Starting phenix.real_space_refine on Thu Jan 18 02:50:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0g_9315/01_2024/6n0g_9315.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0g_9315/01_2024/6n0g_9315.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/6n0g_9315/01_2024/6n0g_9315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0g_9315/01_2024/6n0g_9315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0g_9315/01_2024/6n0g_9315.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n0g_9315/01_2024/6n0g_9315.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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 186 5.16 5 C 35202 2.51 5 N 9867 2.21 5 O 10389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 148": "NH1" <-> "NH2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 199": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "P ARG 199": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 99": "NH1" <-> "NH2" Residue "R TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 50": "NH1" <-> "NH2" Residue "U ARG 115": "NH1" <-> "NH2" Residue "V PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 199": "NH1" <-> "NH2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 70": "NH1" <-> "NH2" Residue "X ARG 99": "NH1" <-> "NH2" Residue "X TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 55644 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "B" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "C" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "GA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "ID" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "G" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "H" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "I" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "J" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "K" 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: "L" 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: "M" 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: "N" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "O" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "P" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "Q" 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: "R" 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: "S" 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: "T" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "U" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "V" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "W" 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: "X" 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} Time building chain proxies: 22.01, per 1000 atoms: 0.40 Number of scatterers: 55644 At special positions: 0 Unit cell: (158.62, 295.61, 259.56, 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 186 16.00 O 10389 8.00 N 9867 7.00 C 35202 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: 15.45 Conformation dependent library (CDL) restraints added in 7.9 seconds 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13686 Finding SS restraints... Secondary structure from input PDB file: 257 helices and 78 sheets defined 43.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.782A pdb=" N GLY A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.935A pdb=" N ARG A 103 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.947A pdb=" N PHE B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 9 " --> pdb=" O GLU B 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5 through 9' Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.536A pdb=" N TRP B 102 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.853A pdb=" N PHE C 8 " --> pdb=" O PRO C 5 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 9 " --> pdb=" O GLU C 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 9' Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.677A pdb=" N GLY C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 removed outlier: 4.021A pdb=" N ARG C 103 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.718A pdb=" N ALA C 132 " --> pdb=" O THR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.592A pdb=" N METGA 16 " --> pdb=" O GLYGA 12 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 4.090A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 removed outlier: 3.524A pdb=" N ASPGA 84 " --> pdb=" O HISGA 80 " (cutoff:3.500A) Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.795A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 63 removed outlier: 3.809A pdb=" N ARGGB 62 " --> pdb=" O GLUGB 58 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 87 Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.532A pdb=" N ALAGC 27 " --> pdb=" O METGC 23 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.894A pdb=" N ARGGC 62 " --> pdb=" O GLUGC 58 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 Processing helix chain 'GD' and resid 12 through 26 Processing helix chain 'GD' and resid 49 through 65 removed outlier: 3.846A 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: 3.606A pdb=" N ALAGE 27 " --> pdb=" O METGE 23 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 4.114A pdb=" N ARGGE 62 " --> pdb=" O GLUGE 58 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 Processing helix chain 'GF' and resid 12 through 27 Processing helix chain 'GF' and resid 49 through 65 removed outlier: 3.987A pdb=" N ARGGF 62 " --> pdb=" O GLUGF 58 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 27 removed outlier: 3.600A pdb=" N ALAHA 27 " --> pdb=" O METHA 23 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 4.100A pdb=" N ARGHA 62 " --> pdb=" O GLUHA 58 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 87 Processing helix chain 'HB' and resid 12 through 26 Processing helix chain 'HB' and resid 49 through 65 removed outlier: 3.709A pdb=" N ARGHB 62 " --> pdb=" O GLUHB 58 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 87 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.634A pdb=" N ALAHC 27 " --> pdb=" O METHC 23 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.733A 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: 3.508A pdb=" N METHD 16 " --> pdb=" O GLYHD 12 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 3.528A pdb=" N ARGHD 62 " --> pdb=" O GLUHD 58 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.622A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 removed outlier: 3.950A pdb=" N ARGHE 62 " --> pdb=" O GLUHE 58 " (cutoff:3.500A) Processing helix chain 'HE' and resid 80 through 87 Processing helix chain 'HF' and resid 12 through 26 Processing helix chain 'HF' and resid 49 through 66 removed outlier: 3.893A pdb=" N ARGHF 62 " --> pdb=" O GLUHF 58 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARGHF 66 " --> pdb=" O ARGHF 62 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 removed outlier: 3.566A pdb=" N ASPHF 84 " --> pdb=" O HISHF 80 " (cutoff:3.500A) Processing helix chain 'IA' and resid 12 through 27 Processing helix chain 'IA' and resid 49 through 65 removed outlier: 4.147A pdb=" N ARGIA 62 " --> pdb=" O GLUIA 58 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.782A pdb=" N ALAIB 27 " --> pdb=" O METIB 23 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 61 Processing helix chain 'IB' and resid 80 through 87 Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.593A pdb=" N ALAIC 27 " --> pdb=" O METIC 23 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 4.090A pdb=" N ARGIC 62 " --> pdb=" O GLUIC 58 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.725A pdb=" N ALAID 27 " --> pdb=" O METID 23 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 3.844A 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: 3.603A pdb=" N ALAIE 27 " --> pdb=" O METIE 23 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 65 removed outlier: 3.982A pdb=" N ARGIE 62 " --> pdb=" O GLUIE 58 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 Processing helix chain 'IF' and resid 49 through 65 removed outlier: 4.088A pdb=" N ARGIF 62 " --> pdb=" O GLUIF 58 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.593A pdb=" N ALAJA 27 " --> pdb=" O METJA 23 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 65 removed outlier: 3.948A pdb=" N ARGJA 62 " --> pdb=" O GLUJA 58 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 Processing helix chain 'JB' and resid 12 through 26 Processing helix chain 'JB' and resid 49 through 65 removed outlier: 3.693A pdb=" N ARGJB 62 " --> pdb=" O GLUJB 58 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 87 Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.612A pdb=" N ALAJC 27 " --> pdb=" O METJC 23 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 65 removed outlier: 3.803A pdb=" N ARGJC 62 " --> pdb=" O GLUJC 58 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.521A pdb=" N METJD 16 " --> pdb=" O GLYJD 12 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 65 removed outlier: 3.611A pdb=" N ARGJD 62 " --> pdb=" O GLUJD 58 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 87 Processing helix chain 'JE' and resid 12 through 26 Processing helix chain 'JE' and resid 49 through 65 removed outlier: 3.921A pdb=" N ARGJE 62 " --> pdb=" O GLUJE 58 " (cutoff:3.500A) Processing helix chain 'JE' and resid 80 through 87 Processing helix chain 'JF' and resid 12 through 27 Processing helix chain 'JF' and resid 49 through 66 removed outlier: 3.845A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARGJF 66 " --> pdb=" O ARGJF 62 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 removed outlier: 3.650A pdb=" N ASPJF 84 " --> pdb=" O HISJF 80 " (cutoff:3.500A) Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.548A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 65 removed outlier: 4.016A pdb=" N ARGKA 62 " --> pdb=" O GLUKA 58 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.705A pdb=" N ALAKB 27 " --> pdb=" O METKB 23 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 3.916A pdb=" N ARGKB 62 " --> pdb=" O GLUKB 58 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 87 Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.618A pdb=" N ALAKC 27 " --> pdb=" O METKC 23 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.981A pdb=" N ARGKC 62 " --> pdb=" O GLUKC 58 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 Processing helix chain 'KD' and resid 12 through 26 Processing helix chain 'KD' and resid 49 through 65 removed outlier: 4.010A 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: 3.600A pdb=" N ALAKE 27 " --> pdb=" O METKE 23 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 4.152A pdb=" N ARGKE 62 " --> pdb=" O GLUKE 58 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 Processing helix chain 'KF' and resid 49 through 65 removed outlier: 4.044A pdb=" N ARGKF 62 " --> pdb=" O GLUKF 58 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.594A pdb=" N ALALA 27 " --> pdb=" O METLA 23 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 65 removed outlier: 3.876A pdb=" N ARGLA 62 " --> pdb=" O GLULA 58 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 87 Processing helix chain 'LB' and resid 12 through 26 Processing helix chain 'LB' and resid 49 through 65 removed outlier: 3.872A pdb=" N ARGLB 62 " --> pdb=" O GLULB 58 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 87 Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.563A pdb=" N ALALC 27 " --> pdb=" O METLC 23 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 65 removed outlier: 3.741A pdb=" N ARGLC 62 " --> pdb=" O GLULC 58 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 25 Processing helix chain 'LD' and resid 49 through 65 removed outlier: 3.645A pdb=" N ARGLD 62 " --> pdb=" O GLULD 58 " (cutoff:3.500A) removed outlier: 3.527A 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: 3.666A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 removed outlier: 4.056A pdb=" N ARGLE 62 " --> pdb=" O GLULE 58 " (cutoff:3.500A) Processing helix chain 'LE' and resid 80 through 87 Processing helix chain 'LF' and resid 12 through 27 removed outlier: 3.562A pdb=" N ALALF 27 " --> pdb=" O METLF 23 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 65 removed outlier: 3.877A pdb=" N ARGLF 62 " --> pdb=" O GLULF 58 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 87 removed outlier: 3.628A pdb=" N ASPLF 84 " --> pdb=" O HISLF 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 47 through 59 removed outlier: 3.898A pdb=" N ASP G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 96 Processing helix chain 'G' and resid 99 through 103 removed outlier: 3.799A pdb=" N GLY G 102 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 128 removed outlier: 3.935A pdb=" N ILE G 124 " --> pdb=" O TYR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 162 removed outlier: 3.845A pdb=" N ALA G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 200 Processing helix chain 'H' and resid 15 through 26 Processing helix chain 'H' and resid 47 through 57 removed outlier: 3.945A pdb=" N ASP H 53 " --> pdb=" O ASN H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 97 Processing helix chain 'H' and resid 99 through 103 removed outlier: 3.636A pdb=" N ARG H 103 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 128 removed outlier: 3.699A pdb=" N ILE H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 162 removed outlier: 3.996A pdb=" N ALA H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 200 removed outlier: 3.666A pdb=" N SER H 200 " --> pdb=" O ALA H 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 26 Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.778A pdb=" N ASP I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 97 Processing helix chain 'I' and resid 99 through 103 removed outlier: 3.573A pdb=" N ARG I 103 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 128 removed outlier: 3.716A pdb=" N ILE I 124 " --> pdb=" O TYR I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 162 removed outlier: 3.898A pdb=" N ALA I 158 " --> pdb=" O ALA I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 199 Processing helix chain 'J' and resid 15 through 26 Processing helix chain 'J' and resid 44 through 46 No H-bonds generated for 'chain 'J' and resid 44 through 46' Processing helix chain 'J' and resid 47 through 57 removed outlier: 3.600A pdb=" N VAL J 51 " --> pdb=" O ALA J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 97 removed outlier: 3.651A pdb=" N VAL J 85 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 103 removed outlier: 3.702A pdb=" N ARG J 103 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 128 removed outlier: 3.940A pdb=" N ILE J 124 " --> pdb=" O TYR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 150 through 160 removed outlier: 4.056A pdb=" N ALA J 158 " --> pdb=" O ALA J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 200 Processing helix chain 'K' and resid 15 through 26 Processing helix chain 'K' and resid 47 through 59 removed outlier: 3.619A pdb=" N ASP K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 96 removed outlier: 3.882A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 103 removed outlier: 3.728A pdb=" N ARG K 103 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 128 removed outlier: 4.251A pdb=" N ILE K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 162 removed outlier: 4.076A pdb=" N ALA K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 200 Processing helix chain 'L' and resid 15 through 26 Processing helix chain 'L' and resid 47 through 57 removed outlier: 3.663A pdb=" N ASP L 53 " --> pdb=" O ASN L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 97 removed outlier: 3.740A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 103 removed outlier: 3.704A pdb=" N ARG L 103 " --> pdb=" O GLU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 128 removed outlier: 3.861A pdb=" N ILE L 124 " --> pdb=" O TYR L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 162 removed outlier: 3.679A pdb=" N ALA L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.508A pdb=" N SER L 200 " --> pdb=" O ALA L 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 26 Processing helix chain 'M' and resid 47 through 57 removed outlier: 3.541A pdb=" N VAL M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP M 53 " --> pdb=" O ASN M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 97 Processing helix chain 'M' and resid 99 through 103 removed outlier: 3.738A pdb=" N GLY M 102 " --> pdb=" O ARG M 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG M 103 " --> pdb=" O GLU M 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 99 through 103' Processing helix chain 'M' and resid 118 through 128 removed outlier: 3.916A pdb=" N ILE M 124 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 162 removed outlier: 3.835A pdb=" N ALA M 158 " --> pdb=" O ALA M 154 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 200 Processing helix chain 'N' and resid 15 through 26 Processing helix chain 'N' and resid 47 through 59 removed outlier: 4.074A pdb=" N ASP N 53 " --> pdb=" O ASN N 49 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 96 Processing helix chain 'N' and resid 99 through 103 removed outlier: 3.545A pdb=" N GLY N 102 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 128 removed outlier: 4.007A pdb=" N ILE N 124 " --> pdb=" O TYR N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 161 removed outlier: 3.830A pdb=" N ALA N 158 " --> pdb=" O ALA N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 200 Processing helix chain 'O' and resid 15 through 26 Processing helix chain 'O' and resid 47 through 57 removed outlier: 3.501A pdb=" N VAL O 51 " --> pdb=" O ALA O 47 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP O 53 " --> pdb=" O ASN O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 96 Processing helix chain 'O' and resid 99 through 103 removed outlier: 3.631A pdb=" N ARG O 103 " --> pdb=" O GLU O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 128 removed outlier: 3.781A pdb=" N ILE O 124 " --> pdb=" O TYR O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 162 removed outlier: 3.994A pdb=" N ALA O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 200 Processing helix chain 'P' and resid 15 through 26 Processing helix chain 'P' and resid 47 through 57 removed outlier: 3.556A pdb=" N VAL P 51 " --> pdb=" O ALA P 47 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP P 53 " --> pdb=" O ASN P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 97 removed outlier: 3.613A pdb=" N VAL P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 103 removed outlier: 3.674A pdb=" N ARG P 103 " --> pdb=" O GLU P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 128 removed outlier: 3.728A pdb=" N ILE P 124 " --> pdb=" O TYR P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 149 No H-bonds generated for 'chain 'P' and resid 147 through 149' Processing helix chain 'P' and resid 150 through 162 removed outlier: 3.986A pdb=" N ALA P 158 " --> pdb=" O ALA P 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 199 Processing helix chain 'Q' and resid 15 through 26 Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 57 Processing helix chain 'Q' and resid 81 through 96 removed outlier: 3.660A pdb=" N VAL Q 85 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 103 removed outlier: 3.689A pdb=" N ARG Q 103 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 128 removed outlier: 4.192A pdb=" N ILE Q 124 " --> pdb=" O TYR Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 162 removed outlier: 4.148A pdb=" N ALA Q 158 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 200 Processing helix chain 'R' and resid 15 through 26 Processing helix chain 'R' and resid 47 through 57 removed outlier: 4.059A pdb=" N ASP R 53 " --> pdb=" O ASN R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 96 removed outlier: 3.780A pdb=" N VAL R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 103 removed outlier: 3.706A pdb=" N ARG R 103 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 128 removed outlier: 3.822A pdb=" N ILE R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 162 removed outlier: 3.912A pdb=" N ALA R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 Processing helix chain 'S' and resid 15 through 26 Processing helix chain 'S' and resid 47 through 57 removed outlier: 3.789A pdb=" N ASP S 53 " --> pdb=" O ASN S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 96 Processing helix chain 'S' and resid 99 through 103 removed outlier: 3.819A pdb=" N GLY S 102 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG S 103 " --> pdb=" O GLU S 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 99 through 103' Processing helix chain 'S' and resid 118 through 128 removed outlier: 4.074A pdb=" N ILE S 124 " --> pdb=" O TYR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 162 removed outlier: 3.889A pdb=" N ALA S 158 " --> pdb=" O ALA S 154 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU S 159 " --> pdb=" O ALA S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 199 Processing helix chain 'T' and resid 15 through 26 Processing helix chain 'T' and resid 47 through 57 removed outlier: 3.914A pdb=" N ASP T 53 " --> pdb=" O ASN T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 96 Processing helix chain 'T' and resid 99 through 103 removed outlier: 3.624A pdb=" N GLY T 102 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 128 removed outlier: 4.003A pdb=" N ILE T 124 " --> pdb=" O TYR T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 150 through 162 removed outlier: 3.916A pdb=" N ALA T 158 " --> pdb=" O ALA T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 200 Processing helix chain 'U' and resid 15 through 26 Processing helix chain 'U' and resid 47 through 57 removed outlier: 3.874A pdb=" N ASP U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 96 Processing helix chain 'U' and resid 99 through 103 removed outlier: 3.665A pdb=" N ARG U 103 " --> pdb=" O GLU U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 128 removed outlier: 3.698A pdb=" N ILE U 124 " --> pdb=" O TYR U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 162 removed outlier: 3.984A pdb=" N ALA U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 200 Processing helix chain 'V' and resid 15 through 26 Processing helix chain 'V' and resid 44 through 46 No H-bonds generated for 'chain 'V' and resid 44 through 46' Processing helix chain 'V' and resid 47 through 57 Processing helix chain 'V' and resid 81 through 97 removed outlier: 3.542A pdb=" N VAL V 85 " --> pdb=" O ASP V 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 99 through 103 removed outlier: 3.725A pdb=" N ARG V 103 " --> pdb=" O GLU V 100 " (cutoff:3.500A) Processing helix chain 'V' and resid 118 through 128 removed outlier: 3.605A pdb=" N ILE V 124 " --> pdb=" O TYR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 149 No H-bonds generated for 'chain 'V' and resid 147 through 149' Processing helix chain 'V' and resid 150 through 162 removed outlier: 3.906A pdb=" N ALA V 158 " --> pdb=" O ALA V 154 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 199 Processing helix chain 'W' and resid 15 through 26 Processing helix chain 'W' and resid 47 through 57 removed outlier: 3.773A pdb=" N ASP W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 96 removed outlier: 3.866A pdb=" N VAL W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 103 removed outlier: 3.647A pdb=" N ARG W 103 " --> pdb=" O GLU W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 128 removed outlier: 4.340A pdb=" N ILE W 124 " --> pdb=" O TYR W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 162 removed outlier: 4.134A pdb=" N ALA W 158 " --> pdb=" O ALA W 154 " (cutoff:3.500A) Processing helix chain 'W' and resid 183 through 200 Processing helix chain 'X' and resid 15 through 26 Processing helix chain 'X' and resid 47 through 57 removed outlier: 4.187A pdb=" N ASP X 53 " --> pdb=" O ASN X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 96 removed outlier: 3.802A pdb=" N VAL X 85 " --> pdb=" O ASP X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 103 removed outlier: 3.661A pdb=" N ARG X 103 " --> pdb=" O GLU X 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 128 Processing helix chain 'X' and resid 150 through 162 removed outlier: 3.745A pdb=" N ALA X 158 " --> pdb=" O ALA X 154 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU X 159 " --> pdb=" O ALA X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 6.322A pdb=" N MET A 62 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 51 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 60 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS A 58 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 65 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 152 removed outlier: 6.869A pdb=" N THR A 163 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET A 150 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A 161 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 188 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 54 removed outlier: 6.386A pdb=" N MET B 62 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 51 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 60 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS B 58 " --> pdb=" O PRO B 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 65 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 5.661A pdb=" N LEU B 147 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 165 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP B 149 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 188 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 54 removed outlier: 6.400A pdb=" N MET C 62 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 51 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 60 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 58 " --> pdb=" O PRO C 53 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 65 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 152 removed outlier: 6.792A pdb=" N THR C 163 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET C 150 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE C 161 " --> pdb=" O MET C 150 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL C 121 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N CYS C 191 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 123 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU C 189 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU C 125 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'GA' and resid 31 through 38 removed outlier: 6.048A pdb=" N LEUGA 31 " --> pdb=" O ARGGA 47 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARGGA 47 " --> pdb=" O LEUGA 31 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLYGA 33 " --> pdb=" O VALGA 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYRGA 41 " --> pdb=" O THRGA 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HISGA 74 " --> pdb=" O METGA 7 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALAGA 72 " --> pdb=" O GLUGA 9 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARGGA 11 " --> pdb=" O VALGA 70 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VALGA 70 " --> pdb=" O ARGGA 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'GB' and resid 31 through 38 removed outlier: 3.683A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYRGB 41 " --> pdb=" O THRGB 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALAGB 72 " --> pdb=" O GLUGB 9 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'GC' and resid 31 through 36 removed outlier: 5.880A pdb=" N LEUGC 31 " --> pdb=" O ARGGC 47 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARGGC 47 " --> pdb=" O LEUGC 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYGC 33 " --> pdb=" O VALGC 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARGGC 11 " --> pdb=" O VALGC 70 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VALGC 70 " --> pdb=" O ARGGC 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'GD' and resid 30 through 36 removed outlier: 5.678A pdb=" N LEUGD 31 " --> pdb=" O ARGGD 47 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARGGD 47 " --> pdb=" O LEUGD 31 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALAGD 72 " --> pdb=" O GLUGD 9 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'GE' and resid 31 through 38 removed outlier: 5.958A pdb=" N LEUGE 31 " --> pdb=" O ARGGE 47 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARGGE 47 " --> pdb=" O LEUGE 31 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLYGE 33 " --> pdb=" O VALGE 45 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYRGE 41 " --> pdb=" O THRGE 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISGE 74 " --> pdb=" O METGE 7 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALAGE 72 " --> pdb=" O GLUGE 9 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARGGE 11 " --> pdb=" O VALGE 70 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VALGE 70 " --> pdb=" O ARGGE 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'GF' and resid 31 through 38 removed outlier: 5.709A pdb=" N LEUGF 31 " --> pdb=" O ARGGF 47 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARGGF 47 " --> pdb=" O LEUGF 31 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLYGF 33 " --> pdb=" O VALGF 45 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THRGF 37 " --> pdb=" O TYRGF 41 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYRGF 41 " --> pdb=" O THRGF 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALAGF 72 " --> pdb=" O GLUGF 9 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARGGF 11 " --> pdb=" O VALGF 70 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VALGF 70 " --> pdb=" O ARGGF 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'HA' and resid 31 through 36 removed outlier: 5.763A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HISHA 74 " --> pdb=" O METHA 7 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALAHA 72 " --> pdb=" O GLUHA 9 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGHA 11 " --> pdb=" O VALHA 70 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VALHA 70 " --> pdb=" O ARGHA 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'HB' and resid 30 through 38 removed outlier: 5.798A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYRHB 41 " --> pdb=" O THRHB 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALAHB 72 " --> pdb=" O GLUHB 9 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'HC' and resid 30 through 36 removed outlier: 5.519A pdb=" N LEUHC 31 " --> pdb=" O ARGHC 47 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARGHC 47 " --> pdb=" O LEUHC 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEUHC 5 " --> pdb=" O VALHC 75 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VALHC 75 " --> pdb=" O LEUHC 5 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N METHC 7 " --> pdb=" O VALHC 73 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VALHC 73 " --> pdb=" O METHC 7 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLUHC 9 " --> pdb=" O VALHC 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'HD' and resid 31 through 38 removed outlier: 5.714A pdb=" N LEUHD 31 " --> pdb=" O ARGHD 47 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARGHD 47 " --> pdb=" O LEUHD 31 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLYHD 33 " --> pdb=" O VALHD 45 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYRHD 41 " --> pdb=" O THRHD 37 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALAHD 72 " --> pdb=" O GLUHD 9 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ARGHD 11 " --> pdb=" O VALHD 70 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VALHD 70 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'HE' and resid 31 through 36 removed outlier: 3.814A pdb=" N GLYHE 33 " --> pdb=" O VALHE 45 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALAHE 72 " --> pdb=" O GLUHE 9 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARGHE 11 " --> pdb=" O VALHE 70 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VALHE 70 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'HF' and resid 30 through 38 removed outlier: 5.739A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYRHF 41 " --> pdb=" O THRHF 37 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HISHF 74 " --> pdb=" O METHF 7 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALAHF 72 " --> pdb=" O GLUHF 9 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'IA' and resid 31 through 38 removed outlier: 5.705A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYRIA 41 " --> pdb=" O THRIA 37 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HISIA 74 " --> pdb=" O METIA 7 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALAIA 72 " --> pdb=" O GLUIA 9 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARGIA 11 " --> pdb=" O VALIA 70 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VALIA 70 " --> pdb=" O ARGIA 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'IB' and resid 31 through 38 removed outlier: 3.716A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEUIB 5 " --> pdb=" O VALIB 75 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VALIB 75 " --> pdb=" O LEUIB 5 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N METIB 7 " --> pdb=" O VALIB 73 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VALIB 73 " --> pdb=" O METIB 7 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLUIB 9 " --> pdb=" O VALIB 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'IC' and resid 31 through 36 removed outlier: 5.728A pdb=" N LEUIC 31 " --> pdb=" O ARGIC 47 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARGIC 47 " --> pdb=" O LEUIC 31 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLYIC 33 " --> pdb=" O VALIC 45 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARGIC 11 " --> pdb=" O VALIC 70 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VALIC 70 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'ID' and resid 30 through 36 removed outlier: 5.767A pdb=" N LEUID 31 " --> pdb=" O ARGID 47 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARGID 47 " --> pdb=" O LEUID 31 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLYID 33 " --> pdb=" O VALID 45 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARGID 11 " --> pdb=" O VALID 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VALID 70 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'IE' and resid 31 through 38 removed outlier: 6.084A pdb=" N LEUIE 31 " --> pdb=" O ARGIE 47 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ARGIE 47 " --> pdb=" O LEUIE 31 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLYIE 33 " --> pdb=" O VALIE 45 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYRIE 41 " --> pdb=" O THRIE 37 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HISIE 74 " --> pdb=" O METIE 7 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALAIE 72 " --> pdb=" O GLUIE 9 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARGIE 11 " --> pdb=" O VALIE 70 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VALIE 70 " --> pdb=" O ARGIE 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'IF' and resid 31 through 38 removed outlier: 5.695A pdb=" N LEUIF 31 " --> pdb=" O ARGIF 47 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARGIF 47 " --> pdb=" O LEUIF 31 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THRIF 37 " --> pdb=" O TYRIF 41 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYRIF 41 " --> pdb=" O THRIF 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALAIF 72 " --> pdb=" O GLUIF 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'JA' and resid 31 through 36 removed outlier: 5.882A pdb=" N LEUJA 31 " --> pdb=" O ARGJA 47 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARGJA 47 " --> pdb=" O LEUJA 31 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HISJA 74 " --> pdb=" O METJA 7 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALAJA 72 " --> pdb=" O GLUJA 9 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARGJA 11 " --> pdb=" O VALJA 70 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VALJA 70 " --> pdb=" O ARGJA 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'JB' and resid 31 through 36 removed outlier: 5.911A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARGJB 11 " --> pdb=" O VALJB 70 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VALJB 70 " --> pdb=" O ARGJB 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'JC' and resid 30 through 36 removed outlier: 5.628A pdb=" N LEUJC 31 " --> pdb=" O ARGJC 47 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARGJC 47 " --> pdb=" O LEUJC 31 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLYJC 33 " --> pdb=" O VALJC 45 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALAJC 72 " --> pdb=" O GLUJC 9 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARGJC 11 " --> pdb=" O VALJC 70 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VALJC 70 " --> pdb=" O ARGJC 11 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'JD' and resid 30 through 36 removed outlier: 5.539A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HISJD 74 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALAJD 72 " --> pdb=" O GLUJD 9 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARGJD 11 " --> pdb=" O VALJD 70 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VALJD 70 " --> pdb=" O ARGJD 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'JE' and resid 30 through 36 removed outlier: 5.507A pdb=" N LEUJE 31 " --> pdb=" O ARGJE 47 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARGJE 47 " --> pdb=" O LEUJE 31 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLYJE 33 " --> pdb=" O VALJE 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALAJE 72 " --> pdb=" O GLUJE 9 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARGJE 11 " --> pdb=" O VALJE 70 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VALJE 70 " --> pdb=" O ARGJE 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'JF' and resid 31 through 38 removed outlier: 5.961A pdb=" N LEUJF 31 " --> pdb=" O ARGJF 47 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARGJF 47 " --> pdb=" O LEUJF 31 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLYJF 33 " --> pdb=" O VALJF 45 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYRJF 41 " --> pdb=" O THRJF 37 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALAJF 72 " --> pdb=" O GLUJF 9 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'KA' and resid 31 through 38 removed outlier: 5.883A pdb=" N LEUKA 31 " --> pdb=" O ARGKA 47 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARGKA 47 " --> pdb=" O LEUKA 31 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLYKA 33 " --> pdb=" O VALKA 45 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYRKA 41 " --> pdb=" O THRKA 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HISKA 74 " --> pdb=" O METKA 7 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALAKA 72 " --> pdb=" O GLUKA 9 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARGKA 11 " --> pdb=" O VALKA 70 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VALKA 70 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'KB' and resid 31 through 38 removed outlier: 3.604A pdb=" N GLYKB 33 " --> pdb=" O VALKB 45 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYRKB 41 " --> pdb=" O THRKB 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HISKB 74 " --> pdb=" O METKB 7 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAKB 72 " --> pdb=" O GLUKB 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'KC' and resid 30 through 36 removed outlier: 5.578A pdb=" N LEUKC 31 " --> pdb=" O ARGKC 47 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARGKC 47 " --> pdb=" O LEUKC 31 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLYKC 33 " --> pdb=" O VALKC 45 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALAKC 72 " --> pdb=" O GLUKC 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARGKC 11 " --> pdb=" O VALKC 70 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VALKC 70 " --> pdb=" O ARGKC 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'KD' and resid 30 through 36 removed outlier: 5.632A pdb=" N LEUKD 31 " --> pdb=" O ARGKD 47 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARGKD 47 " --> pdb=" O LEUKD 31 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALAKD 72 " --> pdb=" O GLUKD 9 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARGKD 11 " --> pdb=" O VALKD 70 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VALKD 70 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'KE' and resid 31 through 36 removed outlier: 6.020A pdb=" N LEUKE 31 " --> pdb=" O ARGKE 47 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARGKE 47 " --> pdb=" O LEUKE 31 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLYKE 33 " --> pdb=" O VALKE 45 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEUKE 5 " --> pdb=" O VALKE 75 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VALKE 75 " --> pdb=" O LEUKE 5 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N METKE 7 " --> pdb=" O VALKE 73 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VALKE 73 " --> pdb=" O METKE 7 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLUKE 9 " --> pdb=" O VALKE 71 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'KF' and resid 30 through 36 removed outlier: 5.321A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HISKF 74 " --> pdb=" O METKF 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALAKF 72 " --> pdb=" O GLUKF 9 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LA' and resid 31 through 36 removed outlier: 5.839A pdb=" N LEULA 31 " --> pdb=" O ARGLA 47 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARGLA 47 " --> pdb=" O LEULA 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HISLA 74 " --> pdb=" O METLA 7 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALALA 72 " --> pdb=" O GLULA 9 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARGLA 11 " --> pdb=" O VALLA 70 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VALLA 70 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LB' and resid 30 through 36 removed outlier: 5.723A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALALB 72 " --> pdb=" O GLULB 9 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARGLB 11 " --> pdb=" O VALLB 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VALLB 70 " --> pdb=" O ARGLB 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LC' and resid 30 through 38 removed outlier: 5.667A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYRLC 41 " --> pdb=" O THRLC 37 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALALC 72 " --> pdb=" O GLULC 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARGLC 11 " --> pdb=" O VALLC 70 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VALLC 70 " --> pdb=" O ARGLC 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LD' and resid 30 through 38 removed outlier: 5.609A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HISLD 74 " --> pdb=" O METLD 7 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALALD 72 " --> pdb=" O GLULD 9 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'LE' and resid 31 through 36 removed outlier: 3.850A pdb=" N GLYLE 33 " --> pdb=" O VALLE 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALALE 72 " --> pdb=" O GLULE 9 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'LF' and resid 30 through 38 removed outlier: 5.777A pdb=" N LEULF 31 " --> pdb=" O ARGLF 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARGLF 47 " --> pdb=" O LEULF 31 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYLF 33 " --> pdb=" O VALLF 45 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYRLF 41 " --> pdb=" O THRLF 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HISLF 74 " --> pdb=" O METLF 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALALF 72 " --> pdb=" O GLULF 9 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARGLF 11 " --> pdb=" O VALLF 70 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VALLF 70 " --> pdb=" O ARGLF 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 5 through 11 removed outlier: 6.437A pdb=" N GLU G 41 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR G 8 " --> pdb=" O TRP G 39 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP G 39 " --> pdb=" O TYR G 8 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N PHE G 10 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER G 37 " --> pdb=" O PHE G 10 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL G 65 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS G 78 " --> pdb=" O PRO G 63 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 107 through 114 removed outlier: 5.580A pdb=" N VAL G 108 " --> pdb=" O GLN G 146 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN G 146 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG G 177 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL G 169 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR G 179 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 11 removed outlier: 5.847A pdb=" N LEU H 5 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA H 43 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU H 74 " --> pdb=" O GLN H 66 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN H 66 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU H 76 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 107 through 114 removed outlier: 5.534A pdb=" N VAL H 108 " --> pdb=" O GLN H 146 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLN H 146 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 110 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG H 177 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL H 169 " --> pdb=" O ARG H 177 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR H 179 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 4 through 11 removed outlier: 5.585A pdb=" N LEU I 5 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA I 43 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU I 74 " --> pdb=" O GLN I 66 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN I 66 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU I 76 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I 64 " --> pdb=" O GLU I 76 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 107 through 114 removed outlier: 5.492A pdb=" N VAL I 108 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN I 146 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA I 181 " --> pdb=" O LEU I 166 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU I 166 " --> pdb=" O ALA I 181 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 11 removed outlier: 6.398A pdb=" N GLU J 41 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR J 8 " --> pdb=" O TRP J 39 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP J 39 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE J 10 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER J 37 " --> pdb=" O PHE J 10 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU J 74 " --> pdb=" O GLN J 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN J 66 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU J 76 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 107 through 114 removed outlier: 5.565A pdb=" N VAL J 108 " --> pdb=" O GLN J 146 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN J 146 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR J 110 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG J 177 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL J 169 " --> pdb=" O ARG J 177 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR J 179 " --> pdb=" O VAL J 167 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 5 through 11 removed outlier: 6.278A pdb=" N LEU K 74 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN K 66 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU K 76 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 107 through 114 removed outlier: 5.511A pdb=" N VAL K 108 " --> pdb=" O GLN K 146 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN K 146 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR K 110 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG K 177 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL K 169 " --> pdb=" O ARG K 177 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR K 179 " --> pdb=" O VAL K 167 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 5 through 11 removed outlier: 4.045A pdb=" N VAL L 65 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS L 78 " --> pdb=" O PRO L 63 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 107 through 114 removed outlier: 5.548A pdb=" N VAL L 108 " --> pdb=" O GLN L 146 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN L 146 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR L 110 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG L 177 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL L 169 " --> pdb=" O ARG L 177 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR L 179 " --> pdb=" O VAL L 167 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 5 through 11 removed outlier: 6.404A pdb=" N LEU M 74 " --> pdb=" O GLN M 66 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN M 66 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU M 76 " --> pdb=" O ALA M 64 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 107 through 114 removed outlier: 5.482A pdb=" N VAL M 108 " --> pdb=" O GLN M 146 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN M 146 " --> pdb=" O VAL M 108 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR M 110 " --> pdb=" O GLU M 144 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA M 181 " --> pdb=" O LEU M 166 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU M 166 " --> pdb=" O ALA M 181 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 4 through 11 removed outlier: 5.931A pdb=" N LEU N 5 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA N 43 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU N 74 " --> pdb=" O GLN N 66 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN N 66 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU N 76 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 107 through 114 removed outlier: 5.726A pdb=" N VAL N 108 " --> pdb=" O GLN N 146 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN N 146 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR N 110 " --> pdb=" O GLU N 144 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG N 177 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL N 169 " --> pdb=" O ARG N 177 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR N 179 " --> pdb=" O VAL N 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 4 through 11 removed outlier: 5.866A pdb=" N LEU O 5 " --> pdb=" O ALA O 43 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ALA O 43 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN O 66 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU O 76 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA O 64 " --> pdb=" O GLU O 76 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 107 through 114 removed outlier: 5.401A pdb=" N VAL O 108 " --> pdb=" O GLN O 146 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN O 146 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG O 177 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL O 169 " --> pdb=" O ARG O 177 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR O 179 " --> pdb=" O VAL O 167 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 4 through 11 removed outlier: 6.413A pdb=" N GLU P 41 " --> pdb=" O ARG P 6 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR P 8 " --> pdb=" O TRP P 39 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP P 39 " --> pdb=" O TYR P 8 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE P 10 " --> pdb=" O SER P 37 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER P 37 " --> pdb=" O PHE P 10 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL P 65 " --> pdb=" O GLU P 76 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS P 78 " --> pdb=" O PRO P 63 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 107 through 114 removed outlier: 5.595A pdb=" N VAL P 108 " --> pdb=" O GLN P 146 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN P 146 " --> pdb=" O VAL P 108 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR P 110 " --> pdb=" O GLU P 144 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG P 177 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL P 169 " --> pdb=" O ARG P 177 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR P 179 " --> pdb=" O VAL P 167 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 5 through 11 removed outlier: 3.985A pdb=" N VAL Q 65 " --> pdb=" O GLU Q 76 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HIS Q 78 " --> pdb=" O PRO Q 63 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 107 through 114 removed outlier: 5.455A pdb=" N VAL Q 108 " --> pdb=" O GLN Q 146 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN Q 146 " --> pdb=" O VAL Q 108 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR Q 110 " --> pdb=" O GLU Q 144 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG Q 177 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL Q 169 " --> pdb=" O ARG Q 177 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR Q 179 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 5 through 11 removed outlier: 4.082A pdb=" N VAL R 65 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N HIS R 78 " --> pdb=" O PRO R 63 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 107 through 114 removed outlier: 5.549A pdb=" N VAL R 108 " --> pdb=" O GLN R 146 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN R 146 " --> pdb=" O VAL R 108 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR R 110 " --> pdb=" O GLU R 144 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG R 177 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL R 169 " --> pdb=" O ARG R 177 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR R 179 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 5 through 11 removed outlier: 6.428A pdb=" N LEU S 74 " --> pdb=" O GLN S 66 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN S 66 " --> pdb=" O LEU S 74 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU S 76 " --> pdb=" O ALA S 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA S 64 " --> pdb=" O GLU S 76 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 107 through 114 removed outlier: 5.539A pdb=" N VAL S 108 " --> pdb=" O GLN S 146 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN S 146 " --> pdb=" O VAL S 108 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG S 177 " --> pdb=" O VAL S 169 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL S 169 " --> pdb=" O ARG S 177 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR S 179 " --> pdb=" O VAL S 167 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 4 through 11 removed outlier: 5.946A pdb=" N LEU T 5 " --> pdb=" O ALA T 43 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA T 43 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU T 74 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN T 66 " --> pdb=" O LEU T 74 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU T 76 " --> pdb=" O ALA T 64 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 107 through 114 removed outlier: 5.781A pdb=" N VAL T 108 " --> pdb=" O GLN T 146 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN T 146 " --> pdb=" O VAL T 108 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR T 110 " --> pdb=" O GLU T 144 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG T 177 " --> pdb=" O VAL T 169 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL T 169 " --> pdb=" O ARG T 177 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR T 179 " --> pdb=" O VAL T 167 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 4 through 11 removed outlier: 5.619A pdb=" N LEU U 5 " --> pdb=" O ALA U 43 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA U 43 " --> pdb=" O LEU U 5 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU U 74 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN U 66 " --> pdb=" O LEU U 74 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU U 76 " --> pdb=" O ALA U 64 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'U' and resid 107 through 114 removed outlier: 5.498A pdb=" N VAL U 108 " --> pdb=" O GLN U 146 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN U 146 " --> pdb=" O VAL U 108 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG U 177 " --> pdb=" O VAL U 169 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL U 169 " --> pdb=" O ARG U 177 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR U 179 " --> pdb=" O VAL U 167 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 4 through 11 removed outlier: 6.349A pdb=" N GLU V 41 " --> pdb=" O ARG V 6 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR V 8 " --> pdb=" O TRP V 39 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP V 39 " --> pdb=" O TYR V 8 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE V 10 " --> pdb=" O SER V 37 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER V 37 " --> pdb=" O PHE V 10 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL V 65 " --> pdb=" O GLU V 76 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS V 78 " --> pdb=" O PRO V 63 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 107 through 114 removed outlier: 5.593A pdb=" N VAL V 108 " --> pdb=" O GLN V 146 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN V 146 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR V 110 " --> pdb=" O GLU V 144 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA V 181 " --> pdb=" O LEU V 166 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU V 166 " --> pdb=" O ALA V 181 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'W' and resid 5 through 11 removed outlier: 6.267A pdb=" N LEU W 74 " --> pdb=" O GLN W 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN W 66 " --> pdb=" O LEU W 74 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU W 76 " --> pdb=" O ALA W 64 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'W' and resid 107 through 114 removed outlier: 5.521A pdb=" N VAL W 108 " --> pdb=" O GLN W 146 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN W 146 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR W 110 " --> pdb=" O GLU W 144 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG W 177 " --> pdb=" O VAL W 169 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL W 169 " --> pdb=" O ARG W 177 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR W 179 " --> pdb=" O VAL W 167 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'X' and resid 5 through 11 removed outlier: 6.233A pdb=" N LEU X 74 " --> pdb=" O GLN X 66 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN X 66 " --> pdb=" O LEU X 74 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU X 76 " --> pdb=" O ALA X 64 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'X' and resid 107 through 114 removed outlier: 5.508A pdb=" N VAL X 108 " --> pdb=" O GLN X 146 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN X 146 " --> pdb=" O VAL X 108 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR X 110 " --> pdb=" O GLU X 144 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG X 177 " --> pdb=" O VAL X 169 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL X 169 " --> pdb=" O ARG X 177 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR X 179 " --> pdb=" O VAL X 167 " (cutoff:3.500A) 3319 hydrogen bonds defined for protein. 9438 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: 18.70 Time building geometry restraints manager: 17.01 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: 18619 1.34 - 1.46: 7401 1.46 - 1.57: 30083 1.57 - 1.69: 0 1.69 - 1.81: 363 Bond restraints: 56466 Sorted by residual: bond pdb=" C GLN O 15 " pdb=" N PRO O 16 " ideal model delta sigma weight residual 1.335 1.371 -0.035 1.36e-02 5.41e+03 6.77e+00 bond pdb=" C GLN S 15 " pdb=" N PRO S 16 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.23e-02 6.61e+03 5.50e+00 bond pdb=" C GLN X 15 " pdb=" N PRO X 16 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.28e-02 6.10e+03 5.23e+00 bond pdb=" C GLN I 15 " pdb=" N PRO I 16 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.88e+00 bond pdb=" C GLN H 15 " pdb=" N PRO H 16 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.71e+00 ... (remaining 56461 not shown) Histogram of bond angle deviations from ideal: 96.32 - 103.85: 896 103.85 - 111.39: 24499 111.39 - 118.92: 21808 118.92 - 126.46: 29041 126.46 - 133.99: 505 Bond angle restraints: 76749 Sorted by residual: angle pdb=" N ILE C 30 " pdb=" CA ILE C 30 " pdb=" C ILE C 30 " ideal model delta sigma weight residual 112.96 108.86 4.10 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N PRO O 16 " pdb=" CA PRO O 16 " pdb=" C PRO O 16 " ideal model delta sigma weight residual 113.53 118.80 -5.27 1.39e+00 5.18e-01 1.44e+01 angle pdb=" N ALA K 71 " pdb=" CA ALA K 71 " pdb=" C ALA K 71 " ideal model delta sigma weight residual 114.56 109.79 4.77 1.27e+00 6.20e-01 1.41e+01 angle pdb=" N PRO S 16 " pdb=" CA PRO S 16 " pdb=" C PRO S 16 " ideal model delta sigma weight residual 113.57 118.14 -4.57 1.31e+00 5.83e-01 1.22e+01 angle pdb=" C VAL G 51 " pdb=" N THR G 52 " pdb=" CA THR G 52 " ideal model delta sigma weight residual 120.54 125.24 -4.70 1.35e+00 5.49e-01 1.21e+01 ... (remaining 76744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 32862 15.71 - 31.42: 948 31.42 - 47.14: 253 47.14 - 62.85: 11 62.85 - 78.56: 12 Dihedral angle restraints: 34086 sinusoidal: 12732 harmonic: 21354 Sorted by residual: dihedral pdb=" CA ASPJF 49 " pdb=" C ASPJF 49 " pdb=" N VALJF 50 " pdb=" CA VALJF 50 " ideal model delta harmonic sigma weight residual 180.00 -146.78 -33.22 0 5.00e+00 4.00e-02 4.41e+01 dihedral pdb=" CA ASPLD 49 " pdb=" C ASPLD 49 " pdb=" N VALLD 50 " pdb=" CA VALLD 50 " ideal model delta harmonic sigma weight residual -180.00 -147.97 -32.03 0 5.00e+00 4.00e-02 4.10e+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 -148.42 -31.58 0 5.00e+00 4.00e-02 3.99e+01 ... (remaining 34083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 6405 0.052 - 0.105: 2127 0.105 - 0.157: 537 0.157 - 0.209: 91 0.209 - 0.262: 14 Chirality restraints: 9174 Sorted by residual: chirality pdb=" CB ILE C 122 " pdb=" CA ILE C 122 " pdb=" CG1 ILE C 122 " pdb=" CG2 ILE C 122 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE A 122 " pdb=" CA ILE A 122 " pdb=" CG1 ILE A 122 " pdb=" CG2 ILE A 122 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE B 122 " pdb=" CA ILE B 122 " pdb=" CG1 ILE B 122 " pdb=" CG2 ILE B 122 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 9171 not shown) Planarity restraints: 10056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 114 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C TRP C 114 " -0.049 2.00e-02 2.50e+03 pdb=" O TRP C 114 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU C 115 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 30 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO G 31 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO G 31 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 31 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P 62 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO P 63 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO P 63 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO P 63 " 0.032 5.00e-02 4.00e+02 ... (remaining 10053 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 9510 2.77 - 3.30: 50242 3.30 - 3.83: 93502 3.83 - 4.37: 108943 4.37 - 4.90: 194078 Nonbonded interactions: 456275 Sorted by model distance: nonbonded pdb=" OD1 ASP A 149 " pdb=" OG1 THR A 163 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP B 149 " pdb=" OG1 THR B 163 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP C 149 " pdb=" OG1 THR C 163 " model vdw 2.259 2.440 nonbonded pdb=" OG SER I 37 " pdb=" OE2 GLU I 76 " model vdw 2.301 2.440 nonbonded pdb=" OG SER T 37 " pdb=" OE2 GLU T 76 " model vdw 2.302 2.440 ... (remaining 456270 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'G' and resid 4 through 204) selection = (chain 'H' and resid 4 through 204) selection = (chain 'I' and resid 4 through 204) selection = (chain 'J' and resid 4 through 204) selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 4 through 204) selection = (chain 'N' and resid 4 through 204) selection = (chain 'O' and resid 4 through 204) selection = (chain 'P' and resid 4 through 204) selection = chain 'Q' selection = chain 'R' selection = (chain 'S' and resid 4 through 204) selection = (chain 'T' and resid 4 through 204) selection = (chain 'U' and resid 4 through 204) selection = (chain 'V' and resid 4 through 204) selection = chain 'W' selection = chain 'X' } 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: 7.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 26.080 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 109.720 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.390 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 56466 Z= 0.520 Angle : 0.869 11.698 76749 Z= 0.502 Chirality : 0.056 0.262 9174 Planarity : 0.007 0.059 10056 Dihedral : 8.895 78.561 20400 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.39 (0.08), residues: 7425 helix: -2.86 (0.06), residues: 3039 sheet: -0.53 (0.11), residues: 1962 loop : -2.58 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP R 39 HIS 0.008 0.002 HISLE 74 PHE 0.030 0.003 PHE S 29 TYR 0.033 0.003 TYRIA 34 ARG 0.010 0.001 ARGLD 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1997 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1987 time to evaluate : 4.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8652 (ptpt) cc_final: 0.8389 (ptpp) REVERT: A 117 ASP cc_start: 0.8054 (p0) cc_final: 0.7685 (p0) REVERT: A 159 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8356 (mtpp) REVERT: B 92 LEU cc_start: 0.8697 (tp) cc_final: 0.8352 (tp) REVERT: GA 31 LEU cc_start: 0.8883 (tp) cc_final: 0.8664 (tp) REVERT: GB 62 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7269 (mtm180) REVERT: GC 21 ASP cc_start: 0.8418 (t70) cc_final: 0.8164 (t70) REVERT: GD 16 MET cc_start: 0.9185 (tmm) cc_final: 0.8938 (tmm) REVERT: GD 18 GLU cc_start: 0.8340 (tp30) cc_final: 0.7880 (tp30) REVERT: GE 16 MET cc_start: 0.8866 (tmm) cc_final: 0.8630 (tmm) REVERT: GE 23 MET cc_start: 0.8255 (mtm) cc_final: 0.8050 (mtp) REVERT: GE 43 THR cc_start: 0.9243 (m) cc_final: 0.8880 (p) REVERT: GF 32 ILE cc_start: 0.9049 (pp) cc_final: 0.8829 (pt) REVERT: HA 82 ASN cc_start: 0.8545 (t160) cc_final: 0.8312 (m-40) REVERT: HD 78 ARG cc_start: 0.8264 (ttt90) cc_final: 0.7863 (ptp90) REVERT: HE 62 ARG cc_start: 0.8874 (ttp-110) cc_final: 0.8583 (mtp-110) REVERT: HF 16 MET cc_start: 0.8703 (tmm) cc_final: 0.8437 (tmm) REVERT: IA 3 ASP cc_start: 0.7709 (m-30) cc_final: 0.7490 (m-30) REVERT: IA 21 ASP cc_start: 0.8998 (t70) cc_final: 0.8329 (t0) REVERT: IC 21 ASP cc_start: 0.8236 (t70) cc_final: 0.7631 (t0) REVERT: IC 82 ASN cc_start: 0.8940 (t160) cc_final: 0.8432 (m-40) REVERT: IC 84 ASP cc_start: 0.8248 (m-30) cc_final: 0.7999 (m-30) REVERT: ID 16 MET cc_start: 0.9328 (tmm) cc_final: 0.9061 (tmm) REVERT: ID 78 ARG cc_start: 0.8322 (ttt90) cc_final: 0.6688 (ptt-90) REVERT: IE 23 MET cc_start: 0.8241 (mtm) cc_final: 0.8022 (mtm) REVERT: IE 43 THR cc_start: 0.9061 (m) cc_final: 0.8703 (t) REVERT: JA 3 ASP cc_start: 0.7049 (m-30) cc_final: 0.6789 (m-30) REVERT: JA 5 LEU cc_start: 0.9250 (tp) cc_final: 0.8846 (tp) REVERT: JA 16 MET cc_start: 0.8942 (tmm) cc_final: 0.8600 (tmm) REVERT: JB 16 MET cc_start: 0.9097 (tmm) cc_final: 0.8774 (tmm) REVERT: JB 18 GLU cc_start: 0.8644 (tp30) cc_final: 0.8289 (tp30) REVERT: JD 18 GLU cc_start: 0.8491 (tp30) cc_final: 0.7841 (tp30) REVERT: JD 78 ARG cc_start: 0.7890 (ttt90) cc_final: 0.7384 (ptp90) REVERT: JE 32 ILE cc_start: 0.9079 (pp) cc_final: 0.8837 (pt) REVERT: KA 8 ILE cc_start: 0.9229 (mm) cc_final: 0.8995 (mm) REVERT: KB 8 ILE cc_start: 0.8620 (mm) cc_final: 0.8373 (mt) REVERT: KC 16 MET cc_start: 0.8886 (tmm) cc_final: 0.8675 (tmm) REVERT: KC 21 ASP cc_start: 0.8162 (t70) cc_final: 0.7952 (t70) REVERT: KC 61 GLN cc_start: 0.8681 (tt0) cc_final: 0.8401 (tt0) REVERT: KE 16 MET cc_start: 0.8737 (tmm) cc_final: 0.8443 (tmm) REVERT: KF 16 MET cc_start: 0.8381 (tmm) cc_final: 0.8002 (tmm) REVERT: KF 21 ASP cc_start: 0.8253 (t70) cc_final: 0.7922 (t0) REVERT: LA 3 ASP cc_start: 0.7441 (m-30) cc_final: 0.7228 (m-30) REVERT: LA 16 MET cc_start: 0.8912 (tmm) cc_final: 0.8520 (tmm) REVERT: LB 10 VAL cc_start: 0.9450 (t) cc_final: 0.9240 (m) REVERT: LB 18 GLU cc_start: 0.8716 (tp30) cc_final: 0.8309 (tp30) REVERT: LB 32 ILE cc_start: 0.8050 (pp) cc_final: 0.7834 (pt) REVERT: LD 16 MET cc_start: 0.8945 (tmm) cc_final: 0.8620 (tmm) REVERT: LD 18 GLU cc_start: 0.8345 (tp30) cc_final: 0.8131 (tp30) REVERT: LD 21 ASP cc_start: 0.8615 (t70) cc_final: 0.8158 (t0) REVERT: LE 32 ILE cc_start: 0.9066 (pp) cc_final: 0.8840 (pt) REVERT: LE 34 TYR cc_start: 0.8746 (p90) cc_final: 0.8499 (p90) REVERT: G 10 PHE cc_start: 0.8412 (t80) cc_final: 0.8156 (t80) REVERT: G 113 ILE cc_start: 0.9187 (mt) cc_final: 0.8957 (tt) REVERT: G 118 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7472 (tp30) REVERT: H 37 SER cc_start: 0.9105 (t) cc_final: 0.8867 (t) REVERT: H 53 ASP cc_start: 0.9230 (t70) cc_final: 0.8909 (t0) REVERT: H 60 LYS cc_start: 0.8454 (mmmm) cc_final: 0.7809 (mmtt) REVERT: H 115 ARG cc_start: 0.4734 (ttt-90) cc_final: 0.3793 (mmt180) REVERT: H 179 TYR cc_start: 0.8812 (m-80) cc_final: 0.8467 (m-10) REVERT: I 17 GLN cc_start: 0.8520 (mt0) cc_final: 0.8018 (mt0) REVERT: J 74 LEU cc_start: 0.8724 (tp) cc_final: 0.8502 (tt) REVERT: J 95 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8223 (ttmm) REVERT: J 110 THR cc_start: 0.9236 (m) cc_final: 0.8950 (p) REVERT: J 183 SER cc_start: 0.7720 (p) cc_final: 0.6960 (m) REVERT: K 7 THR cc_start: 0.8703 (m) cc_final: 0.8206 (m) REVERT: L 10 PHE cc_start: 0.8258 (t80) cc_final: 0.7981 (t80) REVERT: L 37 SER cc_start: 0.8696 (t) cc_final: 0.8485 (t) REVERT: L 132 MET cc_start: 0.7706 (mmt) cc_final: 0.7345 (mmm) REVERT: N 132 MET cc_start: 0.8414 (mmt) cc_final: 0.8035 (mmm) REVERT: N 157 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7610 (mm-30) REVERT: O 60 LYS cc_start: 0.9001 (mttp) cc_final: 0.8756 (mttp) REVERT: O 72 TYR cc_start: 0.8350 (m-10) cc_final: 0.7651 (m-80) REVERT: O 115 ARG cc_start: 0.5186 (mtp180) cc_final: 0.4779 (mpp80) REVERT: O 163 ASN cc_start: 0.7919 (m-40) cc_final: 0.6872 (m110) REVERT: P 134 ILE cc_start: 0.9136 (tt) cc_final: 0.8898 (mt) REVERT: Q 50 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7828 (ttm-80) REVERT: Q 52 THR cc_start: 0.8862 (m) cc_final: 0.8493 (p) REVERT: Q 91 THR cc_start: 0.8749 (m) cc_final: 0.8477 (p) REVERT: Q 132 MET cc_start: 0.8565 (mmt) cc_final: 0.6953 (mmt) REVERT: Q 188 ASP cc_start: 0.7694 (m-30) cc_final: 0.7339 (m-30) REVERT: R 46 ILE cc_start: 0.8902 (tp) cc_final: 0.8549 (tp) REVERT: R 132 MET cc_start: 0.8243 (mmt) cc_final: 0.7934 (mmt) REVERT: S 20 THR cc_start: 0.8953 (m) cc_final: 0.8572 (m) REVERT: S 188 ASP cc_start: 0.8007 (m-30) cc_final: 0.7765 (m-30) REVERT: T 76 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7931 (tm-30) REVERT: T 195 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7468 (mt-10) REVERT: U 9 ILE cc_start: 0.9234 (tp) cc_final: 0.8615 (pt) REVERT: U 30 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8777 (pp) REVERT: U 50 ARG cc_start: 0.7418 (mtp180) cc_final: 0.6930 (mtm110) REVERT: U 72 TYR cc_start: 0.8145 (m-10) cc_final: 0.7678 (m-10) REVERT: U 120 TYR cc_start: 0.8663 (m-10) cc_final: 0.8356 (m-80) REVERT: U 195 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7584 (mt-10) REVERT: V 46 ILE cc_start: 0.8505 (tp) cc_final: 0.8260 (tp) REVERT: V 139 SER cc_start: 0.8923 (m) cc_final: 0.8354 (p) REVERT: V 183 SER cc_start: 0.8364 (p) cc_final: 0.7987 (t) REVERT: X 68 VAL cc_start: 0.9020 (t) cc_final: 0.8800 (m) outliers start: 10 outliers final: 4 residues processed: 1996 average time/residue: 0.6246 time to fit residues: 1955.2304 Evaluate side-chains 1360 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1355 time to evaluate : 6.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain U residue 30 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 625 optimal weight: 0.9990 chunk 561 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 378 optimal weight: 0.0170 chunk 300 optimal weight: 0.9980 chunk 580 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 chunk 432 optimal weight: 0.5980 chunk 672 optimal weight: 0.4980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: GE 82 ASN HB 82 ASN HF 82 ASN IC 82 ASN ID 61 GLN IE 82 ASN IF 82 ASN JA 82 ASN JB 61 GLN JD 82 ASN JF 82 ASN KB 82 ASN KC 82 ASN KE 82 ASN KF 82 ASN LF 82 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN G 168 ASN H 15 GLN H 123 GLN H 168 ASN I 66 GLN I 168 ASN J 121 GLN J 168 ASN K 15 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 HIS L 168 ASN M 168 ASN N 123 GLN N 163 ASN N 168 ASN O 15 GLN O 49 ASN O 78 HIS O 168 ASN P 128 ASN P 165 HIS ** P 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 GLN R 168 ASN S 168 ASN T 123 GLN ** T 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 168 ASN U 78 HIS U 123 GLN ** U 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 168 ASN V 15 GLN V 111 HIS ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 168 ASN W 15 GLN ** W 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 49 ASN ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 56466 Z= 0.225 Angle : 0.582 12.066 76749 Z= 0.313 Chirality : 0.044 0.194 9174 Planarity : 0.005 0.047 10056 Dihedral : 4.798 45.851 8118 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.34 % Allowed : 10.61 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.19 (0.09), residues: 7425 helix: -0.34 (0.09), residues: 3015 sheet: -0.10 (0.11), residues: 1971 loop : -1.76 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP V 39 HIS 0.009 0.001 HIS V 111 PHE 0.025 0.001 PHE V 10 TYR 0.019 0.002 TYR Q 150 ARG 0.009 0.001 ARG K 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1555 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8608 (mtt) cc_final: 0.8357 (mtt) REVERT: B 6 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: B 74 MET cc_start: 0.8936 (tpp) cc_final: 0.8717 (mmm) REVERT: C 71 GLU cc_start: 0.7788 (tp30) cc_final: 0.7325 (tp30) REVERT: C 75 ILE cc_start: 0.9061 (tp) cc_final: 0.8708 (mt) REVERT: C 115 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.4960 (mp0) REVERT: C 117 ASP cc_start: 0.8335 (p0) cc_final: 0.7912 (p0) REVERT: GB 23 MET cc_start: 0.8320 (mtm) cc_final: 0.8091 (mtm) REVERT: GB 62 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7323 (mtm180) REVERT: GC 21 ASP cc_start: 0.8397 (t70) cc_final: 0.8197 (t70) REVERT: GE 16 MET cc_start: 0.8900 (tmm) cc_final: 0.8588 (tmm) REVERT: GE 43 THR cc_start: 0.9158 (m) cc_final: 0.8844 (p) REVERT: GF 16 MET cc_start: 0.8542 (tmm) cc_final: 0.8273 (tmm) REVERT: GF 32 ILE cc_start: 0.9204 (pp) cc_final: 0.8962 (pt) REVERT: HA 34 TYR cc_start: 0.8640 (p90) cc_final: 0.8296 (p90) REVERT: HA 82 ASN cc_start: 0.8464 (t160) cc_final: 0.8168 (m-40) REVERT: HC 78 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7558 (ttp-170) REVERT: HD 78 ARG cc_start: 0.8263 (ttt90) cc_final: 0.7934 (ptp90) REVERT: HE 62 ARG cc_start: 0.8866 (ttp-110) cc_final: 0.8630 (mtm110) REVERT: HF 16 MET cc_start: 0.8756 (tmm) cc_final: 0.8495 (tmm) REVERT: IA 54 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8040 (tttp) REVERT: IC 16 MET cc_start: 0.9019 (tmm) cc_final: 0.8665 (tmm) REVERT: IC 18 GLU cc_start: 0.7923 (tp30) cc_final: 0.7580 (tp30) REVERT: IC 82 ASN cc_start: 0.8989 (t0) cc_final: 0.8443 (m-40) REVERT: ID 28 LYS cc_start: 0.8927 (tptt) cc_final: 0.8694 (tptm) REVERT: ID 78 ARG cc_start: 0.8438 (ttt90) cc_final: 0.6943 (ptt-90) REVERT: IE 43 THR cc_start: 0.8938 (m) cc_final: 0.8659 (p) REVERT: JB 16 MET cc_start: 0.9240 (tmm) cc_final: 0.8767 (tmm) REVERT: JB 18 GLU cc_start: 0.8656 (tp30) cc_final: 0.8293 (tp30) REVERT: JC 62 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.8125 (ttm110) REVERT: JD 18 GLU cc_start: 0.8547 (tp30) cc_final: 0.7847 (tp30) REVERT: JD 78 ARG cc_start: 0.7994 (ttt90) cc_final: 0.7310 (ptp90) REVERT: KB 23 MET cc_start: 0.8701 (mtm) cc_final: 0.8342 (mtp) REVERT: KC 61 GLN cc_start: 0.8648 (tt0) cc_final: 0.8441 (tt0) REVERT: KD 62 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8504 (ttm110) REVERT: KD 89 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8721 (mm) REVERT: KE 16 MET cc_start: 0.8773 (tmm) cc_final: 0.8354 (tmm) REVERT: KE 43 THR cc_start: 0.8931 (m) cc_final: 0.8474 (p) REVERT: KE 49 ASP cc_start: 0.7558 (t0) cc_final: 0.6914 (t70) REVERT: KE 50 VAL cc_start: 0.8730 (p) cc_final: 0.8397 (t) REVERT: KF 16 MET cc_start: 0.8054 (tmm) cc_final: 0.7793 (tmm) REVERT: KF 21 ASP cc_start: 0.8323 (t70) cc_final: 0.7961 (t0) REVERT: KF 58 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7358 (mt-10) REVERT: LA 16 MET cc_start: 0.8958 (tmm) cc_final: 0.8672 (tmm) REVERT: LA 37 THR cc_start: 0.9234 (p) cc_final: 0.9011 (m) REVERT: LA 62 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7673 (mtm110) REVERT: LB 18 GLU cc_start: 0.8752 (tp30) cc_final: 0.8422 (tp30) REVERT: LB 32 ILE cc_start: 0.8224 (pp) cc_final: 0.7919 (pt) REVERT: LC 11 ARG cc_start: 0.8235 (ttt90) cc_final: 0.8023 (ttt90) REVERT: LD 16 MET cc_start: 0.8896 (tmm) cc_final: 0.8668 (tmm) REVERT: LD 18 GLU cc_start: 0.8373 (tp30) cc_final: 0.8039 (tp30) REVERT: LD 21 ASP cc_start: 0.8615 (t70) cc_final: 0.8087 (t0) REVERT: LD 36 LYS cc_start: 0.8802 (mttm) cc_final: 0.8330 (mttt) REVERT: LE 11 ARG cc_start: 0.8340 (ttm170) cc_final: 0.8122 (ttt-90) REVERT: G 30 LEU cc_start: 0.7497 (pp) cc_final: 0.7153 (mt) REVERT: G 113 ILE cc_start: 0.9321 (mt) cc_final: 0.9088 (tt) REVERT: H 27 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7627 (mtp85) REVERT: H 37 SER cc_start: 0.8911 (t) cc_final: 0.8705 (t) REVERT: H 53 ASP cc_start: 0.9228 (t70) cc_final: 0.8879 (t70) REVERT: H 115 ARG cc_start: 0.4990 (ttt-90) cc_final: 0.4072 (mmt180) REVERT: I 95 LYS cc_start: 0.8757 (tppt) cc_final: 0.8545 (tppt) REVERT: I 128 ASN cc_start: 0.8149 (t0) cc_final: 0.7740 (t0) REVERT: I 150 TYR cc_start: 0.8556 (m-80) cc_final: 0.8295 (m-80) REVERT: I 188 ASP cc_start: 0.8281 (m-30) cc_final: 0.8009 (m-30) REVERT: J 60 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8288 (pttp) REVERT: J 74 LEU cc_start: 0.8769 (tp) cc_final: 0.8509 (tt) REVERT: J 110 THR cc_start: 0.9150 (m) cc_final: 0.8831 (p) REVERT: J 128 ASN cc_start: 0.8343 (t0) cc_final: 0.8063 (t0) REVERT: K 9 ILE cc_start: 0.9239 (tp) cc_final: 0.9020 (mm) REVERT: K 139 SER cc_start: 0.9064 (m) cc_final: 0.8531 (p) REVERT: K 177 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8542 (mtt-85) REVERT: L 10 PHE cc_start: 0.8321 (t80) cc_final: 0.8015 (t80) REVERT: L 37 SER cc_start: 0.8809 (t) cc_final: 0.8481 (t) REVERT: L 50 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7096 (ttm-80) REVERT: L 128 ASN cc_start: 0.7980 (t0) cc_final: 0.7696 (t0) REVERT: L 139 SER cc_start: 0.9017 (m) cc_final: 0.8311 (p) REVERT: L 188 ASP cc_start: 0.8369 (t70) cc_final: 0.8158 (t0) REVERT: M 72 TYR cc_start: 0.8152 (m-10) cc_final: 0.7852 (m-80) REVERT: M 94 ASP cc_start: 0.8150 (t70) cc_final: 0.7921 (t70) REVERT: N 132 MET cc_start: 0.8405 (mmt) cc_final: 0.7901 (mmm) REVERT: O 30 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8783 (pp) REVERT: O 60 LYS cc_start: 0.8938 (mttp) cc_final: 0.8715 (mttp) REVERT: O 86 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8576 (mp) REVERT: O 199 ARG cc_start: 0.8342 (ptp-110) cc_final: 0.7764 (ptp-110) REVERT: P 72 TYR cc_start: 0.8307 (m-10) cc_final: 0.7913 (m-80) REVERT: Q 52 THR cc_start: 0.8974 (m) cc_final: 0.8753 (p) REVERT: Q 53 ASP cc_start: 0.8008 (t0) cc_final: 0.7672 (t0) REVERT: Q 57 LYS cc_start: 0.8220 (mmtp) cc_final: 0.7951 (mmtm) REVERT: Q 132 MET cc_start: 0.8463 (mmt) cc_final: 0.6978 (mmt) REVERT: R 8 TYR cc_start: 0.8733 (t80) cc_final: 0.8425 (t80) REVERT: R 46 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8525 (tp) REVERT: R 111 HIS cc_start: 0.7491 (p90) cc_final: 0.7284 (p90) REVERT: R 132 MET cc_start: 0.8139 (mmt) cc_final: 0.7815 (mmm) REVERT: S 72 TYR cc_start: 0.7623 (m-10) cc_final: 0.7199 (m-80) REVERT: S 159 GLU cc_start: 0.7275 (tt0) cc_final: 0.7055 (tt0) REVERT: T 7 THR cc_start: 0.8902 (m) cc_final: 0.8642 (p) REVERT: T 132 MET cc_start: 0.8528 (mmt) cc_final: 0.7997 (mmm) REVERT: T 157 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7809 (mm-30) REVERT: T 175 PHE cc_start: 0.8405 (m-80) cc_final: 0.8185 (m-80) REVERT: U 95 LYS cc_start: 0.8390 (tptt) cc_final: 0.7700 (tptt) REVERT: V 50 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8362 (mtp85) REVERT: V 139 SER cc_start: 0.8859 (m) cc_final: 0.8280 (p) REVERT: W 74 LEU cc_start: 0.8802 (tp) cc_final: 0.8511 (tt) REVERT: W 81 ASP cc_start: 0.8351 (t0) cc_final: 0.8021 (t0) REVERT: X 60 LYS cc_start: 0.8398 (tptt) cc_final: 0.8167 (tptm) outliers start: 129 outliers final: 64 residues processed: 1619 average time/residue: 0.6106 time to fit residues: 1561.8781 Evaluate side-chains 1396 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1325 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain GF residue 76 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JD residue 89 LEU Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 89 LEU Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 111 HIS Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 373 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 560 optimal weight: 0.9990 chunk 458 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 674 optimal weight: 2.9990 chunk 728 optimal weight: 4.9990 chunk 600 optimal weight: 7.9990 chunk 668 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 540 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN GB 82 ASN GF 82 ASN IF 82 ASN KF 82 ASN LB 61 GLN LB 82 ASN G 15 GLN H 78 HIS H 123 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN M 107 GLN N 156 ASN N 163 ASN P 112 GLN P 168 ASN Q 15 GLN R 168 ASN S 107 GLN ** S 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 HIS ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 56466 Z= 0.384 Angle : 0.622 12.196 76749 Z= 0.330 Chirality : 0.045 0.229 9174 Planarity : 0.004 0.043 10056 Dihedral : 4.631 47.329 8118 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.67 % Allowed : 12.68 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.10), residues: 7425 helix: 0.24 (0.10), residues: 3123 sheet: 0.05 (0.11), residues: 1962 loop : -1.75 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 39 HIS 0.008 0.001 HIS V 111 PHE 0.025 0.002 PHE W 10 TYR 0.019 0.002 TYR Q 72 ARG 0.009 0.001 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1354 time to evaluate : 4.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8655 (mtt) cc_final: 0.8402 (mtt) REVERT: C 115 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5158 (mp0) REVERT: C 150 MET cc_start: 0.8913 (ttt) cc_final: 0.8695 (ttt) REVERT: GA 3 ASP cc_start: 0.8381 (m-30) cc_final: 0.8065 (m-30) REVERT: GB 62 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7365 (mtm180) REVERT: GD 16 MET cc_start: 0.9179 (tmm) cc_final: 0.8973 (tmm) REVERT: GD 18 GLU cc_start: 0.8555 (tp30) cc_final: 0.7742 (tp30) REVERT: GE 43 THR cc_start: 0.9282 (m) cc_final: 0.9037 (p) REVERT: GF 32 ILE cc_start: 0.9267 (pp) cc_final: 0.9032 (pt) REVERT: HA 82 ASN cc_start: 0.8558 (t160) cc_final: 0.8161 (m-40) REVERT: HB 23 MET cc_start: 0.8808 (mtm) cc_final: 0.8515 (mtp) REVERT: HB 62 ARG cc_start: 0.8442 (ptp-110) cc_final: 0.8113 (ptp90) REVERT: HE 62 ARG cc_start: 0.8885 (ttp-110) cc_final: 0.8659 (mtm110) REVERT: HF 16 MET cc_start: 0.8780 (tmm) cc_final: 0.8494 (tmm) REVERT: IA 16 MET cc_start: 0.8963 (tmm) cc_final: 0.8751 (tmm) REVERT: IA 21 ASP cc_start: 0.9032 (t0) cc_final: 0.8770 (t0) REVERT: IC 16 MET cc_start: 0.9038 (tmm) cc_final: 0.8612 (tmm) REVERT: IC 18 GLU cc_start: 0.8139 (tp30) cc_final: 0.7677 (tp30) REVERT: IC 21 ASP cc_start: 0.8395 (t70) cc_final: 0.7812 (t0) REVERT: ID 28 LYS cc_start: 0.8830 (tptt) cc_final: 0.8615 (tptm) REVERT: ID 78 ARG cc_start: 0.8521 (ttt90) cc_final: 0.7079 (mtm-85) REVERT: JA 16 MET cc_start: 0.9051 (tmm) cc_final: 0.8727 (tmm) REVERT: JB 16 MET cc_start: 0.9259 (tmm) cc_final: 0.8872 (tmm) REVERT: JB 18 GLU cc_start: 0.8798 (tp30) cc_final: 0.8456 (tp30) REVERT: JC 62 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.8021 (ttm-80) REVERT: JD 18 GLU cc_start: 0.8678 (tp30) cc_final: 0.8084 (tp30) REVERT: JD 78 ARG cc_start: 0.8051 (ttt90) cc_final: 0.7425 (ptp90) REVERT: KB 23 MET cc_start: 0.8761 (mtm) cc_final: 0.8525 (mtp) REVERT: KC 61 GLN cc_start: 0.8737 (tt0) cc_final: 0.8491 (tt0) REVERT: KE 16 MET cc_start: 0.8871 (tmm) cc_final: 0.8355 (tmm) REVERT: KE 43 THR cc_start: 0.9001 (m) cc_final: 0.8656 (p) REVERT: KF 16 MET cc_start: 0.8235 (tmm) cc_final: 0.7907 (tmm) REVERT: KF 21 ASP cc_start: 0.8471 (t70) cc_final: 0.8103 (t0) REVERT: LA 62 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7791 (mtm110) REVERT: LB 18 GLU cc_start: 0.8868 (tp30) cc_final: 0.8602 (tp30) REVERT: LB 32 ILE cc_start: 0.8503 (pp) cc_final: 0.8174 (pt) REVERT: LD 16 MET cc_start: 0.9019 (tmm) cc_final: 0.8734 (tmm) REVERT: LD 18 GLU cc_start: 0.8459 (tp30) cc_final: 0.8157 (tp30) REVERT: LD 21 ASP cc_start: 0.8722 (t70) cc_final: 0.8308 (t0) REVERT: LD 36 LYS cc_start: 0.8844 (mttm) cc_final: 0.8418 (mttt) REVERT: LD 61 GLN cc_start: 0.8352 (tt0) cc_final: 0.8004 (tt0) REVERT: G 132 MET cc_start: 0.8192 (mmm) cc_final: 0.6878 (mmm) REVERT: H 27 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7603 (mtp85) REVERT: H 95 LYS cc_start: 0.8658 (tppt) cc_final: 0.7772 (tppt) REVERT: H 99 ARG cc_start: 0.8309 (mmm160) cc_final: 0.8060 (mmm-85) REVERT: H 115 ARG cc_start: 0.5080 (ttt-90) cc_final: 0.3810 (mmt180) REVERT: I 150 TYR cc_start: 0.8719 (m-80) cc_final: 0.8439 (m-80) REVERT: I 188 ASP cc_start: 0.8304 (m-30) cc_final: 0.8064 (m-30) REVERT: J 110 THR cc_start: 0.9018 (m) cc_final: 0.8811 (p) REVERT: J 128 ASN cc_start: 0.8427 (t0) cc_final: 0.8068 (t0) REVERT: J 132 MET cc_start: 0.8550 (mmt) cc_final: 0.8143 (mmt) REVERT: J 170 THR cc_start: 0.9450 (m) cc_final: 0.8735 (p) REVERT: K 132 MET cc_start: 0.8649 (mmt) cc_final: 0.8144 (mmm) REVERT: K 139 SER cc_start: 0.9042 (m) cc_final: 0.8545 (p) REVERT: L 10 PHE cc_start: 0.8347 (t80) cc_final: 0.8056 (t80) REVERT: L 37 SER cc_start: 0.8891 (t) cc_final: 0.8609 (t) REVERT: L 105 LYS cc_start: 0.9003 (tptp) cc_final: 0.8710 (tptp) REVERT: L 128 ASN cc_start: 0.8074 (t0) cc_final: 0.7852 (t0) REVERT: L 139 SER cc_start: 0.9025 (m) cc_final: 0.8325 (p) REVERT: L 159 GLU cc_start: 0.8317 (tt0) cc_final: 0.7810 (tp30) REVERT: M 94 ASP cc_start: 0.8287 (t70) cc_final: 0.8043 (t70) REVERT: N 132 MET cc_start: 0.8620 (mmt) cc_final: 0.7809 (mmp) REVERT: N 175 PHE cc_start: 0.8412 (m-80) cc_final: 0.8063 (m-80) REVERT: O 30 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8817 (pp) REVERT: O 60 LYS cc_start: 0.8966 (mttp) cc_final: 0.8742 (mttp) REVERT: O 86 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8600 (mp) REVERT: O 199 ARG cc_start: 0.8429 (ptp-110) cc_final: 0.7749 (ptp-110) REVERT: P 72 TYR cc_start: 0.8355 (m-10) cc_final: 0.7896 (m-80) REVERT: P 112 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7690 (tp40) REVERT: Q 132 MET cc_start: 0.8588 (mmt) cc_final: 0.7214 (mmt) REVERT: Q 160 LYS cc_start: 0.9052 (mttm) cc_final: 0.8753 (mmmt) REVERT: S 128 ASN cc_start: 0.8184 (t0) cc_final: 0.7916 (t0) REVERT: T 132 MET cc_start: 0.8601 (mmt) cc_final: 0.8049 (mmm) REVERT: U 50 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7358 (mtm110) REVERT: U 95 LYS cc_start: 0.8351 (tptt) cc_final: 0.8107 (tptt) REVERT: V 46 ILE cc_start: 0.8478 (tp) cc_final: 0.8172 (tp) REVERT: V 50 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8428 (mtp85) REVERT: W 74 LEU cc_start: 0.8799 (tp) cc_final: 0.8506 (tt) outliers start: 202 outliers final: 135 residues processed: 1475 average time/residue: 0.6196 time to fit residues: 1439.5810 Evaluate side-chains 1390 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1251 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 37 THR Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain GF residue 76 ILE Chi-restraints excluded: chain HB residue 89 LEU Chi-restraints excluded: chain HC residue 10 VAL Chi-restraints excluded: chain HC residue 49 ASP Chi-restraints excluded: chain HC residue 62 ARG Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HE residue 10 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 37 THR Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 9 GLU Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 67 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 50 VAL Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KC residue 67 VAL Chi-restraints excluded: chain KD residue 58 GLU Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 92 THR Chi-restraints excluded: chain KE residue 69 GLU Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain KF residue 92 THR Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LD residue 57 THR Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 43 THR Chi-restraints excluded: chain LE residue 67 VAL Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 50 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 107 GLN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 112 GLN Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 107 GLN Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 111 HIS Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 666 optimal weight: 0.5980 chunk 506 optimal weight: 2.9990 chunk 349 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 321 optimal weight: 0.6980 chunk 452 optimal weight: 1.9990 chunk 676 optimal weight: 2.9990 chunk 716 optimal weight: 0.8980 chunk 353 optimal weight: 0.8980 chunk 641 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: GF 82 ASN IF 82 ASN LB 61 GLN I 66 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 ASN ** M 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 ASN S 107 GLN ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 HIS W 66 GLN ** W 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56466 Z= 0.235 Angle : 0.554 11.243 76749 Z= 0.293 Chirality : 0.043 0.203 9174 Planarity : 0.004 0.039 10056 Dihedral : 4.419 56.407 8118 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.20 % Allowed : 14.59 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 (0.10), residues: 7425 helix: 0.66 (0.10), residues: 3114 sheet: 0.26 (0.11), residues: 1962 loop : -1.58 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 39 HIS 0.008 0.001 HIS V 111 PHE 0.025 0.001 PHE W 10 TYR 0.020 0.002 TYR R 150 ARG 0.011 0.001 ARG G 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1541 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1365 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8531 (mtt) cc_final: 0.8301 (mtt) REVERT: C 66 GLN cc_start: 0.7867 (mt0) cc_final: 0.7638 (mp10) REVERT: C 75 ILE cc_start: 0.9041 (tp) cc_final: 0.8808 (mt) REVERT: GA 3 ASP cc_start: 0.8294 (m-30) cc_final: 0.8076 (m-30) REVERT: GB 62 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7287 (mtm180) REVERT: GD 18 GLU cc_start: 0.8502 (tp30) cc_final: 0.7673 (tp30) REVERT: GD 78 ARG cc_start: 0.8565 (ttt90) cc_final: 0.6869 (ptt90) REVERT: GF 32 ILE cc_start: 0.9212 (pp) cc_final: 0.8968 (pt) REVERT: HA 11 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8406 (ttm-80) REVERT: HA 54 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8362 (mtmt) REVERT: HA 82 ASN cc_start: 0.8484 (t160) cc_final: 0.8076 (m-40) REVERT: HE 62 ARG cc_start: 0.8895 (ttp-110) cc_final: 0.8631 (mtm110) REVERT: IA 21 ASP cc_start: 0.9069 (t0) cc_final: 0.8779 (t0) REVERT: IA 61 GLN cc_start: 0.8662 (tt0) cc_final: 0.8429 (tt0) REVERT: IB 47 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8350 (mtm180) REVERT: IC 7 MET cc_start: 0.8364 (mtm) cc_final: 0.8047 (mtm) REVERT: IC 16 MET cc_start: 0.9050 (tmm) cc_final: 0.8656 (tmm) REVERT: IC 18 GLU cc_start: 0.8073 (tp30) cc_final: 0.7642 (tp30) REVERT: IC 21 ASP cc_start: 0.8343 (t70) cc_final: 0.7732 (t0) REVERT: IC 28 LYS cc_start: 0.8570 (tppt) cc_final: 0.8221 (tppt) REVERT: ID 78 ARG cc_start: 0.8470 (ttt90) cc_final: 0.6945 (ptt-90) REVERT: IE 18 GLU cc_start: 0.8370 (tp30) cc_final: 0.8151 (tp30) REVERT: IE 43 THR cc_start: 0.8667 (p) cc_final: 0.8417 (p) REVERT: JA 16 MET cc_start: 0.9067 (tmm) cc_final: 0.8657 (tmm) REVERT: JA 58 GLU cc_start: 0.7325 (mp0) cc_final: 0.6986 (mp0) REVERT: JA 78 ARG cc_start: 0.7932 (tpt170) cc_final: 0.7725 (tpt170) REVERT: JB 7 MET cc_start: 0.8133 (mtp) cc_final: 0.7878 (mtm) REVERT: JB 16 MET cc_start: 0.9225 (tmm) cc_final: 0.8784 (tmm) REVERT: JB 18 GLU cc_start: 0.8697 (tp30) cc_final: 0.8380 (tp30) REVERT: JC 62 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.7975 (ttm-80) REVERT: JD 18 GLU cc_start: 0.8624 (tp30) cc_final: 0.8028 (tp30) REVERT: JD 78 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7429 (ptp90) REVERT: KE 16 MET cc_start: 0.8829 (tmm) cc_final: 0.8403 (tmm) REVERT: KE 43 THR cc_start: 0.8952 (m) cc_final: 0.8595 (p) REVERT: KF 16 MET cc_start: 0.8253 (tmm) cc_final: 0.7960 (tmm) REVERT: KF 21 ASP cc_start: 0.8407 (t70) cc_final: 0.8066 (t0) REVERT: LA 62 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7806 (mtm110) REVERT: LB 18 GLU cc_start: 0.8851 (tp30) cc_final: 0.8562 (tp30) REVERT: LB 61 GLN cc_start: 0.8503 (tt0) cc_final: 0.8270 (tt0) REVERT: LD 16 MET cc_start: 0.9054 (tmm) cc_final: 0.8827 (tmm) REVERT: LD 18 GLU cc_start: 0.8467 (tp30) cc_final: 0.8155 (tp30) REVERT: LD 21 ASP cc_start: 0.8676 (t70) cc_final: 0.8208 (t0) REVERT: LD 36 LYS cc_start: 0.8827 (mttm) cc_final: 0.8322 (mttt) REVERT: LF 16 MET cc_start: 0.8914 (tmm) cc_final: 0.8597 (tmm) REVERT: G 132 MET cc_start: 0.8189 (mmm) cc_final: 0.6999 (mmm) REVERT: H 53 ASP cc_start: 0.9299 (t70) cc_final: 0.8948 (t70) REVERT: H 115 ARG cc_start: 0.5039 (ttt-90) cc_final: 0.3833 (mmt180) REVERT: I 8 TYR cc_start: 0.8807 (t80) cc_final: 0.8295 (t80) REVERT: I 150 TYR cc_start: 0.8657 (m-80) cc_final: 0.8355 (m-80) REVERT: J 128 ASN cc_start: 0.8413 (t0) cc_final: 0.8020 (t0) REVERT: J 132 MET cc_start: 0.8590 (mmt) cc_final: 0.8366 (mmt) REVERT: J 170 THR cc_start: 0.9416 (m) cc_final: 0.8753 (p) REVERT: J 199 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7682 (mmm160) REVERT: K 9 ILE cc_start: 0.9088 (mp) cc_final: 0.8788 (mt) REVERT: K 132 MET cc_start: 0.8668 (mmt) cc_final: 0.8219 (mmm) REVERT: K 139 SER cc_start: 0.9031 (m) cc_final: 0.8821 (t) REVERT: L 37 SER cc_start: 0.8892 (t) cc_final: 0.8606 (t) REVERT: L 50 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.7932 (ttm-80) REVERT: L 128 ASN cc_start: 0.8120 (t0) cc_final: 0.7871 (t0) REVERT: L 132 MET cc_start: 0.7657 (mmt) cc_final: 0.7455 (mmm) REVERT: L 139 SER cc_start: 0.8971 (m) cc_final: 0.8201 (p) REVERT: L 183 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7920 (t) REVERT: M 94 ASP cc_start: 0.8270 (t70) cc_final: 0.8006 (t70) REVERT: N 132 MET cc_start: 0.8405 (mmt) cc_final: 0.8109 (mmm) REVERT: N 199 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6656 (mtm110) REVERT: O 30 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8765 (pp) REVERT: O 86 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8551 (mp) REVERT: O 199 ARG cc_start: 0.8406 (ptp-110) cc_final: 0.7748 (ptp-110) REVERT: P 72 TYR cc_start: 0.8110 (m-10) cc_final: 0.7716 (m-80) REVERT: P 112 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8054 (tp40) REVERT: Q 132 MET cc_start: 0.8640 (mmt) cc_final: 0.8162 (mmm) REVERT: R 8 TYR cc_start: 0.8765 (t80) cc_final: 0.8458 (t80) REVERT: S 69 GLU cc_start: 0.7279 (pm20) cc_final: 0.6986 (pm20) REVERT: S 128 ASN cc_start: 0.8157 (t0) cc_final: 0.7771 (t0) REVERT: T 69 GLU cc_start: 0.7736 (pm20) cc_final: 0.7453 (pm20) REVERT: T 132 MET cc_start: 0.8596 (mmt) cc_final: 0.8067 (mmm) REVERT: U 6 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: U 50 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7231 (mtm110) REVERT: U 95 LYS cc_start: 0.8375 (tptt) cc_final: 0.8151 (tptt) REVERT: U 133 MET cc_start: 0.8321 (mtt) cc_final: 0.7948 (mtt) REVERT: V 46 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8316 (tp) REVERT: W 74 LEU cc_start: 0.8754 (tp) cc_final: 0.8483 (tt) outliers start: 176 outliers final: 118 residues processed: 1468 average time/residue: 0.6387 time to fit residues: 1483.9281 Evaluate side-chains 1384 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1261 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GE residue 65 GLU Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 9 GLU Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 89 LEU Chi-restraints excluded: chain HC residue 62 ARG Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 69 GLU Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 89 LEU Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 49 ASP Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 37 THR Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 54 LYS Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KC residue 67 VAL Chi-restraints excluded: chain KD residue 58 GLU Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KE residue 50 VAL Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LA residue 75 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LD residue 57 THR Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 43 THR Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 168 ASN Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 107 GLN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 107 GLN Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 596 optimal weight: 0.9990 chunk 406 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 533 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 611 optimal weight: 2.9990 chunk 495 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 365 optimal weight: 0.7980 chunk 642 optimal weight: 3.9990 chunk 180 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: IF 82 ASN LB 82 ASN I 66 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 ASN T 78 HIS ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 165 HIS ** W 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56466 Z= 0.225 Angle : 0.548 10.013 76749 Z= 0.289 Chirality : 0.043 0.166 9174 Planarity : 0.004 0.038 10056 Dihedral : 4.288 51.540 8118 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.47 % Allowed : 15.19 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.04 (0.10), residues: 7425 helix: 0.84 (0.10), residues: 3114 sheet: 0.37 (0.11), residues: 1971 loop : -1.50 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP L 39 HIS 0.003 0.001 HISHE 74 PHE 0.025 0.001 PHE P 10 TYR 0.018 0.001 TYRKC 34 ARG 0.011 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1324 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8527 (mtt) cc_final: 0.8264 (mtt) REVERT: B 74 MET cc_start: 0.8758 (tpp) cc_final: 0.8497 (mmm) REVERT: B 96 TYR cc_start: 0.8299 (t80) cc_final: 0.8053 (t80) REVERT: C 66 GLN cc_start: 0.7755 (mt0) cc_final: 0.7467 (mp10) REVERT: C 75 ILE cc_start: 0.9005 (tp) cc_final: 0.8777 (mt) REVERT: GB 62 ARG cc_start: 0.7605 (ttp-110) cc_final: 0.7307 (mtm180) REVERT: GD 18 GLU cc_start: 0.8548 (tp30) cc_final: 0.7766 (tp30) REVERT: GD 78 ARG cc_start: 0.8556 (ttt90) cc_final: 0.6875 (ptt90) REVERT: HA 82 ASN cc_start: 0.8469 (t160) cc_final: 0.8070 (m-40) REVERT: HD 18 GLU cc_start: 0.8622 (tp30) cc_final: 0.8335 (tp30) REVERT: HE 62 ARG cc_start: 0.8914 (ttp-110) cc_final: 0.8673 (mtm110) REVERT: IA 21 ASP cc_start: 0.9092 (t70) cc_final: 0.8799 (t0) REVERT: IB 47 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8505 (mmm160) REVERT: IC 16 MET cc_start: 0.9033 (tmm) cc_final: 0.8618 (tmm) REVERT: IC 18 GLU cc_start: 0.8026 (tp30) cc_final: 0.7604 (tp30) REVERT: IC 21 ASP cc_start: 0.8341 (t70) cc_final: 0.7714 (t0) REVERT: IC 28 LYS cc_start: 0.8582 (tppt) cc_final: 0.8240 (tppt) REVERT: ID 78 ARG cc_start: 0.8463 (ttt90) cc_final: 0.6946 (ptt-90) REVERT: IE 18 GLU cc_start: 0.8406 (tp30) cc_final: 0.8134 (tp30) REVERT: JA 16 MET cc_start: 0.9093 (tmm) cc_final: 0.8714 (tmm) REVERT: JB 16 MET cc_start: 0.9219 (tmm) cc_final: 0.8687 (tmm) REVERT: JB 18 GLU cc_start: 0.8699 (tp30) cc_final: 0.8385 (tp30) REVERT: JC 62 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.7974 (ttm-80) REVERT: JD 8 ILE cc_start: 0.9189 (mm) cc_final: 0.8958 (tp) REVERT: JD 18 GLU cc_start: 0.8629 (tp30) cc_final: 0.8003 (tp30) REVERT: JD 78 ARG cc_start: 0.8067 (ttt90) cc_final: 0.7454 (ptp90) REVERT: KE 16 MET cc_start: 0.8832 (tmm) cc_final: 0.8404 (tmm) REVERT: KE 43 THR cc_start: 0.8903 (m) cc_final: 0.8579 (p) REVERT: KF 16 MET cc_start: 0.8239 (tmm) cc_final: 0.7962 (tmm) REVERT: KF 21 ASP cc_start: 0.8396 (t70) cc_final: 0.8053 (t0) REVERT: LB 18 GLU cc_start: 0.8864 (tp30) cc_final: 0.8586 (tp30) REVERT: LB 61 GLN cc_start: 0.8524 (tt0) cc_final: 0.8261 (tt0) REVERT: LC 28 LYS cc_start: 0.8427 (tmtt) cc_final: 0.7929 (ttpp) REVERT: LD 16 MET cc_start: 0.9090 (tmm) cc_final: 0.8763 (tmm) REVERT: LD 18 GLU cc_start: 0.8441 (tp30) cc_final: 0.8116 (tp30) REVERT: LD 21 ASP cc_start: 0.8676 (t70) cc_final: 0.8244 (t0) REVERT: LD 36 LYS cc_start: 0.8828 (mttm) cc_final: 0.8479 (mttm) REVERT: G 132 MET cc_start: 0.8274 (mmm) cc_final: 0.7640 (mmm) REVERT: H 8 TYR cc_start: 0.9003 (t80) cc_final: 0.8741 (t80) REVERT: H 50 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7277 (ttp80) REVERT: H 95 LYS cc_start: 0.8559 (tppt) cc_final: 0.7645 (tppt) REVERT: H 99 ARG cc_start: 0.8296 (mmm160) cc_final: 0.8041 (mmm-85) REVERT: H 115 ARG cc_start: 0.5075 (ttt-90) cc_final: 0.3854 (mmt180) REVERT: I 150 TYR cc_start: 0.8654 (m-80) cc_final: 0.8341 (m-80) REVERT: I 188 ASP cc_start: 0.8046 (m-30) cc_final: 0.7710 (m-30) REVERT: J 128 ASN cc_start: 0.8435 (t0) cc_final: 0.7972 (t0) REVERT: J 170 THR cc_start: 0.9418 (m) cc_final: 0.8788 (p) REVERT: K 9 ILE cc_start: 0.9063 (mp) cc_final: 0.8826 (mt) REVERT: K 132 MET cc_start: 0.8668 (mmt) cc_final: 0.8242 (mmm) REVERT: L 37 SER cc_start: 0.8718 (t) cc_final: 0.8515 (t) REVERT: L 50 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7973 (ttm-80) REVERT: L 128 ASN cc_start: 0.8115 (t0) cc_final: 0.7870 (t0) REVERT: L 132 MET cc_start: 0.7582 (mmt) cc_final: 0.7206 (mmt) REVERT: M 94 ASP cc_start: 0.8182 (t70) cc_final: 0.7812 (t70) REVERT: N 175 PHE cc_start: 0.8334 (m-80) cc_final: 0.8022 (m-80) REVERT: N 199 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6715 (mtm110) REVERT: O 30 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8736 (pp) REVERT: O 86 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8543 (mp) REVERT: O 184 GLU cc_start: 0.7913 (mp0) cc_final: 0.7677 (pt0) REVERT: O 199 ARG cc_start: 0.8397 (ptp-110) cc_final: 0.7771 (ptp-110) REVERT: P 72 TYR cc_start: 0.7970 (m-10) cc_final: 0.7579 (m-80) REVERT: P 112 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8112 (tp40) REVERT: P 132 MET cc_start: 0.7513 (mmt) cc_final: 0.7303 (mmt) REVERT: Q 60 LYS cc_start: 0.8638 (pttt) cc_final: 0.8437 (pttm) REVERT: R 8 TYR cc_start: 0.8693 (t80) cc_final: 0.8413 (t80) REVERT: S 95 LYS cc_start: 0.8729 (tppt) cc_final: 0.8345 (tppt) REVERT: S 128 ASN cc_start: 0.8098 (t0) cc_final: 0.7818 (t0) REVERT: T 7 THR cc_start: 0.8655 (m) cc_final: 0.8387 (p) REVERT: T 132 MET cc_start: 0.8630 (mmt) cc_final: 0.8298 (mmm) REVERT: T 157 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7546 (mm-30) REVERT: U 99 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7842 (mmm-85) REVERT: V 46 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8216 (tp) REVERT: V 50 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8366 (mtp85) REVERT: V 57 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8586 (mmmt) REVERT: V 105 LYS cc_start: 0.9172 (tptt) cc_final: 0.8947 (tptp) REVERT: W 74 LEU cc_start: 0.8757 (tp) cc_final: 0.8483 (tt) REVERT: X 110 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8215 (p) outliers start: 191 outliers final: 131 residues processed: 1432 average time/residue: 0.6513 time to fit residues: 1481.6055 Evaluate side-chains 1384 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1249 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 9 GLU Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HC residue 49 ASP Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 10 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain ID residue 7 MET Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 49 ASP Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IF residue 10 VAL Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 37 THR Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JE residue 67 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 54 LYS Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KC residue 7 MET Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KC residue 67 VAL Chi-restraints excluded: chain KD residue 58 GLU Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 92 THR Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LA residue 75 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 32 ILE Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LD residue 57 THR Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 168 ASN Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 133 MET Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 109 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 240 optimal weight: 0.8980 chunk 645 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 420 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 716 optimal weight: 0.6980 chunk 595 optimal weight: 1.9990 chunk 331 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 376 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: GF 82 ASN LB 82 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 HIS ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 56466 Z= 0.236 Angle : 0.549 8.812 76749 Z= 0.289 Chirality : 0.043 0.174 9174 Planarity : 0.004 0.050 10056 Dihedral : 4.231 55.705 8118 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.65 % Allowed : 15.68 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.07 (0.10), residues: 7425 helix: 0.92 (0.10), residues: 3114 sheet: 0.44 (0.11), residues: 1968 loop : -1.43 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP L 39 HIS 0.004 0.001 HIS L 78 PHE 0.028 0.001 PHE P 10 TYR 0.026 0.001 TYR K 150 ARG 0.011 0.001 ARG G 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1509 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1308 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8539 (mtt) cc_final: 0.8293 (mtt) REVERT: C 66 GLN cc_start: 0.7741 (mt0) cc_final: 0.7387 (mp10) REVERT: C 75 ILE cc_start: 0.9004 (tp) cc_final: 0.8780 (mt) REVERT: GA 25 LYS cc_start: 0.8583 (mttt) cc_final: 0.8369 (mttt) REVERT: GB 62 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.7301 (mtm180) REVERT: GD 18 GLU cc_start: 0.8559 (tp30) cc_final: 0.7810 (tp30) REVERT: GD 78 ARG cc_start: 0.8532 (ttt90) cc_final: 0.6873 (ptt90) REVERT: GE 36 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7568 (mtpp) REVERT: GF 58 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7721 (mt-10) REVERT: HA 54 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8315 (mtmt) REVERT: HA 82 ASN cc_start: 0.8464 (t160) cc_final: 0.8035 (m-40) REVERT: HD 18 GLU cc_start: 0.8660 (tp30) cc_final: 0.8319 (tp30) REVERT: HE 62 ARG cc_start: 0.8910 (ttp-110) cc_final: 0.8676 (mtm110) REVERT: HF 66 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7693 (mtm-85) REVERT: IA 21 ASP cc_start: 0.9107 (t70) cc_final: 0.8809 (t70) REVERT: IA 61 GLN cc_start: 0.8588 (tt0) cc_final: 0.8361 (tt0) REVERT: IC 16 MET cc_start: 0.9041 (tmm) cc_final: 0.8628 (tmm) REVERT: IC 18 GLU cc_start: 0.8067 (tp30) cc_final: 0.7651 (tp30) REVERT: IC 21 ASP cc_start: 0.8358 (t70) cc_final: 0.7721 (t0) REVERT: IC 28 LYS cc_start: 0.8578 (tppt) cc_final: 0.8233 (tppt) REVERT: ID 78 ARG cc_start: 0.8464 (ttt90) cc_final: 0.6942 (ptt-90) REVERT: IE 18 GLU cc_start: 0.8423 (tp30) cc_final: 0.8123 (tp30) REVERT: JA 16 MET cc_start: 0.9141 (tmm) cc_final: 0.8751 (tmm) REVERT: JA 58 GLU cc_start: 0.7305 (mp0) cc_final: 0.7054 (mp0) REVERT: JB 16 MET cc_start: 0.9169 (tmm) cc_final: 0.8703 (tmm) REVERT: JB 18 GLU cc_start: 0.8704 (tp30) cc_final: 0.8392 (tp30) REVERT: JB 43 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9113 (p) REVERT: JC 62 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.7943 (ttm-80) REVERT: JD 18 GLU cc_start: 0.8648 (tp30) cc_final: 0.8050 (tp30) REVERT: KA 16 MET cc_start: 0.8857 (tmm) cc_final: 0.8629 (tmm) REVERT: KE 16 MET cc_start: 0.8777 (tmm) cc_final: 0.8512 (tmm) REVERT: KF 16 MET cc_start: 0.8215 (tmm) cc_final: 0.7929 (tmm) REVERT: KF 21 ASP cc_start: 0.8377 (t70) cc_final: 0.8111 (t0) REVERT: LA 92 THR cc_start: 0.8564 (m) cc_final: 0.8311 (p) REVERT: LB 18 GLU cc_start: 0.8871 (tp30) cc_final: 0.8595 (tp30) REVERT: LB 61 GLN cc_start: 0.8509 (tt0) cc_final: 0.8263 (tt0) REVERT: LD 16 MET cc_start: 0.9100 (tmm) cc_final: 0.8798 (tmm) REVERT: LD 18 GLU cc_start: 0.8415 (tp30) cc_final: 0.8100 (tp30) REVERT: LD 21 ASP cc_start: 0.8684 (t70) cc_final: 0.8266 (t0) REVERT: LD 36 LYS cc_start: 0.8838 (mttm) cc_final: 0.8431 (mttm) REVERT: LE 89 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (mt) REVERT: LF 16 MET cc_start: 0.8975 (tmm) cc_final: 0.8660 (tmm) REVERT: H 8 TYR cc_start: 0.8972 (t80) cc_final: 0.8752 (t80) REVERT: H 50 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7313 (ttp80) REVERT: H 53 ASP cc_start: 0.9200 (t70) cc_final: 0.8929 (t70) REVERT: H 95 LYS cc_start: 0.8496 (tppt) cc_final: 0.8285 (tppt) REVERT: H 99 ARG cc_start: 0.8286 (mmm160) cc_final: 0.8041 (mmm-85) REVERT: H 115 ARG cc_start: 0.5121 (ttt-90) cc_final: 0.3828 (mmt180) REVERT: I 50 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7651 (mtm110) REVERT: I 150 TYR cc_start: 0.8666 (m-80) cc_final: 0.8357 (m-80) REVERT: I 188 ASP cc_start: 0.8073 (m-30) cc_final: 0.7800 (m-30) REVERT: J 128 ASN cc_start: 0.8412 (t0) cc_final: 0.7957 (t0) REVERT: J 170 THR cc_start: 0.9460 (m) cc_final: 0.8841 (p) REVERT: K 9 ILE cc_start: 0.9116 (mp) cc_final: 0.8820 (mt) REVERT: K 132 MET cc_start: 0.8671 (mmt) cc_final: 0.8259 (mmm) REVERT: L 20 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8390 (m) REVERT: L 128 ASN cc_start: 0.8228 (t0) cc_final: 0.7947 (t0) REVERT: M 94 ASP cc_start: 0.8130 (t70) cc_final: 0.7783 (t70) REVERT: N 175 PHE cc_start: 0.8316 (m-80) cc_final: 0.8017 (m-80) REVERT: N 199 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6787 (mtm110) REVERT: O 30 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8739 (pp) REVERT: O 86 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8569 (mp) REVERT: O 184 GLU cc_start: 0.7831 (mp0) cc_final: 0.7608 (pt0) REVERT: O 199 ARG cc_start: 0.8387 (ptp-110) cc_final: 0.7765 (ptp-110) REVERT: P 112 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8099 (tp40) REVERT: P 186 GLU cc_start: 0.8048 (mp0) cc_final: 0.7719 (mp0) REVERT: S 128 ASN cc_start: 0.8161 (t0) cc_final: 0.7879 (t0) REVERT: T 97 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7816 (pt0) REVERT: T 132 MET cc_start: 0.8637 (mmt) cc_final: 0.7859 (mmp) REVERT: U 95 LYS cc_start: 0.8451 (tptt) cc_final: 0.7995 (tptt) REVERT: U 99 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7707 (mmm-85) REVERT: V 46 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8165 (tp) REVERT: V 50 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8374 (mtp85) REVERT: V 57 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8694 (mmmt) REVERT: W 74 LEU cc_start: 0.8794 (tp) cc_final: 0.8557 (tt) REVERT: X 110 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8214 (p) outliers start: 201 outliers final: 153 residues processed: 1425 average time/residue: 0.6146 time to fit residues: 1381.8963 Evaluate side-chains 1415 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1253 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GE residue 10 VAL Chi-restraints excluded: chain GE residue 36 LYS Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 9 GLU Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 62 ARG Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 10 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 7 MET Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 49 ASP Chi-restraints excluded: chain ID residue 58 GLU Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IF residue 10 VAL Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 37 THR Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 43 THR Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JE residue 67 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 54 LYS Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KC residue 7 MET Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KC residue 67 VAL Chi-restraints excluded: chain KD residue 58 GLU Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 92 THR Chi-restraints excluded: chain KE residue 50 VAL Chi-restraints excluded: chain KE residue 69 GLU Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LA residue 75 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 32 ILE Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LD residue 57 THR Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 50 VAL Chi-restraints excluded: chain LE residue 89 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 133 MET Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 109 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 691 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 408 optimal weight: 2.9990 chunk 523 optimal weight: 0.5980 chunk 405 optimal weight: 0.5980 chunk 603 optimal weight: 3.9990 chunk 400 optimal weight: 0.8980 chunk 714 optimal weight: 0.9990 chunk 446 optimal weight: 0.8980 chunk 435 optimal weight: 0.9980 chunk 329 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: IF 82 ASN KA 61 GLN LB 82 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 ASN ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 56466 Z= 0.240 Angle : 0.551 7.974 76749 Z= 0.290 Chirality : 0.043 0.174 9174 Planarity : 0.004 0.044 10056 Dihedral : 4.188 55.248 8118 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.63 % Allowed : 15.95 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.12 (0.10), residues: 7425 helix: 0.96 (0.10), residues: 3114 sheet: 0.44 (0.11), residues: 1986 loop : -1.39 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP L 39 HIS 0.004 0.001 HIS L 78 PHE 0.024 0.001 PHE W 10 TYR 0.025 0.001 TYR K 150 ARG 0.012 0.001 ARG G 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1288 time to evaluate : 4.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8551 (mtt) cc_final: 0.8302 (mtt) REVERT: B 58 LYS cc_start: 0.9281 (ptpt) cc_final: 0.8961 (ptpp) REVERT: C 75 ILE cc_start: 0.8999 (tp) cc_final: 0.8784 (mt) REVERT: GB 62 ARG cc_start: 0.7602 (ttp-110) cc_final: 0.7251 (mtm180) REVERT: GD 18 GLU cc_start: 0.8548 (tp30) cc_final: 0.7876 (tp30) REVERT: GD 78 ARG cc_start: 0.8533 (ttt90) cc_final: 0.6876 (ptt90) REVERT: GE 36 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7602 (mtpp) REVERT: HA 11 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8417 (ttm-80) REVERT: HA 54 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8298 (mtmt) REVERT: HA 82 ASN cc_start: 0.8462 (t160) cc_final: 0.8034 (m-40) REVERT: HB 28 LYS cc_start: 0.8665 (tttt) cc_final: 0.8304 (ttmm) REVERT: HD 18 GLU cc_start: 0.8648 (tp30) cc_final: 0.8308 (tp30) REVERT: HF 66 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7734 (mtm-85) REVERT: IA 21 ASP cc_start: 0.9127 (t70) cc_final: 0.8767 (t0) REVERT: IA 61 GLN cc_start: 0.8636 (tt0) cc_final: 0.8325 (tt0) REVERT: IC 16 MET cc_start: 0.9033 (tmm) cc_final: 0.8629 (tmm) REVERT: IC 21 ASP cc_start: 0.8363 (t70) cc_final: 0.7756 (t0) REVERT: IC 28 LYS cc_start: 0.8587 (tppt) cc_final: 0.8233 (tppt) REVERT: ID 78 ARG cc_start: 0.8468 (ttt90) cc_final: 0.6957 (ptt-90) REVERT: IE 18 GLU cc_start: 0.8436 (tp30) cc_final: 0.8128 (tp30) REVERT: JA 16 MET cc_start: 0.9145 (tmm) cc_final: 0.8777 (tmm) REVERT: JA 58 GLU cc_start: 0.7340 (mp0) cc_final: 0.7028 (mp0) REVERT: JB 16 MET cc_start: 0.9178 (tmm) cc_final: 0.8841 (tmm) REVERT: JB 18 GLU cc_start: 0.8700 (tp30) cc_final: 0.8382 (tp30) REVERT: JB 43 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9126 (p) REVERT: JC 62 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.7921 (ttm-80) REVERT: JD 18 GLU cc_start: 0.8648 (tp30) cc_final: 0.8015 (tp30) REVERT: KA 16 MET cc_start: 0.8840 (tmm) cc_final: 0.8555 (tmm) REVERT: KE 16 MET cc_start: 0.8811 (tmm) cc_final: 0.8308 (tmm) REVERT: KF 16 MET cc_start: 0.8201 (tmm) cc_final: 0.7924 (tmm) REVERT: KF 21 ASP cc_start: 0.8388 (t70) cc_final: 0.8034 (t0) REVERT: KF 62 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7738 (mtm-85) REVERT: LA 92 THR cc_start: 0.8551 (m) cc_final: 0.8302 (p) REVERT: LD 16 MET cc_start: 0.9107 (tmm) cc_final: 0.8815 (tmm) REVERT: LD 18 GLU cc_start: 0.8417 (tp30) cc_final: 0.8089 (tp30) REVERT: LD 36 LYS cc_start: 0.8821 (mttm) cc_final: 0.8513 (mttm) REVERT: LE 89 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8873 (mt) REVERT: LF 16 MET cc_start: 0.8960 (tmm) cc_final: 0.8630 (tmm) REVERT: H 8 TYR cc_start: 0.8980 (t80) cc_final: 0.8762 (t80) REVERT: H 50 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7185 (ttp80) REVERT: H 53 ASP cc_start: 0.9201 (t70) cc_final: 0.8922 (t70) REVERT: H 95 LYS cc_start: 0.8473 (tppt) cc_final: 0.8236 (tppt) REVERT: H 115 ARG cc_start: 0.5140 (ttt-90) cc_final: 0.3914 (mmt180) REVERT: I 8 TYR cc_start: 0.8770 (t80) cc_final: 0.8487 (t80) REVERT: I 150 TYR cc_start: 0.8697 (m-80) cc_final: 0.8412 (m-80) REVERT: I 188 ASP cc_start: 0.8081 (m-30) cc_final: 0.7844 (m-30) REVERT: J 128 ASN cc_start: 0.8437 (t0) cc_final: 0.7982 (t0) REVERT: J 170 THR cc_start: 0.9497 (m) cc_final: 0.8915 (p) REVERT: K 132 MET cc_start: 0.8665 (mmt) cc_final: 0.8229 (mmm) REVERT: L 20 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8333 (m) REVERT: L 128 ASN cc_start: 0.8214 (t0) cc_final: 0.7957 (t0) REVERT: M 94 ASP cc_start: 0.8183 (t70) cc_final: 0.7913 (t70) REVERT: N 132 MET cc_start: 0.8525 (mmm) cc_final: 0.7802 (tpp) REVERT: N 175 PHE cc_start: 0.8306 (m-80) cc_final: 0.8028 (m-80) REVERT: N 199 ARG cc_start: 0.7160 (mtm110) cc_final: 0.6900 (mtm110) REVERT: O 86 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8571 (mp) REVERT: O 184 GLU cc_start: 0.7815 (mp0) cc_final: 0.7606 (pt0) REVERT: O 199 ARG cc_start: 0.8332 (ptp-110) cc_final: 0.7727 (ptp-110) REVERT: P 112 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8122 (tp40) REVERT: P 186 GLU cc_start: 0.8096 (mp0) cc_final: 0.7744 (mp0) REVERT: R 8 TYR cc_start: 0.8745 (t80) cc_final: 0.8443 (t80) REVERT: S 72 TYR cc_start: 0.7309 (m-10) cc_final: 0.7082 (m-10) REVERT: S 128 ASN cc_start: 0.8087 (t0) cc_final: 0.7839 (t0) REVERT: T 132 MET cc_start: 0.8645 (mmt) cc_final: 0.7842 (mmp) REVERT: U 99 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7703 (mmm-85) REVERT: V 10 PHE cc_start: 0.8205 (t80) cc_final: 0.8004 (t80) REVERT: V 57 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8747 (mmmt) REVERT: V 179 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: W 60 LYS cc_start: 0.7978 (pttm) cc_final: 0.7534 (ptmt) REVERT: W 74 LEU cc_start: 0.8811 (tp) cc_final: 0.8550 (tt) REVERT: W 95 LYS cc_start: 0.9179 (tptt) cc_final: 0.8949 (tptp) REVERT: X 110 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8208 (p) outliers start: 200 outliers final: 163 residues processed: 1406 average time/residue: 0.6559 time to fit residues: 1463.4630 Evaluate side-chains 1399 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1228 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GE residue 10 VAL Chi-restraints excluded: chain GE residue 36 LYS Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 49 ASP Chi-restraints excluded: chain HC residue 62 ARG Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 10 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 50 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 7 MET Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 49 ASP Chi-restraints excluded: chain ID residue 58 GLU Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IF residue 10 VAL Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 37 THR Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 43 THR Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JE residue 67 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 43 THR Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 54 LYS Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KC residue 67 VAL Chi-restraints excluded: chain KD residue 58 GLU Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 92 THR Chi-restraints excluded: chain KE residue 50 VAL Chi-restraints excluded: chain KE residue 69 GLU Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LA residue 75 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 32 ILE Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LD residue 57 THR Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 50 VAL Chi-restraints excluded: chain LE residue 89 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 168 ASN Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain V residue 133 MET Chi-restraints excluded: chain V residue 179 TYR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 60 LYS Chi-restraints excluded: chain X residue 109 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 187 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 441 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 426 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 454 optimal weight: 0.7980 chunk 486 optimal weight: 0.3980 chunk 353 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 561 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 61 GLN LB 82 ASN G 107 GLN I 78 HIS ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 107 GLN X 66 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 56466 Z= 0.223 Angle : 0.554 7.853 76749 Z= 0.290 Chirality : 0.043 0.177 9174 Planarity : 0.004 0.052 10056 Dihedral : 4.142 43.983 8118 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.58 % Allowed : 16.46 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.19 (0.10), residues: 7425 helix: 1.01 (0.10), residues: 3114 sheet: 0.49 (0.11), residues: 1983 loop : -1.34 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP L 39 HIS 0.006 0.001 HIS N 165 PHE 0.028 0.001 PHE P 10 TYR 0.019 0.001 TYR T 72 ARG 0.013 0.001 ARG G 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1501 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1304 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8531 (mtt) cc_final: 0.8280 (mtt) REVERT: B 58 LYS cc_start: 0.9215 (ptpt) cc_final: 0.8979 (ptpp) REVERT: C 75 ILE cc_start: 0.8959 (tp) cc_final: 0.8718 (mt) REVERT: GA 25 LYS cc_start: 0.8575 (mttt) cc_final: 0.8356 (mttt) REVERT: GB 62 ARG cc_start: 0.7611 (ttp-110) cc_final: 0.7254 (mtm180) REVERT: GD 18 GLU cc_start: 0.8544 (tp30) cc_final: 0.7893 (tp30) REVERT: GD 78 ARG cc_start: 0.8529 (ttt90) cc_final: 0.6879 (ptt90) REVERT: HA 11 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8413 (ttm-80) REVERT: HA 54 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8066 (mtmt) REVERT: HA 82 ASN cc_start: 0.8447 (t160) cc_final: 0.8055 (m-40) REVERT: HB 28 LYS cc_start: 0.8737 (tttt) cc_final: 0.8379 (ttmm) REVERT: HD 18 GLU cc_start: 0.8668 (tp30) cc_final: 0.8381 (tp30) REVERT: HF 66 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7675 (mtm-85) REVERT: IA 21 ASP cc_start: 0.9134 (t70) cc_final: 0.8822 (t70) REVERT: IA 61 GLN cc_start: 0.8614 (tt0) cc_final: 0.8316 (tt0) REVERT: IC 16 MET cc_start: 0.9052 (tmm) cc_final: 0.8615 (tmm) REVERT: IC 21 ASP cc_start: 0.8382 (t70) cc_final: 0.7758 (t0) REVERT: IC 28 LYS cc_start: 0.8583 (tppt) cc_final: 0.8233 (tppt) REVERT: ID 78 ARG cc_start: 0.8468 (ttt90) cc_final: 0.6952 (ptt-90) REVERT: JA 16 MET cc_start: 0.9137 (tmm) cc_final: 0.8802 (tmm) REVERT: JA 58 GLU cc_start: 0.7342 (mp0) cc_final: 0.6990 (mp0) REVERT: JB 16 MET cc_start: 0.9182 (tmm) cc_final: 0.8825 (tmm) REVERT: JB 18 GLU cc_start: 0.8692 (tp30) cc_final: 0.8368 (tp30) REVERT: JB 43 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9109 (p) REVERT: JC 62 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.7910 (ttm-80) REVERT: KE 16 MET cc_start: 0.8811 (tmm) cc_final: 0.8336 (tmm) REVERT: KF 16 MET cc_start: 0.8190 (tmm) cc_final: 0.7947 (tmm) REVERT: KF 21 ASP cc_start: 0.8376 (t70) cc_final: 0.8078 (t0) REVERT: KF 62 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7866 (mtm-85) REVERT: LA 92 THR cc_start: 0.8552 (m) cc_final: 0.8321 (p) REVERT: LD 16 MET cc_start: 0.9090 (tmm) cc_final: 0.8774 (tmm) REVERT: LD 18 GLU cc_start: 0.8405 (tp30) cc_final: 0.8120 (tp30) REVERT: LD 36 LYS cc_start: 0.8832 (mttm) cc_final: 0.8517 (mttm) REVERT: LE 16 MET cc_start: 0.8460 (tmm) cc_final: 0.8223 (tmm) REVERT: LE 89 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8863 (mt) REVERT: LF 16 MET cc_start: 0.8947 (tmm) cc_final: 0.8632 (tmm) REVERT: G 62 GLN cc_start: 0.8423 (mt0) cc_final: 0.8135 (mt0) REVERT: H 53 ASP cc_start: 0.9178 (t70) cc_final: 0.8907 (t0) REVERT: H 95 LYS cc_start: 0.8410 (tppt) cc_final: 0.7925 (tppt) REVERT: H 99 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7892 (mmm-85) REVERT: H 115 ARG cc_start: 0.5291 (ttt-90) cc_final: 0.3978 (mmt180) REVERT: I 95 LYS cc_start: 0.8554 (tppt) cc_final: 0.8304 (tppt) REVERT: I 150 TYR cc_start: 0.8668 (m-80) cc_final: 0.8386 (m-80) REVERT: I 188 ASP cc_start: 0.8077 (m-30) cc_final: 0.7857 (m-30) REVERT: J 128 ASN cc_start: 0.8406 (t0) cc_final: 0.7973 (t0) REVERT: J 170 THR cc_start: 0.9501 (m) cc_final: 0.8924 (p) REVERT: K 132 MET cc_start: 0.8657 (mmt) cc_final: 0.8243 (mmm) REVERT: L 128 ASN cc_start: 0.8225 (t0) cc_final: 0.7993 (t0) REVERT: L 132 MET cc_start: 0.7445 (mmt) cc_final: 0.7220 (mmt) REVERT: M 94 ASP cc_start: 0.8159 (t70) cc_final: 0.7823 (t70) REVERT: N 175 PHE cc_start: 0.8376 (m-80) cc_final: 0.8124 (m-80) REVERT: N 199 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6910 (mtm110) REVERT: O 86 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8556 (mp) REVERT: O 184 GLU cc_start: 0.7856 (mp0) cc_final: 0.7614 (pt0) REVERT: O 199 ARG cc_start: 0.8330 (ptp-110) cc_final: 0.7726 (ptp-110) REVERT: P 112 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8071 (tp40) REVERT: P 186 GLU cc_start: 0.8131 (mp0) cc_final: 0.7807 (mp0) REVERT: R 8 TYR cc_start: 0.8772 (t80) cc_final: 0.8500 (t80) REVERT: S 72 TYR cc_start: 0.7375 (m-10) cc_final: 0.7164 (m-10) REVERT: S 128 ASN cc_start: 0.8115 (t0) cc_final: 0.7873 (t0) REVERT: T 132 MET cc_start: 0.8675 (mmt) cc_final: 0.7926 (mmp) REVERT: U 30 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8875 (mt) REVERT: U 72 TYR cc_start: 0.8070 (m-80) cc_final: 0.7856 (m-80) REVERT: U 95 LYS cc_start: 0.8353 (tptt) cc_final: 0.8023 (tptt) REVERT: U 99 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7651 (mmm-85) REVERT: V 57 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8688 (mmmt) REVERT: W 60 LYS cc_start: 0.8011 (pttm) cc_final: 0.7547 (ptmt) REVERT: W 74 LEU cc_start: 0.8833 (tp) cc_final: 0.8629 (tt) REVERT: X 110 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8087 (p) outliers start: 197 outliers final: 155 residues processed: 1416 average time/residue: 0.6508 time to fit residues: 1459.1046 Evaluate side-chains 1403 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1242 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GE residue 10 VAL Chi-restraints excluded: chain GE residue 43 THR Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 49 ASP Chi-restraints excluded: chain HC residue 62 ARG Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 10 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 50 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 58 GLU Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 10 VAL Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 43 THR Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 67 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 43 THR Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KB residue 54 LYS Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 92 THR Chi-restraints excluded: chain KE residue 50 VAL Chi-restraints excluded: chain KE residue 69 GLU Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LA residue 75 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 32 ILE Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 50 VAL Chi-restraints excluded: chain LE residue 89 LEU Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 60 LYS Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 133 MET Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 109 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 187 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 649 optimal weight: 2.9990 chunk 684 optimal weight: 4.9990 chunk 624 optimal weight: 0.6980 chunk 665 optimal weight: 0.6980 chunk 400 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 522 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 601 optimal weight: 4.9990 chunk 629 optimal weight: 0.6980 chunk 663 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: IF 82 ASN KA 61 GLN LB 61 GLN LB 82 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 56466 Z= 0.236 Angle : 0.571 9.568 76749 Z= 0.298 Chirality : 0.043 0.173 9174 Planarity : 0.004 0.100 10056 Dihedral : 4.136 38.726 8118 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.25 % Allowed : 17.46 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.21 (0.10), residues: 7425 helix: 0.95 (0.10), residues: 3150 sheet: 0.50 (0.11), residues: 1986 loop : -1.24 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP P 39 HIS 0.004 0.001 HIS L 78 PHE 0.026 0.001 PHE W 10 TYR 0.019 0.001 TYR T 72 ARG 0.015 0.001 ARGGF 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1457 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1278 time to evaluate : 4.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8527 (mtt) cc_final: 0.8293 (mtt) REVERT: B 58 LYS cc_start: 0.9219 (ptpt) cc_final: 0.8984 (ptpp) REVERT: C 75 ILE cc_start: 0.8947 (tp) cc_final: 0.8710 (mt) REVERT: GB 62 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.7237 (mtm180) REVERT: GC 21 ASP cc_start: 0.8381 (t70) cc_final: 0.8102 (t0) REVERT: GD 18 GLU cc_start: 0.8538 (tp30) cc_final: 0.7841 (tp30) REVERT: GD 78 ARG cc_start: 0.8537 (ttt90) cc_final: 0.6894 (ptt90) REVERT: HA 11 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8416 (ttm-80) REVERT: HA 54 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8206 (mtmt) REVERT: HA 82 ASN cc_start: 0.8483 (t160) cc_final: 0.8052 (m-40) REVERT: HB 28 LYS cc_start: 0.8755 (tttt) cc_final: 0.8393 (ttmm) REVERT: HD 18 GLU cc_start: 0.8677 (tp30) cc_final: 0.8323 (tp30) REVERT: HF 66 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7702 (mtm-85) REVERT: IA 21 ASP cc_start: 0.9129 (t70) cc_final: 0.8816 (t70) REVERT: IA 61 GLN cc_start: 0.8612 (tt0) cc_final: 0.8346 (tt0) REVERT: IC 11 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8222 (ttt90) REVERT: IC 16 MET cc_start: 0.9056 (tmm) cc_final: 0.8610 (tmm) REVERT: IC 21 ASP cc_start: 0.8382 (t70) cc_final: 0.7751 (t0) REVERT: IC 28 LYS cc_start: 0.8587 (tppt) cc_final: 0.8233 (tppt) REVERT: ID 78 ARG cc_start: 0.8471 (ttt90) cc_final: 0.6955 (ptt-90) REVERT: JA 16 MET cc_start: 0.9129 (tmm) cc_final: 0.8805 (tmm) REVERT: JB 16 MET cc_start: 0.9170 (tmm) cc_final: 0.8695 (tmm) REVERT: JB 18 GLU cc_start: 0.8673 (tp30) cc_final: 0.8365 (tp30) REVERT: JB 43 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9152 (p) REVERT: JC 62 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.8078 (ttm-80) REVERT: KA 58 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7607 (mt-10) REVERT: KE 16 MET cc_start: 0.8824 (tmm) cc_final: 0.8326 (tmm) REVERT: KF 16 MET cc_start: 0.8202 (tmm) cc_final: 0.7959 (tmm) REVERT: KF 21 ASP cc_start: 0.8369 (t70) cc_final: 0.8082 (t0) REVERT: KF 62 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7924 (mtm-85) REVERT: LA 92 THR cc_start: 0.8549 (m) cc_final: 0.8323 (p) REVERT: LD 16 MET cc_start: 0.9110 (tmm) cc_final: 0.8867 (tmm) REVERT: LD 36 LYS cc_start: 0.8802 (mttm) cc_final: 0.8563 (mttm) REVERT: LE 16 MET cc_start: 0.8483 (tmm) cc_final: 0.8241 (tmm) REVERT: LF 16 MET cc_start: 0.8923 (tmm) cc_final: 0.8620 (tmm) REVERT: G 62 GLN cc_start: 0.8393 (mt0) cc_final: 0.8141 (mt0) REVERT: G 159 GLU cc_start: 0.6814 (tp30) cc_final: 0.6232 (tp30) REVERT: H 53 ASP cc_start: 0.9181 (t70) cc_final: 0.8907 (t70) REVERT: H 99 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7898 (mmm-85) REVERT: H 115 ARG cc_start: 0.5405 (ttt-90) cc_final: 0.3964 (mmt180) REVERT: I 50 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7716 (ttp80) REVERT: I 95 LYS cc_start: 0.8514 (tppt) cc_final: 0.8299 (tppt) REVERT: I 150 TYR cc_start: 0.8679 (m-80) cc_final: 0.8395 (m-80) REVERT: I 188 ASP cc_start: 0.8119 (m-30) cc_final: 0.7896 (m-30) REVERT: J 128 ASN cc_start: 0.8382 (t0) cc_final: 0.7965 (t0) REVERT: J 170 THR cc_start: 0.9511 (m) cc_final: 0.8938 (p) REVERT: K 132 MET cc_start: 0.8684 (mmt) cc_final: 0.8271 (mmm) REVERT: K 139 SER cc_start: 0.9230 (t) cc_final: 0.8944 (t) REVERT: L 105 LYS cc_start: 0.8951 (tptp) cc_final: 0.8373 (pttm) REVERT: L 128 ASN cc_start: 0.8188 (t0) cc_final: 0.7965 (t0) REVERT: L 132 MET cc_start: 0.7568 (mmt) cc_final: 0.7200 (mmt) REVERT: M 8 TYR cc_start: 0.8755 (t80) cc_final: 0.7950 (t80) REVERT: M 94 ASP cc_start: 0.8163 (t70) cc_final: 0.7797 (t70) REVERT: N 175 PHE cc_start: 0.8414 (m-80) cc_final: 0.8138 (m-80) REVERT: O 86 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8572 (mp) REVERT: O 184 GLU cc_start: 0.7849 (mp0) cc_final: 0.7623 (pt0) REVERT: O 199 ARG cc_start: 0.8309 (ptp-110) cc_final: 0.7703 (ptp-110) REVERT: P 112 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8075 (tp40) REVERT: P 186 GLU cc_start: 0.8152 (mp0) cc_final: 0.7811 (mp0) REVERT: Q 132 MET cc_start: 0.8284 (tpt) cc_final: 0.8072 (mmt) REVERT: R 8 TYR cc_start: 0.8777 (t80) cc_final: 0.8504 (t80) REVERT: S 72 TYR cc_start: 0.7465 (m-10) cc_final: 0.7191 (m-10) REVERT: S 128 ASN cc_start: 0.8149 (t0) cc_final: 0.7894 (t0) REVERT: T 132 MET cc_start: 0.8631 (mmt) cc_final: 0.7896 (mmp) REVERT: U 30 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8962 (mt) REVERT: U 72 TYR cc_start: 0.7935 (m-80) cc_final: 0.7485 (m-80) REVERT: U 99 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7716 (mmm-85) REVERT: W 60 LYS cc_start: 0.8013 (pttm) cc_final: 0.7482 (ptmt) REVERT: W 74 LEU cc_start: 0.8851 (tp) cc_final: 0.8598 (tt) REVERT: X 110 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8089 (p) outliers start: 179 outliers final: 154 residues processed: 1378 average time/residue: 0.6101 time to fit residues: 1330.6914 Evaluate side-chains 1392 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1233 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GE residue 10 VAL Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 49 ASP Chi-restraints excluded: chain HC residue 62 ARG Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 10 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 50 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 7 MET Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 58 GLU Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IF residue 10 VAL Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 37 THR Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JC residue 23 MET Chi-restraints excluded: chain JD residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 43 THR Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JE residue 67 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KB residue 54 LYS Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 92 THR Chi-restraints excluded: chain KE residue 50 VAL Chi-restraints excluded: chain KE residue 69 GLU Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LA residue 75 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 32 ILE Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 50 VAL Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 188 ASP Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 109 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 163 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 437 optimal weight: 0.0980 chunk 703 optimal weight: 3.9990 chunk 429 optimal weight: 1.9990 chunk 333 optimal weight: 0.9990 chunk 489 optimal weight: 6.9990 chunk 738 optimal weight: 0.8980 chunk 679 optimal weight: 4.9990 chunk 587 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 454 optimal weight: 1.9990 chunk 360 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 61 GLN LB 82 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 56466 Z= 0.226 Angle : 0.580 9.831 76749 Z= 0.301 Chirality : 0.043 0.219 9174 Planarity : 0.004 0.059 10056 Dihedral : 4.119 38.538 8118 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.09 % Allowed : 17.53 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.23 (0.10), residues: 7425 helix: 0.95 (0.10), residues: 3153 sheet: 0.54 (0.11), residues: 1983 loop : -1.24 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP L 39 HIS 0.005 0.001 HISIF 74 PHE 0.031 0.001 PHE P 10 TYR 0.017 0.001 TYR K 8 ARG 0.020 0.001 ARG G 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14850 Ramachandran restraints generated. 7425 Oldfield, 0 Emsley, 7425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1286 time to evaluate : 4.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8518 (mtt) cc_final: 0.8280 (mtt) REVERT: C 75 ILE cc_start: 0.8936 (tp) cc_final: 0.8681 (mt) REVERT: GB 62 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7243 (mtm180) REVERT: GD 18 GLU cc_start: 0.8528 (tp30) cc_final: 0.7853 (tp30) REVERT: GD 78 ARG cc_start: 0.8547 (ttt90) cc_final: 0.6903 (ptt90) REVERT: GE 23 MET cc_start: 0.8163 (ttm) cc_final: 0.7779 (mtp) REVERT: HA 11 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8365 (ttm-80) REVERT: HA 54 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7902 (mtmt) REVERT: HA 82 ASN cc_start: 0.8486 (t160) cc_final: 0.8023 (m-40) REVERT: HB 28 LYS cc_start: 0.8756 (tttt) cc_final: 0.8396 (ttmm) REVERT: HD 18 GLU cc_start: 0.8632 (tp30) cc_final: 0.8308 (tp30) REVERT: HF 66 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: IA 7 MET cc_start: 0.8850 (mtm) cc_final: 0.8605 (mtp) REVERT: IA 21 ASP cc_start: 0.9140 (t70) cc_final: 0.8814 (t70) REVERT: IA 61 GLN cc_start: 0.8595 (tt0) cc_final: 0.8359 (tt0) REVERT: IC 11 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8229 (ttt90) REVERT: IC 16 MET cc_start: 0.9065 (tmm) cc_final: 0.8622 (tmm) REVERT: IC 21 ASP cc_start: 0.8370 (t70) cc_final: 0.7731 (t0) REVERT: IC 28 LYS cc_start: 0.8541 (tppt) cc_final: 0.8202 (tppt) REVERT: ID 78 ARG cc_start: 0.8470 (ttt90) cc_final: 0.6947 (ptt-90) REVERT: JA 16 MET cc_start: 0.9146 (tmm) cc_final: 0.8828 (tmm) REVERT: JB 16 MET cc_start: 0.9167 (tmm) cc_final: 0.8681 (tmm) REVERT: JB 18 GLU cc_start: 0.8673 (tp30) cc_final: 0.8363 (tp30) REVERT: JB 43 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9114 (p) REVERT: JC 62 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.8060 (ttm-80) REVERT: KE 16 MET cc_start: 0.8806 (tmm) cc_final: 0.8299 (tmm) REVERT: KF 16 MET cc_start: 0.8183 (tmm) cc_final: 0.7946 (tmm) REVERT: KF 21 ASP cc_start: 0.8365 (t70) cc_final: 0.8070 (t0) REVERT: LD 16 MET cc_start: 0.9116 (tmm) cc_final: 0.8906 (tmm) REVERT: LD 36 LYS cc_start: 0.8818 (mttm) cc_final: 0.8576 (mttm) REVERT: LD 61 GLN cc_start: 0.8550 (tt0) cc_final: 0.8061 (tt0) REVERT: LE 16 MET cc_start: 0.8447 (tmm) cc_final: 0.8221 (tmm) REVERT: LF 16 MET cc_start: 0.8923 (tmm) cc_final: 0.8625 (tmm) REVERT: G 62 GLN cc_start: 0.8396 (mt0) cc_final: 0.8148 (mt0) REVERT: G 159 GLU cc_start: 0.6775 (tp30) cc_final: 0.6217 (tp30) REVERT: H 53 ASP cc_start: 0.9194 (t70) cc_final: 0.8924 (t0) REVERT: H 99 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7823 (mmm-85) REVERT: H 115 ARG cc_start: 0.5555 (ttt-90) cc_final: 0.4058 (mmt180) REVERT: I 50 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7690 (ttp80) REVERT: I 95 LYS cc_start: 0.8566 (tppt) cc_final: 0.8336 (tppt) REVERT: I 132 MET cc_start: 0.8215 (mmm) cc_final: 0.7976 (tpp) REVERT: I 150 TYR cc_start: 0.8653 (m-80) cc_final: 0.8379 (m-80) REVERT: I 188 ASP cc_start: 0.8113 (m-30) cc_final: 0.7881 (m-30) REVERT: J 128 ASN cc_start: 0.8391 (t0) cc_final: 0.8000 (t0) REVERT: J 170 THR cc_start: 0.9513 (m) cc_final: 0.8934 (p) REVERT: K 132 MET cc_start: 0.8648 (mmt) cc_final: 0.8243 (mmm) REVERT: K 139 SER cc_start: 0.9235 (t) cc_final: 0.8949 (t) REVERT: L 105 LYS cc_start: 0.8950 (tptp) cc_final: 0.8289 (pttm) REVERT: L 128 ASN cc_start: 0.8190 (t0) cc_final: 0.7959 (t0) REVERT: L 132 MET cc_start: 0.7544 (mmt) cc_final: 0.7233 (mmt) REVERT: M 8 TYR cc_start: 0.8752 (t80) cc_final: 0.7946 (t80) REVERT: M 94 ASP cc_start: 0.8156 (t70) cc_final: 0.7804 (t70) REVERT: N 175 PHE cc_start: 0.8473 (m-80) cc_final: 0.8186 (m-80) REVERT: O 86 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8554 (mp) REVERT: O 184 GLU cc_start: 0.7837 (mp0) cc_final: 0.7588 (pt0) REVERT: O 199 ARG cc_start: 0.8288 (ptp-110) cc_final: 0.7698 (ptp-110) REVERT: P 186 GLU cc_start: 0.8179 (mp0) cc_final: 0.7829 (mp0) REVERT: Q 50 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7721 (ttp-170) REVERT: R 8 TYR cc_start: 0.8787 (t80) cc_final: 0.8533 (t80) REVERT: S 6 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8390 (mtm180) REVERT: S 72 TYR cc_start: 0.7415 (m-10) cc_final: 0.7180 (m-10) REVERT: S 128 ASN cc_start: 0.8205 (t0) cc_final: 0.7915 (t0) REVERT: T 132 MET cc_start: 0.8656 (mmt) cc_final: 0.7834 (mmp) REVERT: T 186 GLU cc_start: 0.7718 (mp0) cc_final: 0.7372 (mm-30) REVERT: W 60 LYS cc_start: 0.8012 (pttm) cc_final: 0.7482 (ptmt) REVERT: W 74 LEU cc_start: 0.8868 (tp) cc_final: 0.8611 (tt) REVERT: X 110 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8052 (p) outliers start: 170 outliers final: 145 residues processed: 1380 average time/residue: 0.6044 time to fit residues: 1323.8295 Evaluate side-chains 1385 residues out of total 5505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1236 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain GB residue 89 LEU Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 92 THR Chi-restraints excluded: chain GE residue 10 VAL Chi-restraints excluded: chain GF residue 3 ASP Chi-restraints excluded: chain GF residue 49 ASP Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 49 ASP Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 10 VAL Chi-restraints excluded: chain HE residue 49 ASP Chi-restraints excluded: chain HE residue 50 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IB residue 7 MET Chi-restraints excluded: chain IB residue 49 ASP Chi-restraints excluded: chain IC residue 49 ASP Chi-restraints excluded: chain ID residue 7 MET Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 58 GLU Chi-restraints excluded: chain ID residue 92 THR Chi-restraints excluded: chain IF residue 31 LEU Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 43 THR Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JC residue 23 MET Chi-restraints excluded: chain JD residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 43 THR Chi-restraints excluded: chain JE residue 49 ASP Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JE residue 67 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 89 LEU Chi-restraints excluded: chain KA residue 89 LEU Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KB residue 54 LYS Chi-restraints excluded: chain KB residue 89 LEU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 21 ASP Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 58 GLU Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KD residue 92 THR Chi-restraints excluded: chain KE residue 50 VAL Chi-restraints excluded: chain KE residue 69 GLU Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LA residue 75 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 32 ILE Chi-restraints excluded: chain LC residue 49 ASP Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 49 ASP Chi-restraints excluded: chain LE residue 50 VAL Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 32 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 12 ASP Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain X residue 109 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 187 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.3991 > 50: distance: 41 - 61: 3.003 distance: 45 - 66: 5.546 distance: 49 - 71: 9.155 distance: 54 - 57: 3.186 distance: 55 - 56: 6.399 distance: 55 - 61: 3.301 distance: 56 - 79: 4.069 distance: 58 - 59: 5.131 distance: 62 - 63: 7.094 distance: 62 - 65: 7.671 distance: 63 - 64: 13.007 distance: 63 - 66: 5.380 distance: 66 - 67: 7.909 distance: 67 - 68: 3.438 distance: 67 - 70: 10.272 distance: 68 - 69: 8.615 distance: 68 - 71: 11.823 distance: 71 - 72: 6.127 distance: 72 - 73: 8.606 distance: 72 - 75: 6.779 distance: 73 - 74: 12.505 distance: 73 - 79: 5.498 distance: 75 - 76: 9.021 distance: 76 - 77: 10.083 distance: 76 - 78: 18.257 distance: 79 - 80: 28.828 distance: 80 - 81: 49.146 distance: 80 - 83: 43.465 distance: 81 - 82: 8.925 distance: 81 - 88: 36.810 distance: 83 - 84: 36.669 distance: 84 - 85: 9.007 distance: 85 - 86: 24.345 distance: 86 - 87: 27.815 distance: 88 - 89: 17.534 distance: 89 - 90: 27.241 distance: 89 - 92: 26.268 distance: 90 - 91: 31.704 distance: 90 - 93: 26.983 distance: 93 - 94: 20.957 distance: 94 - 95: 16.265 distance: 94 - 97: 35.679 distance: 95 - 96: 28.686 distance: 95 - 100: 30.868 distance: 97 - 98: 4.034 distance: 97 - 99: 67.593 distance: 100 - 101: 13.960 distance: 101 - 102: 23.875 distance: 101 - 104: 15.106 distance: 102 - 103: 38.845 distance: 102 - 109: 21.992 distance: 104 - 105: 22.492 distance: 105 - 106: 26.128 distance: 106 - 107: 7.940 distance: 107 - 108: 25.721 distance: 109 - 110: 16.869 distance: 110 - 111: 20.074 distance: 110 - 113: 38.488 distance: 111 - 112: 30.763 distance: 111 - 116: 6.767 distance: 113 - 114: 18.696 distance: 113 - 115: 6.170 distance: 116 - 117: 23.425 distance: 116 - 147: 23.431 distance: 117 - 118: 17.311 distance: 117 - 120: 20.496 distance: 118 - 119: 9.407 distance: 118 - 125: 5.650 distance: 119 - 144: 5.506 distance: 120 - 121: 25.530 distance: 121 - 122: 17.614 distance: 122 - 123: 9.028 distance: 122 - 124: 11.900