 0.002 PHE D 21 TYR 0.014 0.001 TYR E 8 ARG 0.007 0.000 ARGGB 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 915 time to evaluate : 4.096 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: A 115 ARG cc_start: 0.8319 (mmt180) cc_final: 0.7998 (mmt90) REVERT: A 132 MET cc_start: 0.7965 (ttm) cc_final: 0.7275 (ttm) REVERT: A 163 ASN cc_start: 0.8337 (t0) cc_final: 0.7995 (t0) REVERT: A 165 HIS cc_start: 0.7348 (m-70) cc_final: 0.7135 (m170) REVERT: A 170 THR cc_start: 0.8761 (m) cc_final: 0.8339 (p) REVERT: A 195 GLU cc_start: 0.7629 (tp30) cc_final: 0.6924 (tp30) REVERT: B 170 THR cc_start: 0.8950 (m) cc_final: 0.8519 (p) REVERT: C 170 THR cc_start: 0.9049 (m) cc_final: 0.8790 (p) REVERT: D 150 TYR cc_start: 0.8252 (m-80) cc_final: 0.7930 (m-80) REVERT: F 175 PHE cc_start: 0.8811 (m-10) cc_final: 0.8579 (m-80) REVERT: F 179 TYR cc_start: 0.8697 (m-10) cc_final: 0.8345 (m-80) REVERT: GC 21 ASP cc_start: 0.8523 (t70) cc_final: 0.8197 (t0) REVERT: GC 28 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7633 (mmtm) REVERT: GC 43 THR cc_start: 0.9151 (m) cc_final: 0.8703 (p) REVERT: GC 82 ASN cc_start: 0.8823 (t0) cc_final: 0.8374 (t0) REVERT: GD 11 ARG cc_start: 0.8590 (ttt90) cc_final: 0.8025 (ttt90) REVERT: GD 69 GLU cc_start: 0.7943 (tt0) cc_final: 0.7694 (tt0) REVERT: GD 78 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7191 (mtm180) REVERT: GF 18 GLU cc_start: 0.8785 (tp30) cc_final: 0.8355 (tp30) REVERT: HA 32 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8636 (tp) REVERT: HC 58 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8196 (tm-30) REVERT: HC 78 ARG cc_start: 0.8375 (mtp180) cc_final: 0.6875 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8328 (mttt) REVERT: HD 32 ILE cc_start: 0.9237 (pp) cc_final: 0.9030 (pp) REVERT: IB 18 GLU cc_start: 0.8161 (tp30) cc_final: 0.7911 (tp30) REVERT: IC 18 GLU cc_start: 0.7750 (tp30) cc_final: 0.7398 (tp30) REVERT: IC 21 ASP cc_start: 0.8939 (t70) cc_final: 0.8650 (t0) REVERT: IC 28 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7545 (mptt) REVERT: IC 43 THR cc_start: 0.9120 (m) cc_final: 0.8827 (p) REVERT: IC 62 ARG cc_start: 0.8711 (ttp-110) cc_final: 0.7625 (ttt180) REVERT: JA 16 MET cc_start: 0.8633 (tmm) cc_final: 0.8348 (tmm) REVERT: JA 21 ASP cc_start: 0.8747 (t70) cc_final: 0.8289 (t0) REVERT: JA 58 GLU cc_start: 0.7664 (tp30) cc_final: 0.7422 (tp30) REVERT: JC 78 ARG cc_start: 0.8427 (mtp180) cc_final: 0.6700 (mtt90) REVERT: JE 18 GLU cc_start: 0.8452 (tp30) cc_final: 0.8059 (tp30) REVERT: JE 43 THR cc_start: 0.9053 (m) cc_final: 0.8612 (p) REVERT: JF 82 ASN cc_start: 0.9178 (t0) cc_final: 0.8831 (m-40) REVERT: KA 18 GLU cc_start: 0.8349 (tp30) cc_final: 0.8026 (tp30) REVERT: KB 62 ARG cc_start: 0.8318 (mmt-90) cc_final: 0.7635 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8911 (t70) cc_final: 0.8500 (t0) REVERT: KC 28 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7907 (mptt) REVERT: KC 62 ARG cc_start: 0.8705 (ttp-110) cc_final: 0.7485 (ttt180) REVERT: KD 11 ARG cc_start: 0.8980 (ttt90) cc_final: 0.8405 (ttt90) REVERT: KD 78 ARG cc_start: 0.8288 (tpt-90) cc_final: 0.7231 (mtm110) REVERT: LA 11 ARG cc_start: 0.8600 (ttt90) cc_final: 0.8340 (ttt-90) REVERT: LB 11 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8089 (ttm-80) REVERT: LC 11 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7896 (ttm170) REVERT: LC 78 ARG cc_start: 0.8224 (mtp180) cc_final: 0.6619 (mtm-85) REVERT: LD 16 MET cc_start: 0.9230 (tmm) cc_final: 0.8853 (tmm) REVERT: LD 23 MET cc_start: 0.9160 (mtm) cc_final: 0.8927 (mtp) REVERT: LD 28 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8150 (mttt) REVERT: LD 89 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8964 (mm) REVERT: LE 18 GLU cc_start: 0.8589 (tp30) cc_final: 0.8339 (tp30) REVERT: LF 43 THR cc_start: 0.9517 (m) cc_final: 0.9099 (p) REVERT: LF 82 ASN cc_start: 0.9094 (t0) cc_final: 0.8872 (t0) outliers start: 116 outliers final: 96 residues processed: 971 average time/residue: 0.5221 time to fit residues: 766.1249 Evaluate side-chains 992 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 894 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 5 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HA residue 32 ILE Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 37 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 49 ASP Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 32 ILE Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KF residue 89 LEU Chi-restraints excluded: chain LA residue 37 THR Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 49 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 31 LEU Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 336 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 82 ASN HD 82 ASN KD 82 ASN KE 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33277 Z= 0.292 Angle : 0.589 10.267 45203 Z= 0.307 Chirality : 0.045 0.232 5423 Planarity : 0.003 0.029 5939 Dihedral : 4.052 32.771 4873 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.57 % Allowed : 16.79 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.13 (0.13), residues: 4439 helix: 0.64 (0.13), residues: 1856 sheet: 0.22 (0.15), residues: 1285 loop : -1.30 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 39 HIS 0.005 0.001 HISJB 74 PHE 0.015 0.001 PHE E 21 TYR 0.019 0.001 TYR E 8 ARG 0.007 0.000 ARGJE 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 911 time to evaluate : 3.607 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: A 95 LYS cc_start: 0.9155 (tppp) cc_final: 0.8507 (tppt) REVERT: A 132 MET cc_start: 0.8056 (ttm) cc_final: 0.7373 (ttm) REVERT: A 163 ASN cc_start: 0.8383 (t0) cc_final: 0.8028 (t0) REVERT: A 165 HIS cc_start: 0.7385 (m-70) cc_final: 0.7149 (m-70) REVERT: A 170 THR cc_start: 0.8793 (m) cc_final: 0.8385 (p) REVERT: A 175 PHE cc_start: 0.8609 (m-10) cc_final: 0.8190 (m-10) REVERT: B 159 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6443 (tm-30) REVERT: B 170 THR cc_start: 0.8940 (m) cc_final: 0.8519 (p) REVERT: C 170 THR cc_start: 0.9061 (m) cc_final: 0.8797 (p) REVERT: D 150 TYR cc_start: 0.8286 (m-80) cc_final: 0.7950 (m-80) REVERT: E 115 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8075 (mmt180) REVERT: F 95 LYS cc_start: 0.9189 (tptp) cc_final: 0.8951 (tptp) REVERT: F 175 PHE cc_start: 0.8788 (m-10) cc_final: 0.8559 (m-80) REVERT: F 179 TYR cc_start: 0.8703 (m-10) cc_final: 0.8303 (m-80) REVERT: GC 21 ASP cc_start: 0.8523 (t70) cc_final: 0.8211 (t0) REVERT: GC 28 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7633 (mmtm) REVERT: GC 43 THR cc_start: 0.8973 (m) cc_final: 0.8716 (p) REVERT: GC 82 ASN cc_start: 0.8813 (t0) cc_final: 0.8379 (t0) REVERT: GD 11 ARG cc_start: 0.8625 (ttt90) cc_final: 0.8059 (ttt90) REVERT: GD 69 GLU cc_start: 0.7937 (tt0) cc_final: 0.7686 (tt0) REVERT: GD 78 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7172 (mtm180) REVERT: HC 78 ARG cc_start: 0.8402 (mtp180) cc_final: 0.6911 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8322 (mttt) REVERT: HD 32 ILE cc_start: 0.9255 (pp) cc_final: 0.9048 (pp) REVERT: HE 11 ARG cc_start: 0.8497 (ttt90) cc_final: 0.8007 (ttt90) REVERT: IB 18 GLU cc_start: 0.8195 (tp30) cc_final: 0.7936 (tp30) REVERT: IC 7 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8665 (mtm) REVERT: IC 18 GLU cc_start: 0.7748 (tp30) cc_final: 0.7413 (tp30) REVERT: IC 21 ASP cc_start: 0.8943 (t70) cc_final: 0.8655 (t0) REVERT: IC 28 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7539 (mptt) REVERT: IC 43 THR cc_start: 0.9105 (m) cc_final: 0.8867 (p) REVERT: IC 62 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.7633 (ttt180) REVERT: JA 16 MET cc_start: 0.8648 (tmm) cc_final: 0.8428 (tmm) REVERT: JA 18 GLU cc_start: 0.8548 (tp30) cc_final: 0.7848 (tp30) REVERT: JA 21 ASP cc_start: 0.8791 (t70) cc_final: 0.8364 (t0) REVERT: JA 58 GLU cc_start: 0.7640 (tp30) cc_final: 0.7438 (tp30) REVERT: JC 78 ARG cc_start: 0.8489 (mtp180) cc_final: 0.6657 (mtt90) REVERT: JE 18 GLU cc_start: 0.8440 (tp30) cc_final: 0.8026 (tp30) REVERT: JE 43 THR cc_start: 0.9133 (m) cc_final: 0.8684 (p) REVERT: JF 82 ASN cc_start: 0.9171 (t0) cc_final: 0.8827 (m-40) REVERT: KA 18 GLU cc_start: 0.8379 (tp30) cc_final: 0.8063 (tp30) REVERT: KB 62 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.7541 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8917 (t70) cc_final: 0.8509 (t0) REVERT: KC 28 LYS cc_start: 0.8140 (ttpt) cc_final: 0.7849 (mptt) REVERT: KC 62 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.7509 (ttt180) REVERT: KD 11 ARG cc_start: 0.8977 (ttt90) cc_final: 0.8409 (ttt90) REVERT: KD 78 ARG cc_start: 0.8282 (tpt-90) cc_final: 0.7214 (mtm110) REVERT: LA 11 ARG cc_start: 0.8600 (ttt90) cc_final: 0.8310 (ttt90) REVERT: LC 11 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7927 (ttm170) REVERT: LC 78 ARG cc_start: 0.8231 (mtp180) cc_final: 0.6623 (mtm-85) REVERT: LD 16 MET cc_start: 0.9243 (tmm) cc_final: 0.8874 (tmm) REVERT: LD 23 MET cc_start: 0.9175 (mtm) cc_final: 0.8906 (mtp) REVERT: LD 28 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8144 (mttt) REVERT: LD 89 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8980 (mm) REVERT: LE 18 GLU cc_start: 0.8607 (tp30) cc_final: 0.8348 (tp30) REVERT: LF 43 THR cc_start: 0.9525 (m) cc_final: 0.9122 (p) REVERT: LF 82 ASN cc_start: 0.9112 (t0) cc_final: 0.8871 (t0) outliers start: 114 outliers final: 92 residues processed: 962 average time/residue: 0.5308 time to fit residues: 767.4560 Evaluate side-chains 989 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 895 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IC residue 7 MET Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 49 ASP Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JC residue 89 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 32 ILE Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain LA residue 37 THR Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 49 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.9990 chunk 409 optimal weight: 0.5980 chunk 374 optimal weight: 0.8980 chunk 398 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 173 optimal weight: 0.4980 chunk 313 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 360 optimal weight: 0.4980 chunk 377 optimal weight: 0.8980 chunk 397 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 163 ASN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HD 82 ASN KD 82 ASN KE 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33277 Z= 0.258 Angle : 0.590 10.598 45203 Z= 0.306 Chirality : 0.045 0.189 5423 Planarity : 0.003 0.029 5939 Dihedral : 4.009 28.960 4873 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.41 % Allowed : 17.42 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.00 (0.13), residues: 4439 helix: 0.71 (0.13), residues: 1855 sheet: 0.79 (0.16), residues: 1069 loop : -1.45 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 39 HIS 0.005 0.001 HISKF 74 PHE 0.014 0.001 PHE E 21 TYR 0.021 0.001 TYR E 8 ARG 0.013 0.000 ARGGF 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 912 time to evaluate : 3.678 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: A 132 MET cc_start: 0.8083 (ttm) cc_final: 0.7367 (ttm) REVERT: A 163 ASN cc_start: 0.8332 (t0) cc_final: 0.7987 (t0) REVERT: A 165 HIS cc_start: 0.7400 (m-70) cc_final: 0.7119 (m-70) REVERT: A 170 THR cc_start: 0.8745 (m) cc_final: 0.8346 (p) REVERT: B 159 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6512 (tm-30) REVERT: B 170 THR cc_start: 0.8901 (m) cc_final: 0.8511 (p) REVERT: C 115 ARG cc_start: 0.8154 (mmt180) cc_final: 0.7787 (mtt-85) REVERT: C 170 THR cc_start: 0.9047 (m) cc_final: 0.8791 (p) REVERT: D 150 TYR cc_start: 0.8237 (m-80) cc_final: 0.7979 (m-80) REVERT: F 95 LYS cc_start: 0.9192 (tptp) cc_final: 0.8975 (tptp) REVERT: F 175 PHE cc_start: 0.8755 (m-10) cc_final: 0.8532 (m-80) REVERT: F 179 TYR cc_start: 0.8733 (m-10) cc_final: 0.8341 (m-80) REVERT: GA 16 MET cc_start: 0.8382 (tmm) cc_final: 0.8135 (tmm) REVERT: GC 21 ASP cc_start: 0.8505 (t70) cc_final: 0.8263 (t0) REVERT: GC 28 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7589 (mmtm) REVERT: GC 34 TYR cc_start: 0.8743 (p90) cc_final: 0.8365 (p90) REVERT: GC 43 THR cc_start: 0.8946 (m) cc_final: 0.8616 (p) REVERT: GC 82 ASN cc_start: 0.8823 (t0) cc_final: 0.8378 (t0) REVERT: GD 11 ARG cc_start: 0.8635 (ttt90) cc_final: 0.8092 (ttt90) REVERT: GD 69 GLU cc_start: 0.7935 (tt0) cc_final: 0.7691 (tt0) REVERT: GD 78 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7163 (mtm180) REVERT: HC 11 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7938 (ttm170) REVERT: HC 78 ARG cc_start: 0.8382 (mtp180) cc_final: 0.6928 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8318 (mttt) REVERT: HD 32 ILE cc_start: 0.9237 (pp) cc_final: 0.9031 (pp) REVERT: HE 11 ARG cc_start: 0.8495 (ttt90) cc_final: 0.8003 (ttt90) REVERT: IB 18 GLU cc_start: 0.8192 (tp30) cc_final: 0.7892 (tp30) REVERT: IB 35 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8231 (mm-30) REVERT: IC 7 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8666 (mtm) REVERT: IC 18 GLU cc_start: 0.7722 (tp30) cc_final: 0.7406 (tp30) REVERT: IC 21 ASP cc_start: 0.8944 (t70) cc_final: 0.8647 (t0) REVERT: IC 28 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7538 (mptt) REVERT: IC 43 THR cc_start: 0.9116 (m) cc_final: 0.8888 (p) REVERT: IC 62 ARG cc_start: 0.8732 (ttp-110) cc_final: 0.7628 (ttt180) REVERT: IE 7 MET cc_start: 0.8053 (mtm) cc_final: 0.7806 (mtm) REVERT: JA 16 MET cc_start: 0.8644 (tmm) cc_final: 0.8417 (tmm) REVERT: JA 18 GLU cc_start: 0.8550 (tp30) cc_final: 0.7833 (tp30) REVERT: JA 21 ASP cc_start: 0.8786 (t70) cc_final: 0.8379 (t0) REVERT: JA 58 GLU cc_start: 0.7635 (tp30) cc_final: 0.7427 (tp30) REVERT: JC 78 ARG cc_start: 0.8492 (mtp180) cc_final: 0.6653 (mtt90) REVERT: JE 18 GLU cc_start: 0.8443 (tp30) cc_final: 0.8058 (tp30) REVERT: JE 43 THR cc_start: 0.9129 (m) cc_final: 0.8669 (p) REVERT: JF 82 ASN cc_start: 0.9164 (t0) cc_final: 0.8818 (m-40) REVERT: KA 18 GLU cc_start: 0.8355 (tp30) cc_final: 0.8052 (tp30) REVERT: KB 62 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.7533 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8907 (t70) cc_final: 0.8480 (t0) REVERT: KC 28 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7886 (mptt) REVERT: KC 62 ARG cc_start: 0.8732 (ttp-110) cc_final: 0.7527 (ttt180) REVERT: KD 11 ARG cc_start: 0.8974 (ttt90) cc_final: 0.8407 (ttt90) REVERT: KD 78 ARG cc_start: 0.8285 (tpt-90) cc_final: 0.7243 (mtm110) REVERT: LA 11 ARG cc_start: 0.8600 (ttt90) cc_final: 0.8313 (ttt90) REVERT: LB 11 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.7923 (ttm-80) REVERT: LC 11 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.7863 (ttm170) REVERT: LC 78 ARG cc_start: 0.8222 (mtp180) cc_final: 0.6623 (mtm-85) REVERT: LD 16 MET cc_start: 0.9223 (tmm) cc_final: 0.8857 (tmm) REVERT: LD 23 MET cc_start: 0.9175 (mtm) cc_final: 0.8544 (mtm) REVERT: LD 28 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8154 (mttt) REVERT: LD 89 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8972 (mm) REVERT: LE 18 GLU cc_start: 0.8596 (tp30) cc_final: 0.8325 (tp30) REVERT: LF 43 THR cc_start: 0.9520 (m) cc_final: 0.9119 (p) REVERT: LF 82 ASN cc_start: 0.9103 (t0) cc_final: 0.8854 (t0) outliers start: 109 outliers final: 96 residues processed: 960 average time/residue: 0.5209 time to fit residues: 759.9819 Evaluate side-chains 988 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 890 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 5 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IC residue 7 MET Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 49 ASP Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JC residue 89 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 32 ILE Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain LA residue 37 THR Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 49 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 5 LEU Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.6980 chunk 421 optimal weight: 0.5980 chunk 257 optimal weight: 0.9990 chunk 200 optimal weight: 0.0870 chunk 293 optimal weight: 0.6980 chunk 442 optimal weight: 0.5980 chunk 407 optimal weight: 0.7980 chunk 352 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HD 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33277 Z= 0.236 Angle : 0.585 10.083 45203 Z= 0.303 Chirality : 0.045 0.325 5423 Planarity : 0.003 0.039 5939 Dihedral : 3.982 30.117 4873 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.94 % Allowed : 18.33 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.11 (0.13), residues: 4439 helix: 0.82 (0.13), residues: 1855 sheet: 0.79 (0.15), residues: 1069 loop : -1.36 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 39 HIS 0.005 0.001 HISKF 74 PHE 0.017 0.001 PHE B 29 TYR 0.021 0.001 TYR E 8 ARG 0.011 0.000 ARGGF 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 908 time to evaluate : 3.668 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: A 76 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6189 (tm-30) REVERT: A 132 MET cc_start: 0.8103 (ttm) cc_final: 0.7462 (ttm) REVERT: A 163 ASN cc_start: 0.8315 (t0) cc_final: 0.8093 (t0) REVERT: A 165 HIS cc_start: 0.7383 (m-70) cc_final: 0.7130 (m-70) REVERT: A 170 THR cc_start: 0.8775 (m) cc_final: 0.8371 (p) REVERT: B 159 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6499 (tm-30) REVERT: B 170 THR cc_start: 0.8890 (m) cc_final: 0.8499 (p) REVERT: C 170 THR cc_start: 0.9046 (m) cc_final: 0.8789 (p) REVERT: F 95 LYS cc_start: 0.9204 (tptp) cc_final: 0.8993 (tptp) REVERT: F 179 TYR cc_start: 0.8713 (m-10) cc_final: 0.8388 (m-80) REVERT: GC 21 ASP cc_start: 0.8482 (t70) cc_final: 0.8243 (t0) REVERT: GC 28 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7627 (mmtm) REVERT: GC 34 TYR cc_start: 0.8652 (p90) cc_final: 0.8348 (p90) REVERT: GC 82 ASN cc_start: 0.8794 (t0) cc_final: 0.8356 (t0) REVERT: GD 11 ARG cc_start: 0.8639 (ttt90) cc_final: 0.8133 (ttt90) REVERT: GD 78 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7158 (mtm180) REVERT: GE 25 LYS cc_start: 0.9233 (mtmt) cc_final: 0.9003 (mtmt) REVERT: HC 11 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7904 (ttm170) REVERT: HC 78 ARG cc_start: 0.8421 (mtp180) cc_final: 0.6842 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8321 (mttt) REVERT: HD 32 ILE cc_start: 0.9234 (pp) cc_final: 0.9028 (pp) REVERT: HE 62 ARG cc_start: 0.8882 (ttp-170) cc_final: 0.8667 (ttp-170) REVERT: IB 18 GLU cc_start: 0.8193 (tp30) cc_final: 0.7933 (tp30) REVERT: IC 18 GLU cc_start: 0.7701 (tp30) cc_final: 0.7396 (tp30) REVERT: IC 21 ASP cc_start: 0.8954 (t70) cc_final: 0.8671 (t0) REVERT: IC 28 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7557 (mptt) REVERT: IC 43 THR cc_start: 0.9092 (m) cc_final: 0.8865 (p) REVERT: IC 62 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.7621 (ttt180) REVERT: IE 7 MET cc_start: 0.7983 (mtm) cc_final: 0.7776 (mtm) REVERT: JA 16 MET cc_start: 0.8637 (tmm) cc_final: 0.8382 (tmm) REVERT: JA 21 ASP cc_start: 0.8791 (t70) cc_final: 0.8348 (t0) REVERT: JA 58 GLU cc_start: 0.7602 (tp30) cc_final: 0.7387 (tp30) REVERT: JC 78 ARG cc_start: 0.8490 (mtp180) cc_final: 0.6655 (mtt90) REVERT: JE 18 GLU cc_start: 0.8435 (tp30) cc_final: 0.8058 (tp30) REVERT: JE 43 THR cc_start: 0.9110 (m) cc_final: 0.8645 (p) REVERT: JF 82 ASN cc_start: 0.9160 (t0) cc_final: 0.8816 (m-40) REVERT: KA 18 GLU cc_start: 0.8372 (tp30) cc_final: 0.8100 (tp30) REVERT: KB 62 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7518 (mtm-85) REVERT: KC 7 MET cc_start: 0.7983 (mtp) cc_final: 0.7727 (mtm) REVERT: KC 21 ASP cc_start: 0.8890 (t70) cc_final: 0.8450 (t0) REVERT: KC 28 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7827 (mptt) REVERT: KC 62 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.7503 (ttt180) REVERT: KD 11 ARG cc_start: 0.8975 (ttt90) cc_final: 0.8403 (ttt90) REVERT: KD 78 ARG cc_start: 0.8281 (tpt-90) cc_final: 0.7246 (mtm110) REVERT: LA 11 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8329 (ttt90) REVERT: LC 11 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7915 (ttm170) REVERT: LC 78 ARG cc_start: 0.8221 (mtp180) cc_final: 0.6669 (mtm-85) REVERT: LD 16 MET cc_start: 0.9231 (tmm) cc_final: 0.8882 (tmm) REVERT: LD 23 MET cc_start: 0.9172 (mtm) cc_final: 0.8533 (mtm) REVERT: LD 28 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8157 (mttt) REVERT: LD 89 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8972 (mm) REVERT: LE 18 GLU cc_start: 0.8584 (tp30) cc_final: 0.8377 (tp30) REVERT: LF 43 THR cc_start: 0.9508 (m) cc_final: 0.9097 (p) REVERT: LF 82 ASN cc_start: 0.9079 (t0) cc_final: 0.8824 (t0) outliers start: 94 outliers final: 89 residues processed: 950 average time/residue: 0.5326 time to fit residues: 765.7934 Evaluate side-chains 979 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 889 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 5 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 49 ASP Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 49 ASP Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 49 ASP Chi-restraints excluded: chain JB residue 92 THR Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 32 ILE Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 49 ASP Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 5 LEU Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 49 ASP Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 352 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 82 ASN GB 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.079900 restraints weight = 61556.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.082222 restraints weight = 29140.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.083738 restraints weight = 16418.088| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 33277 Z= 0.529 Angle : 0.710 10.531 45203 Z= 0.371 Chirality : 0.050 0.316 5423 Planarity : 0.004 0.035 5939 Dihedral : 4.350 36.916 4873 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.10 % Allowed : 18.58 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.26 (0.13), residues: 4439 helix: 0.43 (0.13), residues: 1856 sheet: 0.23 (0.15), residues: 1285 loop : -1.29 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 39 HIS 0.007 0.001 HISKE 74 PHE 0.022 0.002 PHE B 29 TYR 0.026 0.002 TYR E 8 ARG 0.013 0.001 ARGGF 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11378.68 seconds wall clock time: 203 minutes 19.18 seconds (12199.18 seconds total)