Starting phenix.real_space_refine on Sun Mar 24 12:50:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv9_14171/03_2024/7qv9_14171_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv9_14171/03_2024/7qv9_14171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv9_14171/03_2024/7qv9_14171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv9_14171/03_2024/7qv9_14171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv9_14171/03_2024/7qv9_14171_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv9_14171/03_2024/7qv9_14171_updated.pdb" } resolution = 3.5 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= 0.006 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: 7 Type Number sf(0) Gaussians Al 4 5.89 5 P 82 5.49 5 S 160 5.16 5 C 25844 2.51 5 N 7325 2.21 5 O 8064 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C ARG 1246": "NH1" <-> "NH2" Residue "C ARG 1269": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1372": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "a GLU 20": "OE1" <-> "OE2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 38": "NH1" <-> "NH2" Residue "a ARG 55": "NH1" <-> "NH2" Residue "a GLU 70": "OE1" <-> "OE2" Residue "a GLU 76": "OE1" <-> "OE2" Residue "a GLU 128": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 158": "OE1" <-> "OE2" Residue "a GLU 211": "OE1" <-> "OE2" Residue "a ARG 212": "NH1" <-> "NH2" Residue "a ARG 227": "NH1" <-> "NH2" Residue "a GLU 234": "OE1" <-> "OE2" Residue "a ARG 257": "NH1" <-> "NH2" Residue "b GLU 3": "OE1" <-> "OE2" Residue "b GLU 11": "OE1" <-> "OE2" Residue "b ARG 55": "NH1" <-> "NH2" Residue "b GLU 76": "OE1" <-> "OE2" Residue "b GLU 81": "OE1" <-> "OE2" Residue "b ARG 91": "NH1" <-> "NH2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b GLU 97": "OE1" <-> "OE2" Residue "b GLU 108": "OE1" <-> "OE2" Residue "b GLU 118": "OE1" <-> "OE2" Residue "b GLU 130": "OE1" <-> "OE2" Residue "b ARG 168": "NH1" <-> "NH2" Residue "b PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 211": "OE1" <-> "OE2" Residue "b ARG 212": "NH1" <-> "NH2" Residue "b GLU 228": "OE1" <-> "OE2" Residue "b GLU 234": "OE1" <-> "OE2" Residue "b ARG 235": "NH1" <-> "NH2" Residue "c GLU 20": "OE1" <-> "OE2" Residue "c GLU 128": "OE1" <-> "OE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "c ARG 162": "NH1" <-> "NH2" Residue "c ARG 168": "NH1" <-> "NH2" Residue "c ARG 199": "NH1" <-> "NH2" Residue "c ARG 227": "NH1" <-> "NH2" Residue "c ARG 239": "NH1" <-> "NH2" Residue "c ARG 257": "NH1" <-> "NH2" Residue "d GLU 37": "OE1" <-> "OE2" Residue "d ARG 48": "NH1" <-> "NH2" Residue "d ARG 98": "NH1" <-> "NH2" Residue "d GLU 118": "OE1" <-> "OE2" Residue "d ARG 122": "NH1" <-> "NH2" Residue "d GLU 125": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "d ARG 131": "NH1" <-> "NH2" Residue "d ARG 143": "NH1" <-> "NH2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 168": "NH1" <-> "NH2" Residue "d GLU 191": "OE1" <-> "OE2" Residue "d GLU 200": "OE1" <-> "OE2" Residue "d ARG 212": "NH1" <-> "NH2" Residue "d ARG 214": "NH1" <-> "NH2" Residue "d ARG 227": "NH1" <-> "NH2" Residue "d ARG 258": "NH1" <-> "NH2" Residue "f PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 20": "OE1" <-> "OE2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f GLU 81": "OE1" <-> "OE2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f GLU 128": "OE1" <-> "OE2" Residue "f PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 181": "OE1" <-> "OE2" Residue "f ARG 182": "NH1" <-> "NH2" Residue "f GLU 211": "OE1" <-> "OE2" Residue "f ARG 214": "NH1" <-> "NH2" Residue "f GLU 228": "OE1" <-> "OE2" Residue "f ARG 257": "NH1" <-> "NH2" Residue "e GLU 3": "OE1" <-> "OE2" Residue "e GLU 11": "OE1" <-> "OE2" Residue "e ARG 38": "NH1" <-> "NH2" Residue "e ARG 55": "NH1" <-> "NH2" Residue "e GLU 70": "OE1" <-> "OE2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 95": "NH1" <-> "NH2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e ARG 98": "NH1" <-> "NH2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e GLU 128": "OE1" <-> "OE2" Residue "e GLU 158": "OE1" <-> "OE2" Residue "e GLU 191": "OE1" <-> "OE2" Residue "e ARG 199": "NH1" <-> "NH2" Residue "e ARG 212": "NH1" <-> "NH2" Residue "e ARG 221": "NH1" <-> "NH2" Residue "e ARG 227": "NH1" <-> "NH2" Residue "e GLU 228": "OE1" <-> "OE2" Residue "e ARG 239": "NH1" <-> "NH2" Residue "e ARG 257": "NH1" <-> "NH2" Residue "e ARG 258": "NH1" <-> "NH2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M ARG 217": "NH1" <-> "NH2" Residue "M ARG 240": "NH1" <-> "NH2" Residue "M ARG 279": "NH1" <-> "NH2" Residue "M ARG 296": "NH1" <-> "NH2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "M PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 455": "NH1" <-> "NH2" Residue "M ARG 473": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41491 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2322 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1676 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 10125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10125 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 293 Chain: "D" Number of atoms: 9634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 9634 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 53, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 963 Unresolved non-hydrogen dihedrals: 648 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 22, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 10, 'GLU:plan': 29, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 477 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "N" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "a" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2052 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 243} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "b" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2052 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 243} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2000 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 241} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "d" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2041 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 241} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2053 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 243} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "e" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2062 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 243} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3301 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 21.19, per 1000 atoms: 0.51 Number of scatterers: 41491 At special positions: 0 Unit cell: (210.1, 204.6, 163.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 160 16.00 P 82 15.00 Al 4 13.00 F 12 9.00 O 8064 8.00 N 7325 7.00 C 25844 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.66 Conformation dependent library (CDL) restraints added in 7.7 seconds 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 38 sheets defined 34.0% alpha, 6.9% beta 34 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 18.35 Creating SS restraints... Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.264A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.006A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.957A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'C' and resid 29 through 39 removed outlier: 4.474A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.672A pdb=" N ARG C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.623A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.970A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 351 No H-bonds generated for 'chain 'C' and resid 348 through 351' Processing helix chain 'C' and resid 359 through 370 removed outlier: 3.646A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 388 Processing helix chain 'C' and resid 399 through 409 removed outlier: 3.726A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 456 through 480 removed outlier: 3.650A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'C' and resid 665 through 667 No H-bonds generated for 'chain 'C' and resid 665 through 667' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 3.930A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 861 through 864 removed outlier: 3.808A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 897 through 905 Processing helix chain 'C' and resid 946 through 978 removed outlier: 3.917A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 994 through 999 removed outlier: 4.417A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1036 Processing helix chain 'C' and resid 1100 through 1106 removed outlier: 3.801A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) Proline residue: C1104 - end of helix No H-bonds generated for 'chain 'C' and resid 1100 through 1106' Processing helix chain 'C' and resid 1109 through 1133 Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1168 through 1175 Processing helix chain 'C' and resid 1192 through 1201 removed outlier: 3.638A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1272 through 1281 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 4.220A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1331 Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.530A pdb=" N GLN D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 7 through 11' Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 140 removed outlier: 4.247A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 406 through 415 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 3.973A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 531 through 537 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.811A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.654A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 3.553A pdb=" N HIS D 651 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE D 654 " --> pdb=" O HIS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 701 Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 734 through 738 Processing helix chain 'D' and resid 769 through 803 removed outlier: 3.889A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 874 Processing helix chain 'D' and resid 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 915 through 918 No H-bonds generated for 'chain 'D' and resid 915 through 918' Processing helix chain 'D' and resid 1138 through 1145 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1227 through 1244 removed outlier: 3.727A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 Processing helix chain 'D' and resid 1280 through 1290 Processing helix chain 'D' and resid 1309 through 1312 No H-bonds generated for 'chain 'D' and resid 1309 through 1312' Processing helix chain 'D' and resid 1329 through 1338 Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 4.118A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D1375 " --> pdb=" O ARG D1372 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.823A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'a' and resid 14 through 24 Processing helix chain 'a' and resid 42 through 48 Processing helix chain 'a' and resid 95 through 98 No H-bonds generated for 'chain 'a' and resid 95 through 98' Processing helix chain 'a' and resid 114 through 124 removed outlier: 3.587A pdb=" N GLU a 118 " --> pdb=" O MET a 114 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU a 120 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU a 121 " --> pdb=" O GLN a 117 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG a 122 " --> pdb=" O GLU a 118 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL a 123 " --> pdb=" O LYS a 119 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE a 124 " --> pdb=" O LEU a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 153 through 158 removed outlier: 3.614A pdb=" N ASN a 157 " --> pdb=" O PRO a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 182 No H-bonds generated for 'chain 'a' and resid 179 through 182' Processing helix chain 'a' and resid 185 through 200 removed outlier: 3.804A pdb=" N GLU a 200 " --> pdb=" O GLN a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 211 through 219 Processing helix chain 'a' and resid 225 through 240 removed outlier: 3.833A pdb=" N ASN a 231 " --> pdb=" O GLU a 228 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL a 232 " --> pdb=" O LEU a 229 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU a 234 " --> pdb=" O ASN a 231 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG a 235 " --> pdb=" O VAL a 232 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 26 removed outlier: 3.591A pdb=" N LEU b 25 " --> pdb=" O GLN b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 50 removed outlier: 3.581A pdb=" N SER b 47 " --> pdb=" O GLU b 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 57 removed outlier: 3.782A pdb=" N GLN b 57 " --> pdb=" O SER b 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 54 through 57' Processing helix chain 'b' and resid 73 through 77 Processing helix chain 'b' and resid 97 through 99 No H-bonds generated for 'chain 'b' and resid 97 through 99' Processing helix chain 'b' and resid 114 through 120 Processing helix chain 'b' and resid 152 through 158 Processing helix chain 'b' and resid 163 through 168 Processing helix chain 'b' and resid 179 through 182 No H-bonds generated for 'chain 'b' and resid 179 through 182' Processing helix chain 'b' and resid 186 through 200 removed outlier: 3.934A pdb=" N ARG b 199 " --> pdb=" O ILE b 195 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU b 200 " --> pdb=" O GLN b 196 " (cutoff:3.500A) Processing helix chain 'b' and resid 211 through 218 Processing helix chain 'b' and resid 226 through 240 removed outlier: 3.641A pdb=" N GLU b 234 " --> pdb=" O ASN b 231 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG b 235 " --> pdb=" O VAL b 232 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL b 237 " --> pdb=" O GLU b 234 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS b 240 " --> pdb=" O VAL b 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 26 removed outlier: 3.816A pdb=" N HIS c 24 " --> pdb=" O GLU c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 51 removed outlier: 3.624A pdb=" N SER c 47 " --> pdb=" O GLU c 43 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG c 48 " --> pdb=" O LEU c 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS c 50 " --> pdb=" O ALA c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 78 removed outlier: 3.662A pdb=" N ASP c 74 " --> pdb=" O GLU c 70 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU c 77 " --> pdb=" O LEU c 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE c 78 " --> pdb=" O ASP c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 99 Processing helix chain 'c' and resid 114 through 127 removed outlier: 5.155A pdb=" N TYR c 126 " --> pdb=" O ARG c 122 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY c 127 " --> pdb=" O VAL c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 152 through 158 removed outlier: 3.764A pdb=" N GLU c 158 " --> pdb=" O ALA c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 163 through 169 removed outlier: 3.751A pdb=" N LEU c 169 " --> pdb=" O LEU c 165 " (cutoff:3.500A) Processing helix chain 'c' and resid 185 through 201 Processing helix chain 'c' and resid 211 through 219 Processing helix chain 'c' and resid 226 through 240 removed outlier: 3.660A pdb=" N ASN c 231 " --> pdb=" O ARG c 227 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS c 240 " --> pdb=" O SER c 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 6 No H-bonds generated for 'chain 'd' and resid 4 through 6' Processing helix chain 'd' and resid 13 through 26 removed outlier: 3.739A pdb=" N HIS d 24 " --> pdb=" O GLU d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 51 Processing helix chain 'd' and resid 71 through 77 Processing helix chain 'd' and resid 109 through 111 No H-bonds generated for 'chain 'd' and resid 109 through 111' Processing helix chain 'd' and resid 114 through 126 removed outlier: 3.643A pdb=" N ARG d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU d 125 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR d 126 " --> pdb=" O ARG d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 157 removed outlier: 3.528A pdb=" N VAL d 156 " --> pdb=" O LEU d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 169 Processing helix chain 'd' and resid 185 through 200 Processing helix chain 'd' and resid 211 through 219 Processing helix chain 'd' and resid 227 through 240 removed outlier: 3.754A pdb=" N ASN d 231 " --> pdb=" O ARG d 227 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL d 232 " --> pdb=" O GLU d 228 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 27 removed outlier: 3.516A pdb=" N SER f 23 " --> pdb=" O LEU f 19 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS f 24 " --> pdb=" O GLU f 20 " (cutoff:3.500A) Proline residue: f 27 - end of helix Processing helix chain 'f' and resid 42 through 52 removed outlier: 4.030A pdb=" N SER f 47 " --> pdb=" O GLU f 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR f 51 " --> pdb=" O SER f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 77 Processing helix chain 'f' and resid 95 through 98 No H-bonds generated for 'chain 'f' and resid 95 through 98' Processing helix chain 'f' and resid 109 through 111 No H-bonds generated for 'chain 'f' and resid 109 through 111' Processing helix chain 'f' and resid 114 through 125 removed outlier: 3.719A pdb=" N LEU f 121 " --> pdb=" O GLN f 117 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG f 122 " --> pdb=" O GLU f 118 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL f 123 " --> pdb=" O LYS f 119 " (cutoff:3.500A) Processing helix chain 'f' and resid 152 through 158 removed outlier: 3.843A pdb=" N ASN f 157 " --> pdb=" O PRO f 153 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU f 158 " --> pdb=" O ALA f 154 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 167 Processing helix chain 'f' and resid 179 through 182 No H-bonds generated for 'chain 'f' and resid 179 through 182' Processing helix chain 'f' and resid 184 through 200 removed outlier: 3.938A pdb=" N MET f 187 " --> pdb=" O SER f 184 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE f 193 " --> pdb=" O ALA f 190 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA f 194 " --> pdb=" O GLU f 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 218 Processing helix chain 'f' and resid 226 through 240 removed outlier: 4.447A pdb=" N TYR f 238 " --> pdb=" O GLU f 234 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 19 Processing helix chain 'e' and resid 22 through 24 No H-bonds generated for 'chain 'e' and resid 22 through 24' Processing helix chain 'e' and resid 44 through 52 removed outlier: 3.717A pdb=" N HIS e 50 " --> pdb=" O ALA e 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR e 51 " --> pdb=" O SER e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 78 removed outlier: 3.634A pdb=" N PHE e 78 " --> pdb=" O ASP e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'e' and resid 114 through 119 removed outlier: 3.535A pdb=" N GLU e 118 " --> pdb=" O MET e 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS e 119 " --> pdb=" O MET e 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 114 through 119' Processing helix chain 'e' and resid 152 through 158 removed outlier: 3.697A pdb=" N ASN e 157 " --> pdb=" O PRO e 153 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU e 158 " --> pdb=" O ALA e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 168 Processing helix chain 'e' and resid 179 through 182 No H-bonds generated for 'chain 'e' and resid 179 through 182' Processing helix chain 'e' and resid 185 through 200 Processing helix chain 'e' and resid 212 through 219 removed outlier: 3.575A pdb=" N LEU e 218 " --> pdb=" O ARG e 214 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN e 219 " --> pdb=" O GLU e 215 " (cutoff:3.500A) Processing helix chain 'e' and resid 229 through 240 Processing helix chain 'M' and resid 17 through 26 removed outlier: 4.608A pdb=" N LEU M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 43 removed outlier: 3.572A pdb=" N GLN M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU M 36 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 40 " --> pdb=" O GLU M 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 129 removed outlier: 3.656A pdb=" N GLN M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 146 Processing helix chain 'M' and resid 158 through 165 Processing helix chain 'M' and resid 172 through 181 Processing helix chain 'M' and resid 197 through 205 Processing helix chain 'M' and resid 213 through 222 removed outlier: 3.922A pdb=" N ASP M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 228 Processing helix chain 'M' and resid 232 through 239 Processing helix chain 'M' and resid 246 through 254 Processing helix chain 'M' and resid 260 through 263 Processing helix chain 'M' and resid 301 through 306 removed outlier: 3.599A pdb=" N MET M 306 " --> pdb=" O GLN M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 350 removed outlier: 3.829A pdb=" N GLN M 350 " --> pdb=" O CYS M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 357 removed outlier: 4.537A pdb=" N GLU M 356 " --> pdb=" O GLN M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.673A pdb=" N ALA M 373 " --> pdb=" O ASP M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 385 Processing helix chain 'M' and resid 399 through 402 removed outlier: 3.688A pdb=" N PHE M 402 " --> pdb=" O LEU M 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 399 through 402' Processing helix chain 'M' and resid 417 through 429 Processing helix chain 'M' and resid 439 through 449 Processing helix chain 'M' and resid 455 through 464 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 170 through 172 removed outlier: 7.161A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.808A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= F, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.741A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 121 through 123 removed outlier: 3.797A pdb=" N VAL C 122 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 98 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 143 through 145 Processing sheet with id= I, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= J, first strand: chain 'C' and resid 154 through 156 removed outlier: 3.713A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= L, first strand: chain 'C' and resid 529 through 531 Processing sheet with id= M, first strand: chain 'C' and resid 589 through 592 Processing sheet with id= N, first strand: chain 'C' and resid 634 through 636 Processing sheet with id= O, first strand: chain 'C' and resid 731 through 735 Processing sheet with id= P, first strand: chain 'C' and resid 1227 through 1232 removed outlier: 6.948A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 830 through 839 removed outlier: 5.665A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 3.696A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= U, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= V, first strand: chain 'D' and resid 355 through 358 removed outlier: 6.749A pdb=" N ILE D 447 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY D 358 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU D 449 " --> pdb=" O GLY D 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 366 through 369 Processing sheet with id= X, first strand: chain 'D' and resid 434 through 438 Processing sheet with id= Y, first strand: chain 'D' and resid 552 through 556 Processing sheet with id= Z, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= AA, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AB, first strand: chain 'a' and resid 145 through 148 removed outlier: 6.046A pdb=" N VAL a 32 " --> pdb=" O CYS a 146 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR a 148 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE a 34 " --> pdb=" O THR a 148 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP a 172 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE a 35 " --> pdb=" O ASP a 172 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL a 174 " --> pdb=" O ILE a 35 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'b' and resid 172 through 175 removed outlier: 3.613A pdb=" N ILE b 35 " --> pdb=" O VAL b 174 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'c' and resid 33 through 36 Processing sheet with id= AE, first strand: chain 'c' and resid 61 through 64 Processing sheet with id= AF, first strand: chain 'd' and resid 172 through 175 removed outlier: 3.506A pdb=" N THR d 148 " --> pdb=" O ILE d 34 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'f' and resid 32 through 35 removed outlier: 3.796A pdb=" N CYS f 146 " --> pdb=" O VAL f 32 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE f 105 " --> pdb=" O ILE f 61 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU f 63 " --> pdb=" O PHE f 105 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'e' and resid 32 through 35 Processing sheet with id= AI, first strand: chain 'e' and resid 61 through 64 removed outlier: 3.923A pdb=" N PHE e 105 " --> pdb=" O ILE e 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP e 107 " --> pdb=" O LEU e 63 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'e' and resid 128 through 130 Processing sheet with id= AK, first strand: chain 'M' and resid 287 through 289 removed outlier: 3.590A pdb=" N PHE M 397 " --> pdb=" O LEU M 390 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 406 through 408 1133 hydrogen bonds defined for protein. 3123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 16.85 Time building geometry restraints manager: 18.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.29: 6940 1.29 - 1.50: 17573 1.50 - 1.70: 17495 1.70 - 1.91: 292 1.91 - 2.11: 6 Bond restraints: 42306 Sorted by residual: bond pdb=" CZ ARG a 98 " pdb=" NH2 ARG a 98 " ideal model delta sigma weight residual 1.330 1.694 -0.364 1.30e-02 5.92e+03 7.83e+02 bond pdb=" C ASP a 185 " pdb=" O ASP a 185 " ideal model delta sigma weight residual 1.235 1.560 -0.325 1.25e-02 6.40e+03 6.77e+02 bond pdb=" C SER e 62 " pdb=" O SER e 62 " ideal model delta sigma weight residual 1.234 1.504 -0.270 1.18e-02 7.18e+03 5.22e+02 bond pdb=" CZ ARG b 143 " pdb=" NH1 ARG b 143 " ideal model delta sigma weight residual 1.323 1.640 -0.317 1.40e-02 5.10e+03 5.14e+02 bond pdb=" CZ ARG a 48 " pdb=" NH1 ARG a 48 " ideal model delta sigma weight residual 1.323 1.599 -0.276 1.40e-02 5.10e+03 3.88e+02 ... (remaining 42301 not shown) Histogram of bond angle deviations from ideal: 76.75 - 90.86: 34 90.86 - 104.97: 1547 104.97 - 119.08: 34175 119.08 - 133.18: 21873 133.18 - 147.29: 72 Bond angle restraints: 57701 Sorted by residual: angle pdb=" C PRO M 258 " pdb=" CA PRO M 258 " pdb=" CB PRO M 258 " ideal model delta sigma weight residual 111.46 82.32 29.14 1.29e+00 6.01e-01 5.10e+02 angle pdb=" NE ARG b 143 " pdb=" CZ ARG b 143 " pdb=" NH2 ARG b 143 " ideal model delta sigma weight residual 119.20 101.29 17.91 9.00e-01 1.23e+00 3.96e+02 angle pdb=" NE ARG a 98 " pdb=" CZ ARG a 98 " pdb=" NH1 ARG a 98 " ideal model delta sigma weight residual 121.50 103.00 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" NE ARG a 48 " pdb=" CZ ARG a 48 " pdb=" NH1 ARG a 48 " ideal model delta sigma weight residual 121.50 139.49 -17.99 1.00e+00 1.00e+00 3.24e+02 angle pdb=" C ILE e 45 " pdb=" CA ILE e 45 " pdb=" CB ILE e 45 " ideal model delta sigma weight residual 112.04 88.60 23.44 1.31e+00 5.83e-01 3.20e+02 ... (remaining 57696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.84: 24346 27.84 - 55.68: 1152 55.68 - 83.52: 101 83.52 - 111.36: 6 111.36 - 139.20: 7 Dihedral angle restraints: 25612 sinusoidal: 10510 harmonic: 15102 Sorted by residual: dihedral pdb=" C PRO M 258 " pdb=" N PRO M 258 " pdb=" CA PRO M 258 " pdb=" CB PRO M 258 " ideal model delta harmonic sigma weight residual -120.70 -84.40 -36.30 0 2.50e+00 1.60e-01 2.11e+02 dihedral pdb=" N LEU b 49 " pdb=" C LEU b 49 " pdb=" CA LEU b 49 " pdb=" CB LEU b 49 " ideal model delta harmonic sigma weight residual 122.80 151.44 -28.64 0 2.50e+00 1.60e-01 1.31e+02 dihedral pdb=" N THR M 119 " pdb=" C THR M 119 " pdb=" CA THR M 119 " pdb=" CB THR M 119 " ideal model delta harmonic sigma weight residual 123.40 151.29 -27.89 0 2.50e+00 1.60e-01 1.24e+02 ... (remaining 25609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 6376 0.287 - 0.573: 240 0.573 - 0.860: 44 0.860 - 1.146: 8 1.146 - 1.433: 4 Chirality restraints: 6672 Sorted by residual: chirality pdb=" C1' ADP f 601 " pdb=" C2' ADP f 601 " pdb=" N9 ADP f 601 " pdb=" O4' ADP f 601 " both_signs ideal model delta sigma weight residual False 2.48 1.05 1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" CA THR M 119 " pdb=" N THR M 119 " pdb=" C THR M 119 " pdb=" CB THR M 119 " both_signs ideal model delta sigma weight residual False 2.53 1.24 1.29 2.00e-01 2.50e+01 4.16e+01 chirality pdb=" CA GLU f 234 " pdb=" N GLU f 234 " pdb=" C GLU f 234 " pdb=" CB GLU f 234 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.20 2.00e-01 2.50e+01 3.57e+01 ... (remaining 6669 not shown) Planarity restraints: 7320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 285 " -0.070 2.00e-02 2.50e+03 1.00e-01 2.52e+02 pdb=" CG TRP M 285 " 0.124 2.00e-02 2.50e+03 pdb=" CD1 TRP M 285 " -0.103 2.00e-02 2.50e+03 pdb=" CD2 TRP M 285 " 0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP M 285 " -0.112 2.00e-02 2.50e+03 pdb=" CE2 TRP M 285 " 0.187 2.00e-02 2.50e+03 pdb=" CE3 TRP M 285 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 285 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 285 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP M 285 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 126 " 0.012 2.00e-02 2.50e+03 6.33e-02 1.00e+02 pdb=" CG TRP M 126 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP M 126 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP M 126 " -0.065 2.00e-02 2.50e+03 pdb=" NE1 TRP M 126 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP M 126 " -0.095 2.00e-02 2.50e+03 pdb=" CE3 TRP M 126 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 126 " 0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 126 " -0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP M 126 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 222 " 0.081 2.00e-02 2.50e+03 5.97e-02 8.92e+01 pdb=" CG TRP a 222 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP a 222 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP a 222 " 0.045 2.00e-02 2.50e+03 pdb=" NE1 TRP a 222 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP a 222 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP a 222 " -0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 222 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 222 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 222 " 0.080 2.00e-02 2.50e+03 ... (remaining 7317 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 408 2.50 - 3.10: 30958 3.10 - 3.70: 62537 3.70 - 4.30: 87186 4.30 - 4.90: 139494 Nonbonded interactions: 320583 Sorted by model distance: nonbonded pdb=" O2A ADP f 601 " pdb=" O2B ADP f 601 " model vdw 1.898 3.040 nonbonded pdb=" N ASP a 185 " pdb=" N ILE a 186 " model vdw 1.973 2.560 nonbonded pdb=" O PRO M 258 " pdb=" CG PRO M 258 " model vdw 2.046 3.440 nonbonded pdb=" O LYS f 5 " pdb=" NZ LYS f 5 " model vdw 2.079 2.520 nonbonded pdb=" N GLU a 130 " pdb=" OE1 GLU a 130 " model vdw 2.081 2.520 ... (remaining 320578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 220 or (resid 221 and (name N or name CA or name C or name O or name \ CB )) or resid 222 through 258)) selection = (chain 'b' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 237 or (resid 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 through 257 or (resid 258 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'c' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 220 or (resid 221 and (name N or name CA or name C or name \ O or name CB )) or resid 222 through 237 or (resid 238 and (name N or name CA or \ name C or name O or name CB )) or resid 239 through 257 or (resid 258 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'd' and (resid 3 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 79 or (resid 80 through 82 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 83 through 86 and (na \ me N or name CA or name C or name O or name CB )) or (resid 87 through 92 and (n \ ame N or name CA or name C or name O or name CB )) or resid 93 through 102 or (r \ esid 103 and (name N or name CA or name C or name O or name CB )) or resid 104 t \ hrough 134 or (resid 135 and (name N or name CA or name C or name O or name CB ) \ ) or resid 136 through 220 or (resid 221 and (name N or name CA or name C or nam \ e O or name CB )) or resid 222 through 237 or (resid 238 and (name N or name CA \ or name C or name O or name CB )) or resid 239 through 257 or (resid 258 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'e' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 220 or (resid 221 and (name N or name CA or name C or name O or name \ CB )) or resid 222 through 237 or (resid 238 and (name N or name CA or name C o \ r name O or name CB )) or resid 239 through 257 or (resid 258 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'f' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 237 or (resid 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 through 258)) } 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=0.20 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.140 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 116.650 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.170 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 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 : 0.021 0.364 42306 Z= 1.343 Angle : 2.212 35.602 57701 Z= 1.353 Chirality : 0.126 1.433 6672 Planarity : 0.009 0.113 7320 Dihedral : 14.787 139.204 15864 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 37.15 Ramachandran Plot: Outliers : 1.33 % Allowed : 8.18 % Favored : 90.49 % Rotamer: Outliers : 10.34 % Allowed : 10.80 % Favored : 78.87 % Cbeta Deviations : 3.75 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.11), residues: 5205 helix: -0.85 (0.12), residues: 1796 sheet: -1.71 (0.24), residues: 438 loop : -2.87 (0.10), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.187 0.014 TRP M 285 HIS 0.042 0.002 HIS d 50 PHE 0.119 0.007 PHE f 15 TYR 0.117 0.004 TYR M 153 ARG 0.063 0.001 ARG b 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 425 poor density : 841 time to evaluate : 4.740 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: 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: B 131 CYS cc_start: 0.7606 (t) cc_final: 0.7292 (t) REVERT: C 160 ASP cc_start: 0.6747 (m-30) cc_final: 0.5526 (m-30) REVERT: C 208 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7278 (mt) REVERT: C 437 ASN cc_start: 0.8003 (m-40) cc_final: 0.7625 (m-40) REVERT: C 696 ASP cc_start: 0.8019 (t70) cc_final: 0.7576 (t0) REVERT: C 843 THR cc_start: 0.7159 (p) cc_final: 0.6921 (p) REVERT: C 917 SER cc_start: 0.7854 (p) cc_final: 0.7545 (t) REVERT: C 955 GLN cc_start: 0.8473 (tp40) cc_final: 0.8118 (tm-30) REVERT: C 1026 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: C 1030 GLU cc_start: 0.8292 (tp30) cc_final: 0.8058 (tp30) REVERT: C 1304 MET cc_start: 0.8140 (tpp) cc_final: 0.7790 (tpt) REVERT: D 48 THR cc_start: 0.8142 (p) cc_final: 0.7711 (p) REVERT: D 265 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6445 (mp) REVERT: D 340 GLN cc_start: 0.1882 (OUTLIER) cc_final: 0.0638 (pp30) REVERT: D 505 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6701 (m-30) REVERT: D 517 CYS cc_start: 0.2835 (OUTLIER) cc_final: 0.2452 (p) REVERT: D 781 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6843 (mtmt) REVERT: D 826 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6063 (pt) REVERT: D 901 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.4554 (ppt-90) REVERT: D 1040 MET cc_start: 0.3980 (mtp) cc_final: 0.2567 (mmt) REVERT: a 118 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.4886 (pt0) REVERT: a 143 ARG cc_start: 0.5092 (OUTLIER) cc_final: 0.4552 (ttp-170) REVERT: a 250 ILE cc_start: 0.0307 (OUTLIER) cc_final: -0.0218 (tt) REVERT: b 57 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8805 (pp30) REVERT: b 139 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.9080 (tm-30) REVERT: c 136 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: c 138 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5151 (tt) REVERT: c 187 MET cc_start: 0.5721 (mmm) cc_final: 0.5508 (mmm) REVERT: d 42 LYS cc_start: 0.6906 (mmmt) cc_final: 0.6523 (mtmm) REVERT: d 55 ARG cc_start: 0.3239 (OUTLIER) cc_final: 0.2816 (pmt-80) REVERT: d 69 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7459 (p0) REVERT: d 222 TRP cc_start: 0.6086 (m-10) cc_final: 0.3531 (m-10) REVERT: e 42 LYS cc_start: 0.4467 (OUTLIER) cc_final: 0.4183 (mtmm) REVERT: e 49 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8730 (tt) REVERT: e 255 PHE cc_start: 0.3298 (OUTLIER) cc_final: 0.2584 (m-80) REVERT: M 11 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: M 31 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7999 (mm) REVERT: M 127 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: M 185 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8470 (m-10) REVERT: M 259 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8227 (ttm170) REVERT: M 416 SER cc_start: 0.9489 (OUTLIER) cc_final: 0.9199 (m) REVERT: M 441 LYS cc_start: 0.9636 (OUTLIER) cc_final: 0.9323 (mmmm) outliers start: 425 outliers final: 113 residues processed: 1197 average time/residue: 0.5922 time to fit residues: 1108.7965 Evaluate side-chains 594 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 453 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1026 GLU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 56 TRP Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 118 GLU Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain a residue 143 ARG Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 171 PHE Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 196 GLN Chi-restraints excluded: chain a residue 225 ASN Chi-restraints excluded: chain a residue 226 ILE Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 48 ARG Chi-restraints excluded: chain b residue 57 GLN Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 139 GLN Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 204 PRO Chi-restraints excluded: chain b residue 235 ARG Chi-restraints excluded: chain b residue 239 ARG Chi-restraints excluded: chain b residue 256 LYS Chi-restraints excluded: chain c residue 5 LYS Chi-restraints excluded: chain c residue 29 ASP Chi-restraints excluded: chain c residue 56 TRP Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 136 GLN Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain c residue 236 SER Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 56 TRP Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 95 ARG Chi-restraints excluded: chain d residue 96 PHE Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 235 ARG Chi-restraints excluded: chain f residue 5 LYS Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 15 PHE Chi-restraints excluded: chain f residue 34 ILE Chi-restraints excluded: chain f residue 50 HIS Chi-restraints excluded: chain f residue 51 TYR Chi-restraints excluded: chain f residue 55 ARG Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain f residue 129 LEU Chi-restraints excluded: chain f residue 136 GLN Chi-restraints excluded: chain f residue 214 ARG Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 158 GLU Chi-restraints excluded: chain e residue 174 VAL Chi-restraints excluded: chain e residue 199 ARG Chi-restraints excluded: chain e residue 255 PHE Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 8 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 11 GLN Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 118 GLN Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 259 ARG Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 292 ASP Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 355 PHE Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 372 GLN Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 416 SER Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 455 ARG Chi-restraints excluded: chain M residue 460 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 441 optimal weight: 10.0000 chunk 396 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 211 optimal weight: 0.0470 chunk 409 optimal weight: 40.0000 chunk 158 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 474 optimal weight: 40.0000 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 117 HIS B 147 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 649 GLN C 684 ASN C 686 GLN C 761 GLN ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN C1268 GLN D 94 GLN D 232 ASN D 340 GLN D 341 ASN D 430 HIS D 450 HIS D 465 GLN D 700 ASN E 29 GLN a 21 GLN a 80 HIS a 92 HIS a 225 ASN a 231 ASN b 21 GLN b 92 HIS ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 ASN c 64 ASN c 157 ASN c 225 ASN d 92 HIS f 7 ASN f 13 ASN f 24 HIS f 50 HIS f 136 GLN f 157 ASN f 175 GLN e 24 HIS e 50 HIS e 89 GLN ** e 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 157 ASN e 225 ASN ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN M 118 GLN M 127 GLN M 229 ASN M 322 ASN M 324 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 42306 Z= 0.399 Angle : 0.862 15.181 57701 Z= 0.424 Chirality : 0.049 0.237 6672 Planarity : 0.006 0.069 7320 Dihedral : 14.124 158.666 6874 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.78 % Favored : 92.03 % Rotamer: Outliers : 5.54 % Allowed : 16.49 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.11), residues: 5205 helix: -0.36 (0.12), residues: 1832 sheet: -1.42 (0.24), residues: 449 loop : -2.61 (0.10), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP M 285 HIS 0.010 0.002 HIS D 419 PHE 0.032 0.003 PHE c 15 TYR 0.030 0.003 TYR b 51 ARG 0.013 0.001 ARG a 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 464 time to evaluate : 5.186 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: A 321 TRP cc_start: 0.5218 (m100) cc_final: 0.4800 (m-90) REVERT: B 95 LYS cc_start: 0.7662 (ttmt) cc_final: 0.7327 (ttpt) REVERT: B 174 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: C 176 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8624 (mt) REVERT: C 195 PHE cc_start: 0.8384 (m-80) cc_final: 0.8120 (m-80) REVERT: C 310 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4549 (tp) REVERT: C 644 LEU cc_start: 0.8554 (mm) cc_final: 0.8270 (tp) REVERT: C 696 ASP cc_start: 0.8100 (t70) cc_final: 0.7455 (t0) REVERT: C 937 ASP cc_start: 0.8024 (t0) cc_final: 0.7753 (m-30) REVERT: C 1085 MET cc_start: 0.9321 (mmm) cc_final: 0.8978 (mmm) REVERT: C 1166 ASP cc_start: 0.7836 (t0) cc_final: 0.7591 (t0) REVERT: D 144 TYR cc_start: 0.8343 (m-80) cc_final: 0.8102 (t80) REVERT: D 227 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7713 (t80) REVERT: D 281 ARG cc_start: 0.8114 (tpt90) cc_final: 0.7568 (tpp-160) REVERT: D 298 MET cc_start: 0.8005 (tpp) cc_final: 0.7714 (mpp) REVERT: D 299 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8821 (tp) REVERT: D 428 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7964 (t) REVERT: D 901 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.4534 (ppt-90) REVERT: D 1040 MET cc_start: 0.4015 (mtp) cc_final: 0.3429 (mtt) REVERT: a 1 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5495 (tmm) REVERT: a 205 LEU cc_start: 0.9038 (tp) cc_final: 0.8721 (tp) REVERT: a 225 ASN cc_start: 0.6902 (OUTLIER) cc_final: 0.6583 (m110) REVERT: a 229 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8696 (pp) REVERT: a 250 ILE cc_start: -0.0681 (OUTLIER) cc_final: -0.1596 (mp) REVERT: c 115 MET cc_start: 0.8469 (mmm) cc_final: 0.8107 (mmm) REVERT: d 55 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.3871 (pmt-80) REVERT: d 69 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6503 (p0) REVERT: f 63 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6371 (pt) REVERT: e 104 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5782 (mt) REVERT: M 28 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8411 (pp) REVERT: M 185 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: M 271 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7610 (p90) REVERT: M 409 THR cc_start: 0.8573 (p) cc_final: 0.8292 (t) outliers start: 228 outliers final: 111 residues processed: 656 average time/residue: 0.5642 time to fit residues: 596.1203 Evaluate side-chains 512 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 383 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 225 ASN Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 24 HIS Chi-restraints excluded: chain d residue 43 GLU Chi-restraints excluded: chain d residue 45 ILE Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 235 ARG Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 164 ASP Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 308 ASN Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 263 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 395 optimal weight: 2.9990 chunk 323 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 475 optimal weight: 50.0000 chunk 513 optimal weight: 0.0770 chunk 423 optimal weight: 9.9990 chunk 471 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 381 optimal weight: 8.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 465 GLN D 667 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 196 GLN ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN e 149 ASN ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42306 Z= 0.182 Angle : 0.681 11.158 57701 Z= 0.331 Chirality : 0.043 0.222 6672 Planarity : 0.004 0.065 7320 Dihedral : 13.298 145.402 6649 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.92 % Favored : 92.87 % Rotamer: Outliers : 4.23 % Allowed : 18.51 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.11), residues: 5205 helix: 0.24 (0.12), residues: 1810 sheet: -1.01 (0.25), residues: 429 loop : -2.40 (0.10), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP c 222 HIS 0.010 0.001 HIS b 50 PHE 0.019 0.001 PHE C 337 TYR 0.026 0.001 TYR b 51 ARG 0.010 0.000 ARG a 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 385 time to evaluate : 4.813 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: B 27 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8255 (p) REVERT: B 174 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: C 158 ASP cc_start: 0.7515 (p0) cc_final: 0.6515 (p0) REVERT: C 176 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8571 (mt) REVERT: C 310 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4664 (tp) REVERT: C 644 LEU cc_start: 0.8496 (mm) cc_final: 0.8203 (tp) REVERT: C 696 ASP cc_start: 0.8145 (t70) cc_final: 0.7556 (t0) REVERT: C 796 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7850 (pp) REVERT: C 1107 MET cc_start: 0.8210 (mpp) cc_final: 0.7498 (mtm) REVERT: C 1166 ASP cc_start: 0.7735 (t0) cc_final: 0.7484 (t0) REVERT: D 281 ARG cc_start: 0.8132 (tpt90) cc_final: 0.7557 (tpp-160) REVERT: D 298 MET cc_start: 0.8017 (tpp) cc_final: 0.7706 (mpp) REVERT: D 428 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7754 (t) REVERT: D 901 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.4657 (ppt-90) REVERT: D 1040 MET cc_start: 0.4040 (mtp) cc_final: 0.3508 (mtt) REVERT: a 51 TYR cc_start: 0.8524 (m-80) cc_final: 0.7930 (m-80) REVERT: a 205 LEU cc_start: 0.9129 (tp) cc_final: 0.8839 (tp) REVERT: a 250 ILE cc_start: -0.1345 (OUTLIER) cc_final: -0.2422 (mp) REVERT: c 227 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.5264 (tpt170) REVERT: d 55 ARG cc_start: 0.4261 (OUTLIER) cc_final: 0.3386 (pmt-80) REVERT: d 69 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6725 (p0) REVERT: f 1 MET cc_start: 0.4438 (mmt) cc_final: 0.3882 (mmt) REVERT: f 63 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6668 (pt) REVERT: e 104 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5694 (mt) REVERT: M 28 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8610 (pp) REVERT: M 185 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: M 271 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7618 (p90) REVERT: M 446 LEU cc_start: 0.9367 (mt) cc_final: 0.9158 (mm) outliers start: 174 outliers final: 98 residues processed: 527 average time/residue: 0.5331 time to fit residues: 462.6724 Evaluate side-chains 459 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 345 time to evaluate : 5.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 MET Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 227 ARG Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain d residue 125 GLU Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 15 PHE Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 470 optimal weight: 30.0000 chunk 357 optimal weight: 40.0000 chunk 246 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 319 optimal weight: 0.0370 chunk 477 optimal weight: 30.0000 chunk 505 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 452 optimal weight: 50.0000 chunk 136 optimal weight: 8.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 465 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** b 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 HIS ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 42306 Z= 0.386 Angle : 0.753 12.959 57701 Z= 0.372 Chirality : 0.046 0.195 6672 Planarity : 0.005 0.058 7320 Dihedral : 13.279 138.453 6633 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.95 % Favored : 91.82 % Rotamer: Outliers : 5.42 % Allowed : 18.31 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.89 (0.11), residues: 5205 helix: 0.06 (0.12), residues: 1830 sheet: -0.93 (0.26), residues: 420 loop : -2.28 (0.10), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP c 222 HIS 0.022 0.002 HIS d 24 PHE 0.029 0.002 PHE C 57 TYR 0.028 0.002 TYR b 51 ARG 0.011 0.001 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 369 time to evaluate : 5.101 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 117 HIS cc_start: 0.6809 (t-90) cc_final: 0.6581 (t-90) REVERT: B 204 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: C 37 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8195 (pttm) REVERT: C 176 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8693 (mt) REVERT: C 195 PHE cc_start: 0.8465 (m-80) cc_final: 0.8258 (m-80) REVERT: C 219 GLN cc_start: 0.8496 (mt0) cc_final: 0.8289 (mt0) REVERT: C 310 ILE cc_start: 0.4982 (OUTLIER) cc_final: 0.4596 (tp) REVERT: C 955 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 1107 MET cc_start: 0.8455 (mpp) cc_final: 0.7961 (mtm) REVERT: C 1321 GLU cc_start: 0.8229 (tp30) cc_final: 0.7689 (tp30) REVERT: D 48 THR cc_start: 0.8625 (p) cc_final: 0.8368 (t) REVERT: D 281 ARG cc_start: 0.8213 (tpt90) cc_final: 0.7688 (tpp-160) REVERT: D 298 MET cc_start: 0.8016 (tpp) cc_final: 0.7695 (mpp) REVERT: D 479 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8446 (mt-10) REVERT: D 504 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7413 (mm-40) REVERT: D 901 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.5019 (ppt-90) REVERT: D 1040 MET cc_start: 0.4157 (mtp) cc_final: 0.3590 (mtt) REVERT: a 205 LEU cc_start: 0.9145 (tp) cc_final: 0.8863 (tp) REVERT: a 250 ILE cc_start: -0.0873 (OUTLIER) cc_final: -0.1913 (tt) REVERT: c 227 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.5319 (tpt90) REVERT: d 55 ARG cc_start: 0.4263 (OUTLIER) cc_final: 0.3426 (pmt-80) REVERT: d 69 ASN cc_start: 0.7132 (OUTLIER) cc_final: 0.6670 (p0) REVERT: f 1 MET cc_start: 0.3855 (mmt) cc_final: 0.3183 (mmt) REVERT: f 63 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7118 (mp) REVERT: M 1 MET cc_start: 0.7376 (tmm) cc_final: 0.7026 (tmm) REVERT: M 28 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8636 (pp) REVERT: M 185 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8135 (m-10) REVERT: M 271 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7630 (p90) REVERT: M 365 MET cc_start: 0.9251 (ptm) cc_final: 0.8861 (ptp) REVERT: M 446 LEU cc_start: 0.9431 (mt) cc_final: 0.9214 (mm) outliers start: 223 outliers final: 133 residues processed: 560 average time/residue: 0.5386 time to fit residues: 495.3045 Evaluate side-chains 479 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 332 time to evaluate : 4.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 103 THR Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 227 ARG Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 125 GLU Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 315 ASP Chi-restraints excluded: chain M residue 441 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 421 optimal weight: 20.0000 chunk 286 optimal weight: 0.0470 chunk 7 optimal weight: 3.9990 chunk 376 optimal weight: 50.0000 chunk 208 optimal weight: 2.9990 chunk 431 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 chunk 453 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 HIS b 50 HIS ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** c 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN d 24 HIS ** d 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN M 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 42306 Z= 0.261 Angle : 0.683 13.194 57701 Z= 0.334 Chirality : 0.043 0.243 6672 Planarity : 0.004 0.078 7320 Dihedral : 13.138 136.661 6625 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.47 % Favored : 92.35 % Rotamer: Outliers : 4.82 % Allowed : 19.41 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.73 (0.11), residues: 5205 helix: 0.21 (0.12), residues: 1825 sheet: -0.55 (0.26), residues: 434 loop : -2.25 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP c 222 HIS 0.009 0.001 HIS d 24 PHE 0.017 0.001 PHE C 57 TYR 0.057 0.002 TYR b 51 ARG 0.005 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 350 time to evaluate : 4.748 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 117 HIS cc_start: 0.6784 (t-90) cc_final: 0.6565 (t-90) REVERT: B 204 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: C 37 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8162 (pttm) REVERT: C 176 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8712 (mt) REVERT: C 195 PHE cc_start: 0.8416 (m-80) cc_final: 0.8216 (m-80) REVERT: C 219 GLN cc_start: 0.8484 (mt0) cc_final: 0.8284 (mt0) REVERT: C 310 ILE cc_start: 0.4806 (OUTLIER) cc_final: 0.4460 (tp) REVERT: C 741 MET cc_start: 0.8889 (tpt) cc_final: 0.8677 (tpt) REVERT: C 899 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7507 (tm-30) REVERT: C 955 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7759 (tm-30) REVERT: C 1107 MET cc_start: 0.8388 (mpp) cc_final: 0.7934 (mtm) REVERT: C 1158 LYS cc_start: 0.7434 (ttpp) cc_final: 0.7103 (ttmm) REVERT: D 29 MET cc_start: 0.7512 (mmm) cc_final: 0.7300 (tpp) REVERT: D 48 THR cc_start: 0.8744 (p) cc_final: 0.8469 (t) REVERT: D 281 ARG cc_start: 0.8256 (tpt90) cc_final: 0.7683 (tpp-160) REVERT: D 298 MET cc_start: 0.8057 (tpp) cc_final: 0.7711 (mpp) REVERT: D 479 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8366 (mt-10) REVERT: D 901 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5271 (ppt-90) REVERT: D 1040 MET cc_start: 0.4100 (mtp) cc_final: 0.3529 (mtt) REVERT: a 205 LEU cc_start: 0.9140 (tp) cc_final: 0.8893 (tp) REVERT: a 250 ILE cc_start: -0.0943 (OUTLIER) cc_final: -0.1986 (tt) REVERT: c 227 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.5303 (tpt90) REVERT: d 55 ARG cc_start: 0.4395 (OUTLIER) cc_final: 0.2711 (pmt170) REVERT: d 69 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6779 (p0) REVERT: d 176 LEU cc_start: 0.0088 (OUTLIER) cc_final: -0.1437 (pp) REVERT: f 1 MET cc_start: 0.3394 (mmt) cc_final: 0.2618 (mmt) REVERT: f 8 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5934 (mt) REVERT: e 157 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8602 (p0) REVERT: M 1 MET cc_start: 0.7261 (tmm) cc_final: 0.7038 (tmm) REVERT: M 28 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8629 (pp) REVERT: M 185 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: M 271 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7701 (p90) REVERT: M 365 MET cc_start: 0.9312 (ptm) cc_final: 0.8921 (ptp) REVERT: M 446 LEU cc_start: 0.9394 (mt) cc_final: 0.9155 (mm) outliers start: 198 outliers final: 134 residues processed: 520 average time/residue: 0.5314 time to fit residues: 455.0966 Evaluate side-chains 483 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 334 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 103 THR Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 103 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 227 ARG Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 43 GLU Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 125 GLU Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 15 PHE Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain e residue 157 ASN Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 315 ASP Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 170 optimal weight: 1.9990 chunk 455 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 296 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 506 optimal weight: 8.9990 chunk 420 optimal weight: 30.0000 chunk 234 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 167 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN b 80 HIS ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 HIS d 175 GLN ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 42306 Z= 0.181 Angle : 0.652 12.355 57701 Z= 0.315 Chirality : 0.042 0.245 6672 Planarity : 0.004 0.056 7320 Dihedral : 13.003 137.082 6619 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.57 % Favored : 92.26 % Rotamer: Outliers : 4.57 % Allowed : 20.31 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.11), residues: 5205 helix: 0.42 (0.12), residues: 1823 sheet: -0.43 (0.26), residues: 418 loop : -2.17 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP c 222 HIS 0.012 0.001 HIS d 24 PHE 0.016 0.001 PHE D 141 TYR 0.024 0.001 TYR D1282 ARG 0.005 0.000 ARG c 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 352 time to evaluate : 4.761 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: C 37 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8092 (pttm) REVERT: C 176 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8723 (mt) REVERT: C 310 ILE cc_start: 0.4717 (OUTLIER) cc_final: 0.4397 (tp) REVERT: C 337 PHE cc_start: 0.7018 (t80) cc_final: 0.6599 (t80) REVERT: C 644 LEU cc_start: 0.8538 (mm) cc_final: 0.8274 (tp) REVERT: C 800 MET cc_start: 0.8697 (mmm) cc_final: 0.8425 (mmp) REVERT: C 899 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7460 (tm-30) REVERT: C 1085 MET cc_start: 0.9387 (mmm) cc_final: 0.9048 (mmm) REVERT: C 1107 MET cc_start: 0.8381 (mpp) cc_final: 0.7865 (mtm) REVERT: C 1158 LYS cc_start: 0.7321 (ttpp) cc_final: 0.7103 (ttmt) REVERT: D 48 THR cc_start: 0.8762 (p) cc_final: 0.8501 (t) REVERT: D 137 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7834 (mtm110) REVERT: D 227 PHE cc_start: 0.7948 (m-80) cc_final: 0.7745 (t80) REVERT: D 281 ARG cc_start: 0.8278 (tpt90) cc_final: 0.7695 (tpp-160) REVERT: D 298 MET cc_start: 0.8045 (tpp) cc_final: 0.7700 (mpp) REVERT: D 447 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8091 (mt) REVERT: D 901 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.4730 (ppt-90) REVERT: D 1040 MET cc_start: 0.4130 (mtp) cc_final: 0.3574 (mtt) REVERT: a 1 MET cc_start: 0.6078 (mmm) cc_final: 0.5852 (tpp) REVERT: a 205 LEU cc_start: 0.9199 (tp) cc_final: 0.8956 (tp) REVERT: a 250 ILE cc_start: -0.0979 (OUTLIER) cc_final: -0.2008 (tt) REVERT: b 51 TYR cc_start: 0.7973 (p90) cc_final: 0.7604 (p90) REVERT: b 68 LEU cc_start: 0.7756 (mt) cc_final: 0.7338 (mp) REVERT: b 136 GLN cc_start: 0.7681 (pm20) cc_final: 0.7077 (tm-30) REVERT: c 227 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4922 (tpt90) REVERT: d 55 ARG cc_start: 0.4482 (OUTLIER) cc_final: 0.2774 (pmt170) REVERT: d 69 ASN cc_start: 0.7175 (OUTLIER) cc_final: 0.6900 (p0) REVERT: d 176 LEU cc_start: 0.0030 (OUTLIER) cc_final: -0.1468 (pp) REVERT: f 1 MET cc_start: 0.3371 (mmt) cc_final: 0.2497 (mmt) REVERT: f 8 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6250 (mt) REVERT: e 63 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7377 (pt) REVERT: e 157 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8516 (p0) REVERT: M 28 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8622 (pp) REVERT: M 185 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8177 (m-10) REVERT: M 271 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7714 (p90) REVERT: M 279 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7282 (ppt90) REVERT: M 401 TYR cc_start: 0.8827 (t80) cc_final: 0.8384 (t80) REVERT: M 446 LEU cc_start: 0.9358 (mt) cc_final: 0.9152 (mm) outliers start: 188 outliers final: 125 residues processed: 509 average time/residue: 0.5548 time to fit residues: 470.3256 Evaluate side-chains 469 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 327 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 80 HIS Chi-restraints excluded: chain b residue 103 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 227 ARG Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 43 GLU Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 125 GLU Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 15 PHE Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain e residue 157 ASN Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 315 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 487 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 chunk 369 optimal weight: 40.0000 chunk 286 optimal weight: 30.0000 chunk 425 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 chunk 504 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 196 GLN b 71 ASN b 80 HIS ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 GLN ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 42306 Z= 0.243 Angle : 0.669 15.410 57701 Z= 0.324 Chirality : 0.043 0.263 6672 Planarity : 0.004 0.053 7320 Dihedral : 12.979 138.126 6615 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.85 % Rotamer: Outliers : 4.35 % Allowed : 20.84 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.49 (0.11), residues: 5205 helix: 0.41 (0.12), residues: 1837 sheet: -0.43 (0.26), residues: 422 loop : -2.11 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP c 222 HIS 0.036 0.001 HIS b 80 PHE 0.017 0.001 PHE C 57 TYR 0.033 0.001 TYR b 192 ARG 0.007 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 336 time to evaluate : 4.961 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: B 95 LYS cc_start: 0.7796 (tttt) cc_final: 0.7077 (tmmt) REVERT: C 37 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8160 (pttm) REVERT: C 176 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8739 (mt) REVERT: C 310 ILE cc_start: 0.4753 (OUTLIER) cc_final: 0.4428 (tp) REVERT: C 337 PHE cc_start: 0.7161 (t80) cc_final: 0.6742 (t80) REVERT: C 800 MET cc_start: 0.8721 (mmm) cc_final: 0.8463 (mmp) REVERT: C 899 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7418 (tm-30) REVERT: C 1107 MET cc_start: 0.8395 (mpp) cc_final: 0.7842 (mtm) REVERT: C 1158 LYS cc_start: 0.7572 (ttpp) cc_final: 0.7264 (ttmt) REVERT: C 1321 GLU cc_start: 0.8052 (tp30) cc_final: 0.7588 (tp30) REVERT: D 48 THR cc_start: 0.8710 (p) cc_final: 0.8465 (t) REVERT: D 133 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7253 (mmm160) REVERT: D 227 PHE cc_start: 0.7996 (m-80) cc_final: 0.7764 (t80) REVERT: D 281 ARG cc_start: 0.8297 (tpt90) cc_final: 0.7715 (tpp-160) REVERT: D 298 MET cc_start: 0.8028 (tpp) cc_final: 0.7686 (mpp) REVERT: D 447 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8226 (mt) REVERT: D 901 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.4755 (ppt-90) REVERT: D 1040 MET cc_start: 0.4217 (mtp) cc_final: 0.3619 (mtt) REVERT: a 1 MET cc_start: 0.6010 (mmm) cc_final: 0.5573 (tpp) REVERT: a 205 LEU cc_start: 0.9195 (tp) cc_final: 0.8957 (tp) REVERT: a 250 ILE cc_start: -0.0465 (OUTLIER) cc_final: -0.1579 (tt) REVERT: b 51 TYR cc_start: 0.7996 (p90) cc_final: 0.7701 (p90) REVERT: b 68 LEU cc_start: 0.7719 (mt) cc_final: 0.7321 (mp) REVERT: b 136 GLN cc_start: 0.7384 (pm20) cc_final: 0.6930 (tm-30) REVERT: c 115 MET cc_start: 0.8369 (mmm) cc_final: 0.7994 (mmm) REVERT: c 227 ARG cc_start: 0.5178 (OUTLIER) cc_final: 0.4942 (tpt90) REVERT: d 55 ARG cc_start: 0.4928 (OUTLIER) cc_final: 0.3199 (pmt170) REVERT: f 1 MET cc_start: 0.3346 (mmt) cc_final: 0.2545 (mmt) REVERT: e 63 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7381 (pt) REVERT: e 157 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8513 (p0) REVERT: e 189 MET cc_start: 0.6326 (mmm) cc_final: 0.5606 (mmt) REVERT: M 28 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8682 (pp) REVERT: M 185 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8169 (m-10) REVERT: M 271 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7784 (p90) REVERT: M 279 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7024 (ppt90) REVERT: M 285 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.5685 (m100) REVERT: M 288 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7848 (pt0) REVERT: M 401 TYR cc_start: 0.8837 (t80) cc_final: 0.8405 (t80) outliers start: 179 outliers final: 134 residues processed: 487 average time/residue: 0.5176 time to fit residues: 417.1688 Evaluate side-chains 469 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 320 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 80 HIS Chi-restraints excluded: chain b residue 103 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 227 ARG Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 15 PHE Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 157 ASN Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 315 ASP Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 311 optimal weight: 0.5980 chunk 201 optimal weight: 10.0000 chunk 301 optimal weight: 0.3980 chunk 151 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 320 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 396 optimal weight: 9.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 ASN b 80 HIS ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42306 Z= 0.175 Angle : 0.643 11.581 57701 Z= 0.309 Chirality : 0.041 0.188 6672 Planarity : 0.004 0.052 7320 Dihedral : 12.832 139.017 6605 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.47 % Favored : 92.35 % Rotamer: Outliers : 4.11 % Allowed : 21.11 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.35 (0.11), residues: 5205 helix: 0.56 (0.13), residues: 1832 sheet: -0.32 (0.26), residues: 427 loop : -2.05 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP c 222 HIS 0.019 0.001 HIS b 80 PHE 0.016 0.001 PHE D 141 TYR 0.022 0.001 TYR M 361 ARG 0.010 0.000 ARG C 903 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 338 time to evaluate : 4.814 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: B 95 LYS cc_start: 0.7722 (tttt) cc_final: 0.7027 (tmmt) REVERT: C 37 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8104 (pttm) REVERT: C 176 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8696 (mt) REVERT: C 310 ILE cc_start: 0.4710 (OUTLIER) cc_final: 0.4397 (tp) REVERT: C 337 PHE cc_start: 0.7117 (t80) cc_final: 0.6680 (t80) REVERT: C 644 LEU cc_start: 0.8552 (mm) cc_final: 0.8309 (tp) REVERT: C 800 MET cc_start: 0.8697 (mmm) cc_final: 0.8425 (mmp) REVERT: C 899 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7325 (tm-30) REVERT: C 1026 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8351 (mm-30) REVERT: C 1085 MET cc_start: 0.9345 (mmm) cc_final: 0.8939 (mmm) REVERT: C 1107 MET cc_start: 0.8345 (mpp) cc_final: 0.7795 (mtm) REVERT: D 48 THR cc_start: 0.8742 (p) cc_final: 0.8503 (t) REVERT: D 133 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7352 (mmm160) REVERT: D 281 ARG cc_start: 0.8301 (tpt90) cc_final: 0.7701 (tpp-160) REVERT: D 298 MET cc_start: 0.7973 (tpp) cc_final: 0.7672 (mpp) REVERT: D 447 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8368 (mt) REVERT: D 901 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.4721 (ppt-90) REVERT: D 1040 MET cc_start: 0.4275 (mtp) cc_final: 0.3012 (mpp) REVERT: a 1 MET cc_start: 0.5930 (mmm) cc_final: 0.5699 (tpp) REVERT: a 205 LEU cc_start: 0.9188 (tp) cc_final: 0.8953 (tp) REVERT: a 250 ILE cc_start: -0.0447 (OUTLIER) cc_final: -0.1622 (tt) REVERT: b 68 LEU cc_start: 0.7685 (mt) cc_final: 0.7266 (mp) REVERT: b 136 GLN cc_start: 0.7408 (pm20) cc_final: 0.7083 (tm-30) REVERT: c 63 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7408 (tm) REVERT: d 55 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.2996 (pmt170) REVERT: f 1 MET cc_start: 0.3179 (mmt) cc_final: 0.2384 (mmt) REVERT: e 63 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7420 (pt) REVERT: e 157 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8504 (p0) REVERT: e 189 MET cc_start: 0.6482 (mmm) cc_final: 0.5752 (mmt) REVERT: e 197 MET cc_start: 0.1263 (OUTLIER) cc_final: 0.0817 (ptp) REVERT: M 28 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8723 (pp) REVERT: M 125 MET cc_start: 0.8947 (mmm) cc_final: 0.8704 (mmm) REVERT: M 185 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: M 279 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6924 (ppt90) REVERT: M 285 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.5901 (m100) REVERT: M 288 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7868 (pt0) REVERT: M 401 TYR cc_start: 0.8803 (t80) cc_final: 0.8352 (t80) REVERT: M 446 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8773 (mm) outliers start: 169 outliers final: 127 residues processed: 477 average time/residue: 0.5317 time to fit residues: 417.2950 Evaluate side-chains 470 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 327 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 80 HIS Chi-restraints excluded: chain b residue 103 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 15 PHE Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 157 ASN Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 197 MET Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 458 optimal weight: 30.0000 chunk 482 optimal weight: 30.0000 chunk 440 optimal weight: 20.0000 chunk 469 optimal weight: 50.0000 chunk 282 optimal weight: 30.0000 chunk 204 optimal weight: 4.9990 chunk 368 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 424 optimal weight: 9.9990 chunk 444 optimal weight: 3.9990 chunk 468 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS a 69 ASN b 80 HIS ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 42306 Z= 0.550 Angle : 0.824 15.128 57701 Z= 0.411 Chirality : 0.048 0.224 6672 Planarity : 0.006 0.076 7320 Dihedral : 13.083 137.617 6603 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.30 % Favored : 90.49 % Rotamer: Outliers : 4.09 % Allowed : 21.38 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.78 (0.11), residues: 5205 helix: 0.01 (0.12), residues: 1861 sheet: -0.67 (0.26), residues: 446 loop : -2.17 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP c 222 HIS 0.027 0.002 HIS b 80 PHE 0.035 0.002 PHE C 57 TYR 0.028 0.002 TYR M 361 ARG 0.013 0.001 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 334 time to evaluate : 4.702 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: B 95 LYS cc_start: 0.7933 (tttt) cc_final: 0.7215 (tmmt) REVERT: C 37 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8219 (pttm) REVERT: C 176 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8734 (mt) REVERT: C 295 LYS cc_start: 0.8301 (ttpt) cc_final: 0.8088 (mtpt) REVERT: C 1107 MET cc_start: 0.8567 (mpp) cc_final: 0.8072 (mtm) REVERT: C 1321 GLU cc_start: 0.8537 (tp30) cc_final: 0.8181 (tp30) REVERT: D 77 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6635 (tpp-160) REVERT: D 281 ARG cc_start: 0.8364 (tpt90) cc_final: 0.7701 (tpp-160) REVERT: D 298 MET cc_start: 0.8055 (tpp) cc_final: 0.7712 (mpp) REVERT: D 1040 MET cc_start: 0.4565 (mtp) cc_final: 0.3744 (mtt) REVERT: E 30 MET cc_start: 0.8431 (mtt) cc_final: 0.8211 (mtt) REVERT: a 1 MET cc_start: 0.5974 (mmm) cc_final: 0.5650 (tpp) REVERT: a 205 LEU cc_start: 0.9202 (tp) cc_final: 0.8965 (tp) REVERT: a 250 ILE cc_start: -0.0226 (OUTLIER) cc_final: -0.1315 (tt) REVERT: b 68 LEU cc_start: 0.7761 (mt) cc_final: 0.7380 (mp) REVERT: b 136 GLN cc_start: 0.7107 (pm20) cc_final: 0.6805 (tm-30) REVERT: d 55 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.2848 (pmt170) REVERT: d 69 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.6947 (p0) REVERT: d 117 GLN cc_start: 0.7969 (mt0) cc_final: 0.7739 (mp10) REVERT: f 1 MET cc_start: 0.2987 (mmt) cc_final: 0.2164 (mmt) REVERT: f 155 MET cc_start: 0.4228 (pmm) cc_final: 0.4022 (pmm) REVERT: e 63 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7434 (pt) REVERT: e 157 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8601 (p0) REVERT: e 189 MET cc_start: 0.6563 (mmm) cc_final: 0.5828 (mmt) REVERT: M 28 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8761 (pp) REVERT: M 279 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6866 (ppt90) REVERT: M 285 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.5952 (m100) outliers start: 168 outliers final: 130 residues processed: 478 average time/residue: 0.5357 time to fit residues: 421.0796 Evaluate side-chains 453 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 312 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 80 HIS Chi-restraints excluded: chain b residue 103 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 157 ASN Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 192 TYR Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 308 optimal weight: 10.0000 chunk 496 optimal weight: 3.9990 chunk 303 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 chunk 345 optimal weight: 30.0000 chunk 521 optimal weight: 6.9990 chunk 479 optimal weight: 5.9990 chunk 414 optimal weight: 50.0000 chunk 43 optimal weight: 40.0000 chunk 320 optimal weight: 0.7980 chunk 254 optimal weight: 0.7980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN b 24 HIS b 80 HIS ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 HIS f 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 42306 Z= 0.291 Angle : 0.704 13.291 57701 Z= 0.343 Chirality : 0.043 0.220 6672 Planarity : 0.005 0.094 7320 Dihedral : 12.949 137.208 6603 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.09 % Favored : 91.78 % Rotamer: Outliers : 3.57 % Allowed : 22.11 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.61 (0.11), residues: 5205 helix: 0.19 (0.12), residues: 1856 sheet: -0.49 (0.26), residues: 435 loop : -2.10 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP c 222 HIS 0.016 0.001 HIS d 24 PHE 0.021 0.001 PHE D 141 TYR 0.025 0.001 TYR M 361 ARG 0.008 0.000 ARG C 903 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 323 time to evaluate : 4.804 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: B 95 LYS cc_start: 0.7889 (tttt) cc_final: 0.7146 (tmmt) REVERT: C 37 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8267 (pttm) REVERT: C 239 MET cc_start: 0.6894 (mmp) cc_final: 0.6691 (mmp) REVERT: C 392 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7189 (tp30) REVERT: C 1107 MET cc_start: 0.8457 (mpp) cc_final: 0.8025 (mtm) REVERT: C 1321 GLU cc_start: 0.8273 (tp30) cc_final: 0.7844 (tp30) REVERT: D 281 ARG cc_start: 0.8297 (tpt90) cc_final: 0.7624 (tpp-160) REVERT: D 298 MET cc_start: 0.8064 (tpp) cc_final: 0.7706 (mpp) REVERT: D 322 ARG cc_start: 0.7512 (ppt170) cc_final: 0.7212 (ppt170) REVERT: D 901 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5209 (ppt-90) REVERT: D 1040 MET cc_start: 0.4631 (mtp) cc_final: 0.3765 (mtt) REVERT: E 30 MET cc_start: 0.8058 (mtt) cc_final: 0.7788 (mtt) REVERT: a 1 MET cc_start: 0.5933 (mmm) cc_final: 0.5582 (tpp) REVERT: a 205 LEU cc_start: 0.9213 (tp) cc_final: 0.8984 (tp) REVERT: a 250 ILE cc_start: -0.0199 (OUTLIER) cc_final: -0.1294 (tt) REVERT: b 68 LEU cc_start: 0.7694 (mt) cc_final: 0.7288 (mp) REVERT: b 136 GLN cc_start: 0.7236 (pm20) cc_final: 0.6978 (tm-30) REVERT: c 115 MET cc_start: 0.8349 (mmm) cc_final: 0.8119 (mpp) REVERT: d 55 ARG cc_start: 0.4134 (OUTLIER) cc_final: 0.2486 (pmt170) REVERT: d 69 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.7043 (p0) REVERT: f 1 MET cc_start: 0.3065 (mmt) cc_final: 0.2217 (mmt) REVERT: e 63 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7384 (pt) REVERT: e 157 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8618 (p0) REVERT: M 28 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8747 (pp) REVERT: M 279 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6757 (ppt90) REVERT: M 285 TRP cc_start: 0.8394 (OUTLIER) cc_final: 0.6402 (m100) REVERT: M 401 TYR cc_start: 0.8821 (t80) cc_final: 0.8581 (t80) outliers start: 147 outliers final: 125 residues processed: 451 average time/residue: 0.5430 time to fit residues: 403.7175 Evaluate side-chains 447 residues out of total 4492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 312 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 107 ASP Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 80 HIS Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 164 ASP Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 157 ASN Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 192 TYR Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain e residue 238 TYR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 329 optimal weight: 20.0000 chunk 441 optimal weight: 40.0000 chunk 127 optimal weight: 2.9990 chunk 382 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 415 optimal weight: 50.0000 chunk 173 optimal weight: 0.0170 chunk 426 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN D 424 ASN D 667 GLN a 69 ASN b 80 HIS ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.183226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.153375 restraints weight = 77030.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.149096 restraints weight = 136943.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.146709 restraints weight = 123565.180| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42306 Z= 0.165 Angle : 0.657 11.613 57701 Z= 0.316 Chirality : 0.041 0.194 6672 Planarity : 0.004 0.121 7320 Dihedral : 12.731 139.066 6597 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.92 % Favored : 91.97 % Rotamer: Outliers : 2.80 % Allowed : 22.88 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 5205 helix: 0.48 (0.12), residues: 1845 sheet: -0.31 (0.26), residues: 429 loop : -2.00 (0.11), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP c 222 HIS 0.022 0.001 HIS b 80 PHE 0.031 0.001 PHE C 337 TYR 0.033 0.001 TYR b 192 ARG 0.008 0.000 ARG M 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9714.67 seconds wall clock time: 174 minutes 46.70 seconds (10486.70 seconds total)