Starting phenix.real_space_refine on Fri Feb 23 01:23:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2f_22006/02_2024/6x2f_22006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2f_22006/02_2024/6x2f_22006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2f_22006/02_2024/6x2f_22006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2f_22006/02_2024/6x2f_22006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2f_22006/02_2024/6x2f_22006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2f_22006/02_2024/6x2f_22006_updated.pdb" } resolution = 4.0 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= 0.008 sd= 1.068 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 Zn 2 6.06 5 P 114 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 22296 2.51 5 N 6401 2.21 5 O 7099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A ASP 436": "OD1" <-> "OD2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 957": "OE1" <-> "OE2" Residue "A GLU 977": "OE1" <-> "OE2" Residue "A TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 96": "OD1" <-> "OD2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 14": "OD1" <-> "OD2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I ASP 81": "OD1" <-> "OD2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I ASP 158": "OD1" <-> "OD2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 396": "OD1" <-> "OD2" Residue "I GLU 413": "OE1" <-> "OE2" Residue "I ASP 434": "OD1" <-> "OD2" Residue "I GLU 472": "OE1" <-> "OE2" Residue "I ASP 485": "OD1" <-> "OD2" Residue "I GLU 523": "OE1" <-> "OE2" Residue "I ASP 601": "OD1" <-> "OD2" Residue "I TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I ASP 674": "OD1" <-> "OD2" Residue "I GLU 705": "OE1" <-> "OE2" Residue "I GLU 738": "OE1" <-> "OE2" Residue "I GLU 740": "OE1" <-> "OE2" Residue "I TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 793": "OE1" <-> "OE2" Residue "I ASP 814": "OD1" <-> "OD2" Residue "I GLU 820": "OE1" <-> "OE2" Residue "I GLU 825": "OE1" <-> "OE2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I ASP 930": "OD1" <-> "OD2" Residue "I PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 949": "OE1" <-> "OE2" Residue "I TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1024": "OE1" <-> "OE2" Residue "I GLU 1026": "OE1" <-> "OE2" Residue "I ASP 1126": "OD1" <-> "OD2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I GLU 1167": "OE1" <-> "OE2" Residue "I GLU 1168": "OE1" <-> "OE2" Residue "I GLU 1192": "OE1" <-> "OE2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J ASP 410": "OD1" <-> "OD2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J ASP 505": "OD1" <-> "OD2" Residue "J TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 622": "OD1" <-> "OD2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J GLU 713": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J GLU 765": "OE1" <-> "OE2" Residue "J TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J ASP 1007": "OD1" <-> "OD2" Residue "J GLU 1030": "OE1" <-> "OE2" Residue "J PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J GLU 1281": "OE1" <-> "OE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K ASP 65": "OD1" <-> "OD2" Residue "K GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36054 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8934 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1088} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1721 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10368 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 10383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10383 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 201 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23139 SG CYS J 70 27.729 99.970 85.446 1.00139.65 S ATOM 23153 SG CYS J 72 27.808 103.669 84.394 1.00141.32 S ATOM 23261 SG CYS J 85 25.989 100.923 82.417 1.00146.72 S ATOM 23285 SG CYS J 88 29.659 101.045 82.330 1.00134.74 S ATOM 28961 SG CYS J 814 53.224 38.369 92.070 1.00 96.55 S ATOM 29526 SG CYS J 888 54.225 41.984 91.005 1.00 81.59 S ATOM 29598 SG CYS J 898 55.996 38.784 93.474 1.00 76.52 S Time building chain proxies: 19.20, per 1000 atoms: 0.53 Number of scatterers: 36054 At special positions: 0 Unit cell: (139.1, 209.3, 179.4, 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) Zn 2 29.99 S 141 16.00 P 114 15.00 Mg 1 11.99 O 7099 8.00 N 6401 7.00 C 22296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.48 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 6 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 47 sheets defined 32.5% alpha, 11.9% beta 51 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 19.35 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 49 through 62 removed outlier: 5.053A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 removed outlier: 5.549A pdb=" N LEU A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 98 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 288 through 306 removed outlier: 4.503A pdb=" N GLU A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.955A pdb=" N ASN A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.529A pdb=" N THR A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.958A pdb=" N GLU A 400 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 402 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 463 through 466 No H-bonds generated for 'chain 'A' and resid 463 through 466' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.561A pdb=" N ASP A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.628A pdb=" N SER A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 617 Processing helix chain 'A' and resid 634 through 647 Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 689 through 701 Processing helix chain 'A' and resid 738 through 745 removed outlier: 4.577A pdb=" N ILE A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 795 through 807 removed outlier: 3.885A pdb=" N GLU A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 832 Processing helix chain 'A' and resid 849 through 858 Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 924 through 935 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 972 through 987 removed outlier: 3.502A pdb=" N GLU A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1000 Processing helix chain 'A' and resid 1020 through 1032 Processing helix chain 'A' and resid 1036 through 1050 Processing helix chain 'A' and resid 1055 through 1073 removed outlier: 3.843A pdb=" N ILE A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1128 through 1144 removed outlier: 3.971A pdb=" N GLU A1144 " --> pdb=" O ARG A1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 231 removed outlier: 3.550A pdb=" N THR G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.932A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 230 removed outlier: 3.791A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 223 Processing helix chain 'I' and resid 243 through 245 No H-bonds generated for 'chain 'I' and resid 243 through 245' Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 289 through 291 No H-bonds generated for 'chain 'I' and resid 289 through 291' Processing helix chain 'I' and resid 319 through 327 Processing helix chain 'I' and resid 348 through 352 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.722A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 486 No H-bonds generated for 'chain 'I' and resid 484 through 486' Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 540 through 542 No H-bonds generated for 'chain 'I' and resid 540 through 542' Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 657 through 659 No H-bonds generated for 'chain 'I' and resid 657 through 659' Processing helix chain 'I' and resid 676 through 686 Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 859 through 864 removed outlier: 5.173A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 943 through 977 Processing helix chain 'I' and resid 994 through 996 No H-bonds generated for 'chain 'I' and resid 994 through 996' Processing helix chain 'I' and resid 1006 through 1037 removed outlier: 3.791A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR I1037 " --> pdb=" O ARG I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1100 through 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1168 through 1178 removed outlier: 3.698A pdb=" N ARG I1177 " --> pdb=" O ALA I1173 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS I1178 " --> pdb=" O GLU I1174 " (cutoff:3.500A) Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1272 through 1280 removed outlier: 3.870A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1285 through 1292 Processing helix chain 'I' and resid 1298 through 1310 removed outlier: 3.754A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 removed outlier: 3.606A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.887A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 181 through 190 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 213 through 229 Processing helix chain 'J' and resid 234 through 237 removed outlier: 3.742A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 234 through 237' Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 330 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 416 removed outlier: 4.127A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.764A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 592 Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 648 through 669 removed outlier: 3.742A pdb=" N HIS J 651 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE J 654 " --> pdb=" O HIS J 651 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL J 661 " --> pdb=" O GLU J 658 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN J 669 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 803 removed outlier: 3.912A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 915 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.553A pdb=" N THR J1230 " --> pdb=" O VAL J1226 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1262 removed outlier: 3.621A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG J1262 " --> pdb=" O ARG J1258 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 removed outlier: 3.997A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1314 removed outlier: 4.134A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1328 through 1337 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.887A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG J1369 " --> pdb=" O HIS J1366 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG J1371 " --> pdb=" O ASP J1368 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 17 through 31 removed outlier: 3.608A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 77 Processing sheet with id= A, first strand: chain 'A' and resid 350 through 352 removed outlier: 9.156A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG A 336 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU A 19 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A 338 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 43 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 285 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= C, first strand: chain 'A' and resid 162 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 355 through 357 Processing sheet with id= E, first strand: chain 'A' and resid 422 through 424 Processing sheet with id= F, first strand: chain 'A' and resid 489 through 492 Processing sheet with id= G, first strand: chain 'A' and resid 496 through 500 Processing sheet with id= H, first strand: chain 'A' and resid 623 through 627 removed outlier: 7.151A pdb=" N ILE A 751 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL A 626 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR A 753 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 653 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP A 729 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 655 " --> pdb=" O ASP A 729 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 787 through 792 removed outlier: 3.573A pdb=" N LEU A 915 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR A 813 " --> pdb=" O ILE A 884 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id= K, first strand: chain 'A' and resid 1084 through 1088 Processing sheet with id= L, first strand: chain 'A' and resid 192 through 195 removed outlier: 3.709A pdb=" N LEU A 192 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 204 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.657A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.850A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 108 through 110 removed outlier: 4.086A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.764A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 14 through 18 Processing sheet with id= R, first strand: chain 'H' and resid 53 through 56 Processing sheet with id= S, first strand: chain 'H' and resid 59 through 61 Processing sheet with id= T, first strand: chain 'H' and resid 188 through 190 removed outlier: 3.584A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 108 through 111 Processing sheet with id= V, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= W, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= X, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= Y, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.526A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 226 through 231 removed outlier: 4.501A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= AB, first strand: chain 'I' and resid 529 through 531 Processing sheet with id= AC, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= AD, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= AE, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.705A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 1096 through 1098 removed outlier: 4.604A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.907A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 68 through 75 removed outlier: 6.965A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.017A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.698A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= AL, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AM, first strand: chain 'J' and resid 365 through 369 removed outlier: 5.773A pdb=" N GLU J 438 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU J 368 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL J 440 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AO, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AP, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= AQ, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.096A pdb=" N ALA J1001 " --> pdb=" O ILE J 975 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= AS, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.617A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AU, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.656A pdb=" N VAL J1280 " --> pdb=" O ALA J1264 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 20.02 Time building geometry restraints manager: 17.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9695 1.33 - 1.45: 6929 1.45 - 1.57: 19777 1.57 - 1.70: 225 1.70 - 1.82: 247 Bond restraints: 36873 Sorted by residual: bond pdb=" N PRO I 489 " pdb=" CD PRO I 489 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.71e+01 bond pdb=" N PRO I 552 " pdb=" CD PRO I 552 " ideal model delta sigma weight residual 1.473 1.405 0.068 1.40e-02 5.10e+03 2.34e+01 bond pdb=" CA ARG A 837 " pdb=" CB ARG A 837 " ideal model delta sigma weight residual 1.524 1.456 0.069 1.46e-02 4.69e+03 2.22e+01 bond pdb=" CA PHE J 116 " pdb=" C PHE J 116 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.37e-02 5.33e+03 1.63e+01 bond pdb=" CA ILE J 416 " pdb=" CB ILE J 416 " ideal model delta sigma weight residual 1.540 1.487 0.053 1.36e-02 5.41e+03 1.53e+01 ... (remaining 36868 not shown) Histogram of bond angle deviations from ideal: 93.04 - 102.21: 282 102.21 - 111.37: 15602 111.37 - 120.53: 21224 120.53 - 129.69: 13038 129.69 - 138.86: 210 Bond angle restraints: 50356 Sorted by residual: angle pdb=" C LEU A 344 " pdb=" N PRO A 345 " pdb=" CA PRO A 345 " ideal model delta sigma weight residual 119.84 130.93 -11.09 1.25e+00 6.40e-01 7.87e+01 angle pdb=" C CYS A 617 " pdb=" N GLN A 618 " pdb=" CA GLN A 618 " ideal model delta sigma weight residual 120.39 131.36 -10.97 1.39e+00 5.18e-01 6.22e+01 angle pdb=" N VAL A 564 " pdb=" CA VAL A 564 " pdb=" C VAL A 564 " ideal model delta sigma weight residual 113.20 106.43 6.77 9.60e-01 1.09e+00 4.97e+01 angle pdb=" C THR A 346 " pdb=" N LYS A 347 " pdb=" CA LYS A 347 " ideal model delta sigma weight residual 121.80 133.31 -11.51 1.71e+00 3.42e-01 4.53e+01 angle pdb=" N VAL J 839 " pdb=" CA VAL J 839 " pdb=" C VAL J 839 " ideal model delta sigma weight residual 111.88 104.87 7.01 1.06e+00 8.90e-01 4.37e+01 ... (remaining 50351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 21506 35.82 - 71.65: 761 71.65 - 107.47: 35 107.47 - 143.29: 1 143.29 - 179.11: 2 Dihedral angle restraints: 22305 sinusoidal: 9876 harmonic: 12429 Sorted by residual: dihedral pdb=" C5' ADP A2000 " pdb=" O5' ADP A2000 " pdb=" PA ADP A2000 " pdb=" O2A ADP A2000 " ideal model delta sinusoidal sigma weight residual -60.00 118.71 -178.70 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA ASN J 768 " pdb=" C ASN J 768 " pdb=" N VAL J 769 " pdb=" CA VAL J 769 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASN J1249 " pdb=" C ASN J1249 " pdb=" N ASP J1250 " pdb=" CA ASP J1250 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 22302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5125 0.099 - 0.199: 574 0.199 - 0.298: 38 0.298 - 0.398: 5 0.398 - 0.497: 2 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CB ILE I 117 " pdb=" CA ILE I 117 " pdb=" CG1 ILE I 117 " pdb=" CG2 ILE I 117 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CB VAL A 389 " pdb=" CA VAL A 389 " pdb=" CG1 VAL A 389 " pdb=" CG2 VAL A 389 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CG LEU A 402 " pdb=" CB LEU A 402 " pdb=" CD1 LEU A 402 " pdb=" CD2 LEU A 402 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 5741 not shown) Planarity restraints: 6194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 183 " -0.017 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP I 183 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP I 183 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP I 183 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 183 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP I 183 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 183 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 183 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 183 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 183 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 10 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LYS H 10 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS H 10 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO H 11 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 626 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C VAL A 626 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL A 626 " 0.022 2.00e-02 2.50e+03 pdb=" N CYS A 627 " 0.019 2.00e-02 2.50e+03 ... (remaining 6191 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 622 2.62 - 3.19: 31758 3.19 - 3.76: 60598 3.76 - 4.33: 79502 4.33 - 4.90: 124441 Nonbonded interactions: 296921 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 2.054 2.170 nonbonded pdb=" O SER J 210 " pdb=" CB ARG J 214 " model vdw 2.070 3.440 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.079 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.100 2.170 nonbonded pdb=" CG1 VAL A 786 " pdb=" CB ALA A 910 " model vdw 2.107 3.880 ... (remaining 296916 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 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 190 or (resid 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.950 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 117.650 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.160 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.149 36873 Z= 0.510 Angle : 1.196 12.664 50356 Z= 0.674 Chirality : 0.064 0.497 5744 Planarity : 0.007 0.077 6194 Dihedral : 17.062 179.114 14293 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.76 % Favored : 91.87 % Rotamer: Outliers : 0.25 % Allowed : 0.86 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -2.72 (0.11), residues: 4294 helix: -1.64 (0.12), residues: 1474 sheet: -0.99 (0.22), residues: 580 loop : -2.15 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP I 183 HIS 0.012 0.003 HIS A 842 PHE 0.037 0.003 PHE A1138 TYR 0.049 0.003 TYR A 150 ARG 0.024 0.002 ARG I 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 497 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8612 (mm) cc_final: 0.8379 (tp) REVERT: A 315 LEU cc_start: 0.7371 (pt) cc_final: 0.7032 (pt) REVERT: A 622 MET cc_start: 0.5991 (mpp) cc_final: 0.5239 (mmt) REVERT: A 745 MET cc_start: 0.5189 (ttt) cc_final: 0.4548 (tpp) REVERT: H 84 ASN cc_start: 0.8560 (m110) cc_final: 0.8154 (m110) REVERT: H 185 TYR cc_start: 0.8779 (p90) cc_final: 0.8071 (p90) REVERT: I 524 ILE cc_start: 0.9574 (tp) cc_final: 0.9270 (tp) REVERT: I 1230 MET cc_start: 0.7880 (ttt) cc_final: 0.7430 (ttt) REVERT: I 1285 TYR cc_start: 0.8559 (m-80) cc_final: 0.8281 (m-80) REVERT: J 29 MET cc_start: 0.7971 (tpt) cc_final: 0.7570 (tpp) REVERT: J 180 MET cc_start: 0.7339 (mpp) cc_final: 0.7058 (mpp) REVERT: J 259 ARG cc_start: 0.5433 (mtm180) cc_final: 0.5017 (mtp180) REVERT: J 264 ASP cc_start: 0.7550 (t0) cc_final: 0.7263 (t0) REVERT: J 479 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7038 (mt-10) REVERT: J 505 ASP cc_start: 0.7603 (t0) cc_final: 0.7007 (t0) REVERT: J 512 TYR cc_start: 0.8464 (t80) cc_final: 0.7894 (t80) REVERT: J 582 ILE cc_start: 0.8924 (mm) cc_final: 0.8591 (tt) REVERT: J 698 MET cc_start: 0.9039 (mmm) cc_final: 0.8701 (mmm) REVERT: J 707 ILE cc_start: 0.8261 (pt) cc_final: 0.8031 (tp) REVERT: J 772 TYR cc_start: 0.9006 (t80) cc_final: 0.8511 (t80) REVERT: J 921 GLN cc_start: 0.8808 (mt0) cc_final: 0.8374 (mt0) REVERT: K 31 GLN cc_start: 0.8357 (tt0) cc_final: 0.8136 (tt0) REVERT: K 32 VAL cc_start: 0.7992 (t) cc_final: 0.7744 (p) outliers start: 9 outliers final: 2 residues processed: 504 average time/residue: 0.4761 time to fit residues: 391.5302 Evaluate side-chains 378 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 376 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 1170 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 369 optimal weight: 20.0000 chunk 331 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 223 optimal weight: 0.4980 chunk 176 optimal weight: 8.9990 chunk 342 optimal weight: 4.9990 chunk 132 optimal weight: 0.2980 chunk 208 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 396 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1021 ASN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN I 462 ASN I 517 GLN ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1070 HIS J 477 GLN J 861 ASN J 875 ASN J 962 ASN J1350 ASN K 62 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36873 Z= 0.183 Angle : 0.658 11.889 50356 Z= 0.342 Chirality : 0.043 0.165 5744 Planarity : 0.005 0.060 6194 Dihedral : 16.245 178.429 5991 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 1.33 % Allowed : 9.38 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -2.04 (0.12), residues: 4294 helix: -0.73 (0.13), residues: 1486 sheet: -1.03 (0.21), residues: 589 loop : -1.88 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J1193 HIS 0.006 0.001 HIS A 485 PHE 0.020 0.002 PHE A1138 TYR 0.028 0.001 TYR G 185 ARG 0.010 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 446 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8561 (mm) cc_final: 0.8319 (tp) REVERT: A 203 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7699 (mm) REVERT: A 361 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5600 (mt) REVERT: A 426 MET cc_start: 0.4846 (tpt) cc_final: 0.4638 (tpp) REVERT: A 622 MET cc_start: 0.6182 (mpp) cc_final: 0.5236 (mmt) REVERT: A 858 HIS cc_start: 0.5408 (OUTLIER) cc_final: 0.5063 (t-90) REVERT: G 75 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6803 (pp30) REVERT: H 185 TYR cc_start: 0.8676 (p90) cc_final: 0.8133 (p90) REVERT: H 186 ASN cc_start: 0.8015 (t0) cc_final: 0.7795 (t0) REVERT: I 386 GLU cc_start: 0.6056 (mp0) cc_final: 0.5809 (mp0) REVERT: I 516 ASP cc_start: 0.7713 (m-30) cc_final: 0.7481 (m-30) REVERT: I 524 ILE cc_start: 0.9572 (tp) cc_final: 0.9228 (tp) REVERT: I 653 MET cc_start: 0.6032 (ttp) cc_final: 0.5637 (ptm) REVERT: I 671 LEU cc_start: 0.9591 (tp) cc_final: 0.9374 (tp) REVERT: I 1109 ILE cc_start: 0.9265 (mm) cc_final: 0.8808 (mm) REVERT: I 1230 MET cc_start: 0.7805 (ttt) cc_final: 0.7366 (ttt) REVERT: I 1328 LYS cc_start: 0.8829 (mppt) cc_final: 0.8586 (mppt) REVERT: J 29 MET cc_start: 0.7922 (tpt) cc_final: 0.7530 (tpp) REVERT: J 47 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7342 (ptm160) REVERT: J 48 THR cc_start: 0.7741 (p) cc_final: 0.7375 (p) REVERT: J 320 ASN cc_start: 0.8267 (t0) cc_final: 0.8030 (t0) REVERT: J 479 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6921 (mt-10) REVERT: J 512 TYR cc_start: 0.8402 (t80) cc_final: 0.7890 (t80) REVERT: J 707 ILE cc_start: 0.8269 (pt) cc_final: 0.7979 (tp) REVERT: J 725 MET cc_start: 0.8703 (mtm) cc_final: 0.8474 (mtm) REVERT: J 802 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7768 (t0) REVERT: J 921 GLN cc_start: 0.8656 (mt0) cc_final: 0.8240 (mt0) REVERT: K 30 MET cc_start: 0.8309 (tmm) cc_final: 0.7870 (tmm) REVERT: K 31 GLN cc_start: 0.8389 (tt0) cc_final: 0.8140 (tp40) REVERT: K 52 ARG cc_start: 0.7500 (ptp90) cc_final: 0.6995 (ptt180) outliers start: 48 outliers final: 31 residues processed: 474 average time/residue: 0.4748 time to fit residues: 369.2359 Evaluate side-chains 412 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 375 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 220 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 397 optimal weight: 0.0010 chunk 429 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 394 optimal weight: 0.2980 chunk 135 optimal weight: 9.9990 chunk 318 optimal weight: 7.9990 overall best weight: 2.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 85 GLN A 111 ASN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 462 ASN I 551 HIS I 725 GLN ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1017 GLN J 477 GLN J1350 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 36873 Z= 0.238 Angle : 0.644 11.502 50356 Z= 0.335 Chirality : 0.043 0.157 5744 Planarity : 0.004 0.060 6194 Dihedral : 16.079 177.923 5986 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 1.91 % Allowed : 13.23 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4294 helix: -0.43 (0.13), residues: 1490 sheet: -0.98 (0.21), residues: 606 loop : -1.81 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J1193 HIS 0.011 0.001 HIS I 551 PHE 0.023 0.001 PHE A1138 TYR 0.022 0.002 TYR H 177 ARG 0.005 0.000 ARG J 709 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 377 time to evaluate : 5.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8617 (mm) cc_final: 0.8336 (tp) REVERT: A 203 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7628 (mm) REVERT: A 361 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5651 (mt) REVERT: A 426 MET cc_start: 0.5193 (tpt) cc_final: 0.4967 (tpp) REVERT: A 858 HIS cc_start: 0.5375 (OUTLIER) cc_final: 0.5158 (t-90) REVERT: A 959 LEU cc_start: 0.6635 (tp) cc_final: 0.5976 (tp) REVERT: H 177 TYR cc_start: 0.8690 (m-80) cc_final: 0.7992 (m-80) REVERT: H 185 TYR cc_start: 0.8726 (p90) cc_final: 0.8208 (p90) REVERT: I 386 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.4873 (mp0) REVERT: I 462 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7928 (m110) REVERT: I 524 ILE cc_start: 0.9573 (tp) cc_final: 0.9219 (tp) REVERT: I 686 GLN cc_start: 0.9345 (mm110) cc_final: 0.8767 (mm-40) REVERT: I 781 ASP cc_start: 0.7216 (t0) cc_final: 0.6919 (t0) REVERT: I 1230 MET cc_start: 0.7838 (ttt) cc_final: 0.7364 (ttt) REVERT: I 1326 LEU cc_start: 0.9453 (tp) cc_final: 0.9252 (tp) REVERT: I 1328 LYS cc_start: 0.8837 (mppt) cc_final: 0.8541 (mppt) REVERT: J 29 MET cc_start: 0.7930 (tpt) cc_final: 0.7440 (tpp) REVERT: J 320 ASN cc_start: 0.8246 (t0) cc_final: 0.8046 (t0) REVERT: J 479 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6896 (mt-10) REVERT: J 512 TYR cc_start: 0.8498 (t80) cc_final: 0.7814 (t80) REVERT: J 725 MET cc_start: 0.8818 (mtm) cc_final: 0.8575 (mtp) REVERT: J 921 GLN cc_start: 0.8788 (mt0) cc_final: 0.8301 (mt0) REVERT: K 30 MET cc_start: 0.8358 (tmm) cc_final: 0.7799 (tmm) REVERT: K 31 GLN cc_start: 0.8377 (tt0) cc_final: 0.8084 (tp40) REVERT: K 52 ARG cc_start: 0.7706 (ptp90) cc_final: 0.7167 (ptp-170) REVERT: K 54 ILE cc_start: 0.8629 (mm) cc_final: 0.8349 (tp) outliers start: 69 outliers final: 47 residues processed: 416 average time/residue: 0.4509 time to fit residues: 312.6695 Evaluate side-chains 405 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 353 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1243 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 392 optimal weight: 30.0000 chunk 298 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 398 optimal weight: 1.9990 chunk 422 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 378 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 462 ASN ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1350 ASN J1367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36873 Z= 0.206 Angle : 0.613 11.821 50356 Z= 0.317 Chirality : 0.042 0.189 5744 Planarity : 0.004 0.056 6194 Dihedral : 15.969 177.465 5986 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.53 % Rotamer: Outliers : 2.24 % Allowed : 15.33 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4294 helix: -0.17 (0.13), residues: 1479 sheet: -0.85 (0.21), residues: 616 loop : -1.73 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J1193 HIS 0.004 0.001 HIS A 485 PHE 0.025 0.001 PHE A 972 TYR 0.018 0.001 TYR A 975 ARG 0.005 0.000 ARG J1194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 372 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 HIS cc_start: 0.6531 (t70) cc_final: 0.5779 (t70) REVERT: A 92 LEU cc_start: 0.8597 (mm) cc_final: 0.8333 (tp) REVERT: A 203 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7647 (mm) REVERT: A 361 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5697 (mt) REVERT: A 858 HIS cc_start: 0.5383 (OUTLIER) cc_final: 0.5094 (t-90) REVERT: A 959 LEU cc_start: 0.6112 (tp) cc_final: 0.5825 (tp) REVERT: H 177 TYR cc_start: 0.8656 (m-80) cc_final: 0.8155 (m-80) REVERT: H 185 TYR cc_start: 0.8692 (p90) cc_final: 0.8246 (p90) REVERT: I 386 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5009 (mp0) REVERT: I 459 MET cc_start: 0.8552 (mpp) cc_final: 0.8201 (mpp) REVERT: I 524 ILE cc_start: 0.9583 (tp) cc_final: 0.9210 (tp) REVERT: I 562 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: I 781 ASP cc_start: 0.7211 (t0) cc_final: 0.6885 (t0) REVERT: I 1230 MET cc_start: 0.7856 (ttt) cc_final: 0.7367 (ttt) REVERT: I 1328 LYS cc_start: 0.8807 (mppt) cc_final: 0.8436 (mmmt) REVERT: J 29 MET cc_start: 0.7913 (tpt) cc_final: 0.7382 (tpp) REVERT: J 180 MET cc_start: 0.6248 (mpp) cc_final: 0.5713 (mpp) REVERT: J 298 MET cc_start: 0.8437 (ppp) cc_final: 0.8155 (tmm) REVERT: J 308 ASP cc_start: 0.8285 (t0) cc_final: 0.8005 (t0) REVERT: J 479 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6957 (mt-10) REVERT: J 512 TYR cc_start: 0.8525 (t80) cc_final: 0.7967 (t80) REVERT: J 725 MET cc_start: 0.8841 (mtm) cc_final: 0.8589 (mtp) REVERT: J 921 GLN cc_start: 0.8770 (mt0) cc_final: 0.8278 (mt0) REVERT: J 1327 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: K 30 MET cc_start: 0.8429 (tmm) cc_final: 0.7822 (tmm) REVERT: K 31 GLN cc_start: 0.8298 (tt0) cc_final: 0.7935 (tp40) REVERT: K 52 ARG cc_start: 0.7702 (ptp90) cc_final: 0.7121 (ptp-170) REVERT: K 54 ILE cc_start: 0.8638 (mm) cc_final: 0.8372 (tp) outliers start: 81 outliers final: 54 residues processed: 416 average time/residue: 0.4530 time to fit residues: 315.5486 Evaluate side-chains 408 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 348 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1243 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 379 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS A 748 ASN A1071 GLN ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 462 ASN I 686 GLN I 832 HIS J 488 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36873 Z= 0.296 Angle : 0.658 13.096 50356 Z= 0.339 Chirality : 0.043 0.213 5744 Planarity : 0.004 0.062 6194 Dihedral : 15.981 176.129 5986 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 2.96 % Allowed : 16.63 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4294 helix: -0.06 (0.13), residues: 1466 sheet: -0.89 (0.21), residues: 603 loop : -1.72 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 868 HIS 0.007 0.001 HIS A 711 PHE 0.029 0.002 PHE A1138 TYR 0.019 0.002 TYR I1305 ARG 0.005 0.001 ARG J1194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 364 time to evaluate : 4.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8539 (mm) cc_final: 0.8285 (tp) REVERT: A 361 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.5983 (mt) REVERT: A 858 HIS cc_start: 0.5756 (OUTLIER) cc_final: 0.5299 (t-90) REVERT: H 177 TYR cc_start: 0.8621 (m-80) cc_final: 0.7957 (m-80) REVERT: H 185 TYR cc_start: 0.8841 (p90) cc_final: 0.8351 (p90) REVERT: H 193 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: I 272 ARG cc_start: 0.7997 (ptt180) cc_final: 0.7696 (ptp90) REVERT: I 386 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.4937 (mp0) REVERT: I 462 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8009 (m110) REVERT: I 524 ILE cc_start: 0.9609 (tp) cc_final: 0.9239 (tp) REVERT: I 781 ASP cc_start: 0.7368 (t0) cc_final: 0.7073 (t0) REVERT: I 1230 MET cc_start: 0.7853 (ttt) cc_final: 0.7242 (ttt) REVERT: I 1328 LYS cc_start: 0.8909 (mppt) cc_final: 0.8627 (mppt) REVERT: J 29 MET cc_start: 0.8040 (tpt) cc_final: 0.7473 (tpp) REVERT: J 151 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6025 (tmm) REVERT: J 180 MET cc_start: 0.6271 (mpp) cc_final: 0.6035 (mpp) REVERT: J 297 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7827 (ttp80) REVERT: J 400 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7997 (ttm) REVERT: J 512 TYR cc_start: 0.8677 (t80) cc_final: 0.8168 (t80) REVERT: J 725 MET cc_start: 0.8872 (mtm) cc_final: 0.8607 (mtp) REVERT: J 772 TYR cc_start: 0.8956 (t80) cc_final: 0.8741 (t80) REVERT: J 781 LYS cc_start: 0.9129 (tppt) cc_final: 0.8826 (tppt) REVERT: J 921 GLN cc_start: 0.8854 (mt0) cc_final: 0.8592 (mt0) REVERT: J 1327 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: K 30 MET cc_start: 0.8367 (tmm) cc_final: 0.7793 (tmm) REVERT: K 31 GLN cc_start: 0.8226 (tt0) cc_final: 0.7900 (tt0) REVERT: K 52 ARG cc_start: 0.7762 (ptp90) cc_final: 0.7408 (ptp-170) REVERT: K 54 ILE cc_start: 0.8691 (mm) cc_final: 0.8479 (tp) outliers start: 107 outliers final: 66 residues processed: 431 average time/residue: 0.4555 time to fit residues: 328.7260 Evaluate side-chains 422 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 348 time to evaluate : 4.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1217 THR Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 699 ASP Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 142 optimal weight: 0.9990 chunk 380 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 422 optimal weight: 9.9990 chunk 350 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 HIS ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN J1098 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 36873 Z= 0.424 Angle : 0.758 12.257 50356 Z= 0.392 Chirality : 0.046 0.210 5744 Planarity : 0.005 0.066 6194 Dihedral : 16.175 175.416 5986 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 27.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.38 % Favored : 91.57 % Rotamer: Outliers : 3.65 % Allowed : 18.48 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.12), residues: 4294 helix: -0.37 (0.13), residues: 1472 sheet: -1.13 (0.20), residues: 615 loop : -1.84 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 231 HIS 0.011 0.002 HIS A 711 PHE 0.034 0.002 PHE A1138 TYR 0.030 0.002 TYR I1305 ARG 0.012 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 354 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8587 (mm) cc_final: 0.8355 (tp) REVERT: A 157 MET cc_start: 0.7495 (mmm) cc_final: 0.7004 (mmm) REVERT: A 311 MET cc_start: 0.8329 (tpt) cc_final: 0.7954 (tpp) REVERT: A 361 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5745 (mt) REVERT: A 858 HIS cc_start: 0.6300 (OUTLIER) cc_final: 0.6060 (t-90) REVERT: H 193 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: I 71 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8624 (t) REVERT: I 272 ARG cc_start: 0.7948 (ptt180) cc_final: 0.7688 (ptp90) REVERT: I 315 MET cc_start: 0.9005 (tpp) cc_final: 0.8562 (tmm) REVERT: I 386 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.4777 (mp0) REVERT: I 524 ILE cc_start: 0.9602 (tp) cc_final: 0.9209 (tp) REVERT: I 545 PHE cc_start: 0.7518 (m-80) cc_final: 0.7304 (m-80) REVERT: I 1230 MET cc_start: 0.7889 (ttt) cc_final: 0.7177 (ttt) REVERT: I 1329 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: J 29 MET cc_start: 0.8152 (tpt) cc_final: 0.7540 (tpp) REVERT: J 151 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6099 (tmm) REVERT: J 180 MET cc_start: 0.6360 (mpp) cc_final: 0.6020 (mpp) REVERT: J 297 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7808 (ttp80) REVERT: J 298 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8447 (tmm) REVERT: J 400 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8006 (ttm) REVERT: J 512 TYR cc_start: 0.8850 (t80) cc_final: 0.8410 (t80) REVERT: J 725 MET cc_start: 0.8978 (mtm) cc_final: 0.8724 (mtm) REVERT: J 781 LYS cc_start: 0.9099 (tppt) cc_final: 0.8746 (tppt) REVERT: J 921 GLN cc_start: 0.8915 (mt0) cc_final: 0.8538 (mt0) REVERT: J 1327 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: K 30 MET cc_start: 0.8424 (tmm) cc_final: 0.7821 (tmm) REVERT: K 31 GLN cc_start: 0.8339 (tt0) cc_final: 0.8004 (tt0) REVERT: K 54 ILE cc_start: 0.8706 (mm) cc_final: 0.8483 (tp) outliers start: 132 outliers final: 87 residues processed: 443 average time/residue: 0.4666 time to fit residues: 345.0345 Evaluate side-chains 432 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 335 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1217 THR Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 699 ASP Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 407 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 308 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 355 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 421 optimal weight: 0.0770 chunk 263 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36873 Z= 0.177 Angle : 0.642 12.407 50356 Z= 0.324 Chirality : 0.043 0.280 5744 Planarity : 0.004 0.061 6194 Dihedral : 15.975 176.643 5986 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.57 % Favored : 93.41 % Rotamer: Outliers : 2.43 % Allowed : 20.59 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 4294 helix: 0.01 (0.13), residues: 1463 sheet: -0.89 (0.21), residues: 603 loop : -1.68 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 231 HIS 0.016 0.001 HIS A 159 PHE 0.021 0.002 PHE A 172 TYR 0.017 0.001 TYR G 185 ARG 0.013 0.000 ARG I1069 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 386 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8592 (mm) cc_final: 0.8350 (tp) REVERT: A 361 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6168 (mt) REVERT: A 410 GLN cc_start: 0.6398 (mm-40) cc_final: 0.6146 (mm-40) REVERT: A 423 ARG cc_start: 0.6983 (mmt180) cc_final: 0.6753 (mmp80) REVERT: A 745 MET cc_start: 0.5464 (mtt) cc_final: 0.4898 (mtt) REVERT: G 32 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: H 177 TYR cc_start: 0.8629 (m-80) cc_final: 0.7979 (m-80) REVERT: H 185 TYR cc_start: 0.8658 (p90) cc_final: 0.8186 (p90) REVERT: H 193 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: I 130 MET cc_start: 0.9085 (ttm) cc_final: 0.8610 (ttm) REVERT: I 272 ARG cc_start: 0.7910 (ptt180) cc_final: 0.7605 (ptp90) REVERT: I 386 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4951 (mp0) REVERT: I 459 MET cc_start: 0.8376 (mpp) cc_final: 0.8062 (mpp) REVERT: I 524 ILE cc_start: 0.9574 (tp) cc_final: 0.9149 (tp) REVERT: I 653 MET cc_start: 0.6121 (ttp) cc_final: 0.5492 (ptm) REVERT: I 1230 MET cc_start: 0.7779 (ttt) cc_final: 0.7076 (ttt) REVERT: I 1328 LYS cc_start: 0.8769 (mppt) cc_final: 0.8500 (mppt) REVERT: J 29 MET cc_start: 0.7952 (tpt) cc_final: 0.7421 (tpp) REVERT: J 180 MET cc_start: 0.6139 (mpp) cc_final: 0.5815 (mpp) REVERT: J 297 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7719 (ttp80) REVERT: J 424 ASN cc_start: 0.8850 (t0) cc_final: 0.8227 (p0) REVERT: J 479 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7222 (mt-10) REVERT: J 512 TYR cc_start: 0.8621 (t80) cc_final: 0.8036 (t80) REVERT: J 544 LEU cc_start: 0.9167 (tp) cc_final: 0.8811 (tp) REVERT: J 725 MET cc_start: 0.8888 (mtm) cc_final: 0.8653 (mtm) REVERT: J 781 LYS cc_start: 0.9097 (tppt) cc_final: 0.8857 (tppt) REVERT: J 921 GLN cc_start: 0.8729 (mt0) cc_final: 0.8409 (mt0) REVERT: K 30 MET cc_start: 0.8233 (tmm) cc_final: 0.7770 (tmm) REVERT: K 31 GLN cc_start: 0.8255 (tt0) cc_final: 0.7909 (tt0) outliers start: 88 outliers final: 63 residues processed: 442 average time/residue: 0.4619 time to fit residues: 341.1469 Evaluate side-chains 426 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 359 time to evaluate : 4.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 260 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN J1350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36873 Z= 0.186 Angle : 0.627 11.693 50356 Z= 0.318 Chirality : 0.043 0.217 5744 Planarity : 0.004 0.052 6194 Dihedral : 15.843 175.607 5986 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 2.57 % Allowed : 20.97 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4294 helix: 0.12 (0.13), residues: 1471 sheet: -0.84 (0.22), residues: 590 loop : -1.67 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP J1193 HIS 0.012 0.001 HIS A 159 PHE 0.034 0.001 PHE A 972 TYR 0.016 0.001 TYR A 814 ARG 0.008 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 381 time to evaluate : 4.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8557 (mm) cc_final: 0.8343 (tp) REVERT: A 157 MET cc_start: 0.7036 (mmm) cc_final: 0.6603 (mmm) REVERT: A 174 MET cc_start: 0.3945 (mmt) cc_final: 0.2734 (mpp) REVERT: A 361 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6144 (mt) REVERT: A 410 GLN cc_start: 0.6266 (mm-40) cc_final: 0.5968 (mm-40) REVERT: A 423 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6703 (mmp80) REVERT: A 858 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.5198 (t-90) REVERT: G 32 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: H 185 TYR cc_start: 0.8659 (p90) cc_final: 0.8180 (p90) REVERT: H 193 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: I 130 MET cc_start: 0.9080 (ttm) cc_final: 0.8563 (ttm) REVERT: I 386 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.4926 (mp0) REVERT: I 524 ILE cc_start: 0.9583 (tp) cc_final: 0.9144 (tp) REVERT: I 653 MET cc_start: 0.6030 (ttp) cc_final: 0.5445 (ptm) REVERT: I 1114 GLU cc_start: 0.8974 (tt0) cc_final: 0.8484 (tt0) REVERT: I 1219 GLU cc_start: 0.7628 (tp30) cc_final: 0.7396 (tp30) REVERT: I 1230 MET cc_start: 0.7775 (ttt) cc_final: 0.7122 (ttt) REVERT: I 1328 LYS cc_start: 0.8809 (mppt) cc_final: 0.8585 (mmmt) REVERT: J 29 MET cc_start: 0.7884 (tpt) cc_final: 0.7311 (tpp) REVERT: J 180 MET cc_start: 0.6004 (mpp) cc_final: 0.5669 (mpp) REVERT: J 297 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7876 (ttp80) REVERT: J 304 ASP cc_start: 0.8214 (t70) cc_final: 0.7983 (t70) REVERT: J 479 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6972 (mt-10) REVERT: J 512 TYR cc_start: 0.8640 (t80) cc_final: 0.7892 (t80) REVERT: J 544 LEU cc_start: 0.9138 (tp) cc_final: 0.8836 (tp) REVERT: J 725 MET cc_start: 0.8892 (mtm) cc_final: 0.8657 (mtm) REVERT: J 921 GLN cc_start: 0.8688 (mt0) cc_final: 0.8440 (mt0) REVERT: J 1048 ARG cc_start: 0.6660 (tpt170) cc_final: 0.5807 (tpt90) REVERT: K 30 MET cc_start: 0.8315 (tmm) cc_final: 0.8085 (tmm) REVERT: K 31 GLN cc_start: 0.8255 (tt0) cc_final: 0.7993 (tt0) outliers start: 93 outliers final: 71 residues processed: 441 average time/residue: 0.4572 time to fit residues: 335.3812 Evaluate side-chains 428 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 352 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 383 optimal weight: 20.0000 chunk 403 optimal weight: 10.0000 chunk 368 optimal weight: 1.9990 chunk 392 optimal weight: 30.0000 chunk 236 optimal weight: 7.9990 chunk 170 optimal weight: 0.2980 chunk 308 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 354 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 391 optimal weight: 0.7980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 462 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN J 488 ASN J1350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36873 Z= 0.224 Angle : 0.645 13.292 50356 Z= 0.326 Chirality : 0.043 0.224 5744 Planarity : 0.004 0.054 6194 Dihedral : 15.816 174.850 5986 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.85 % Favored : 93.13 % Rotamer: Outliers : 2.60 % Allowed : 21.36 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 4294 helix: 0.16 (0.14), residues: 1475 sheet: -0.89 (0.21), residues: 611 loop : -1.67 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J1193 HIS 0.011 0.001 HIS A 159 PHE 0.022 0.001 PHE A1138 TYR 0.015 0.001 TYR J 772 ARG 0.009 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 359 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.4038 (mmt) cc_final: 0.2831 (mpp) REVERT: A 311 MET cc_start: 0.7750 (tpt) cc_final: 0.7543 (tpp) REVERT: A 361 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6304 (mt) REVERT: A 410 GLN cc_start: 0.6367 (mm-40) cc_final: 0.6080 (mm110) REVERT: A 802 ILE cc_start: 0.8101 (mt) cc_final: 0.7850 (mm) REVERT: G 32 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: H 185 TYR cc_start: 0.8754 (p90) cc_final: 0.8227 (p90) REVERT: H 193 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: I 130 MET cc_start: 0.9109 (ttm) cc_final: 0.8601 (ttm) REVERT: I 386 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.4937 (mp0) REVERT: I 459 MET cc_start: 0.8422 (mpp) cc_final: 0.8168 (mpp) REVERT: I 524 ILE cc_start: 0.9598 (tp) cc_final: 0.9174 (tp) REVERT: I 653 MET cc_start: 0.6103 (ttp) cc_final: 0.5541 (ptm) REVERT: I 1114 GLU cc_start: 0.8977 (tt0) cc_final: 0.8695 (tt0) REVERT: I 1219 GLU cc_start: 0.7581 (tp30) cc_final: 0.7283 (tp30) REVERT: I 1230 MET cc_start: 0.7772 (ttt) cc_final: 0.7166 (ttt) REVERT: I 1328 LYS cc_start: 0.8873 (mppt) cc_final: 0.8558 (mmmt) REVERT: J 29 MET cc_start: 0.7924 (tpt) cc_final: 0.7335 (tpp) REVERT: J 180 MET cc_start: 0.6023 (mpp) cc_final: 0.5668 (mpp) REVERT: J 297 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7932 (ttp80) REVERT: J 304 ASP cc_start: 0.8208 (t70) cc_final: 0.7961 (t70) REVERT: J 479 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6950 (mt-10) REVERT: J 512 TYR cc_start: 0.8624 (t80) cc_final: 0.7787 (t80) REVERT: J 725 MET cc_start: 0.8915 (mtm) cc_final: 0.8668 (mtm) REVERT: J 921 GLN cc_start: 0.8787 (mt0) cc_final: 0.8487 (mt0) REVERT: J 1048 ARG cc_start: 0.6697 (tpt170) cc_final: 0.5795 (tpt90) REVERT: K 30 MET cc_start: 0.8324 (tmm) cc_final: 0.8094 (tmm) REVERT: K 31 GLN cc_start: 0.8259 (tt0) cc_final: 0.7986 (tt0) REVERT: K 69 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7205 (mtm110) outliers start: 94 outliers final: 81 residues processed: 420 average time/residue: 0.4643 time to fit residues: 328.5048 Evaluate side-chains 433 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 348 time to evaluate : 4.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 257 optimal weight: 4.9990 chunk 415 optimal weight: 0.0040 chunk 253 optimal weight: 0.4980 chunk 196 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 chunk 346 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN ** J 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36873 Z= 0.191 Angle : 0.640 13.480 50356 Z= 0.321 Chirality : 0.042 0.205 5744 Planarity : 0.004 0.051 6194 Dihedral : 15.746 175.833 5986 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 2.27 % Allowed : 21.78 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4294 helix: 0.24 (0.14), residues: 1470 sheet: -0.86 (0.21), residues: 606 loop : -1.62 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J1193 HIS 0.009 0.001 HIS A 159 PHE 0.037 0.001 PHE A 972 TYR 0.016 0.001 TYR A 814 ARG 0.014 0.000 ARG A 741 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 386 time to evaluate : 4.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.4141 (mmt) cc_final: 0.3025 (mpp) REVERT: A 410 GLN cc_start: 0.6334 (mm-40) cc_final: 0.6032 (mm110) REVERT: A 509 LEU cc_start: 0.7715 (mm) cc_final: 0.6842 (mm) REVERT: G 32 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: H 147 GLN cc_start: 0.8429 (mt0) cc_final: 0.8095 (mt0) REVERT: H 185 TYR cc_start: 0.8713 (p90) cc_final: 0.8189 (p90) REVERT: H 193 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: I 130 MET cc_start: 0.9112 (ttm) cc_final: 0.8586 (ttm) REVERT: I 386 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.4913 (mp0) REVERT: I 524 ILE cc_start: 0.9596 (tp) cc_final: 0.9161 (tp) REVERT: I 653 MET cc_start: 0.6076 (ttp) cc_final: 0.5530 (ptm) REVERT: I 1072 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7483 (t0) REVERT: I 1114 GLU cc_start: 0.8942 (tt0) cc_final: 0.8631 (tt0) REVERT: I 1219 GLU cc_start: 0.7495 (tp30) cc_final: 0.7082 (tp30) REVERT: I 1230 MET cc_start: 0.7758 (ttt) cc_final: 0.7277 (ttt) REVERT: I 1328 LYS cc_start: 0.8797 (mppt) cc_final: 0.8583 (mmmt) REVERT: J 29 MET cc_start: 0.7868 (tpt) cc_final: 0.7271 (tpp) REVERT: J 180 MET cc_start: 0.5965 (mpp) cc_final: 0.5614 (mpp) REVERT: J 297 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7951 (ttp80) REVERT: J 304 ASP cc_start: 0.8126 (t70) cc_final: 0.7906 (t70) REVERT: J 479 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6957 (mt-10) REVERT: J 512 TYR cc_start: 0.8579 (t80) cc_final: 0.8005 (t80) REVERT: J 725 MET cc_start: 0.8869 (mtm) cc_final: 0.8627 (mtm) REVERT: J 921 GLN cc_start: 0.8735 (mt0) cc_final: 0.8436 (mt0) REVERT: J 1048 ARG cc_start: 0.6690 (tpt170) cc_final: 0.5789 (tpt90) REVERT: J 1095 MET cc_start: 0.6676 (mpp) cc_final: 0.6344 (ttt) REVERT: K 30 MET cc_start: 0.8302 (tmm) cc_final: 0.8065 (tmm) REVERT: K 31 GLN cc_start: 0.8203 (tt0) cc_final: 0.7974 (tt0) REVERT: K 69 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7223 (mtm110) outliers start: 82 outliers final: 73 residues processed: 439 average time/residue: 0.4576 time to fit residues: 334.9769 Evaluate side-chains 438 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 361 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 275 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 319 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 347 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN J1350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.103219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.085659 restraints weight = 155072.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087122 restraints weight = 101388.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.087482 restraints weight = 68880.798| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36873 Z= 0.305 Angle : 0.699 13.112 50356 Z= 0.355 Chirality : 0.044 0.260 5744 Planarity : 0.005 0.054 6194 Dihedral : 15.840 173.549 5986 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.59 % Favored : 92.36 % Rotamer: Outliers : 2.49 % Allowed : 21.86 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 4294 helix: 0.11 (0.14), residues: 1472 sheet: -0.94 (0.21), residues: 644 loop : -1.66 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J1193 HIS 0.014 0.002 HIS A 159 PHE 0.025 0.002 PHE A1138 TYR 0.031 0.002 TYR A 814 ARG 0.010 0.001 ARG A 741 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7112.22 seconds wall clock time: 131 minutes 4.64 seconds (7864.64 seconds total)