Starting phenix.real_space_refine on Sat Mar 23 07:52:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2n_22012/03_2024/6x2n_22012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2n_22012/03_2024/6x2n_22012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2n_22012/03_2024/6x2n_22012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2n_22012/03_2024/6x2n_22012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2n_22012/03_2024/6x2n_22012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2n_22012/03_2024/6x2n_22012_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.081 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 115 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 22308 2.51 5 N 6402 2.21 5 O 7110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 849": "OE1" <-> "OE2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I GLU 286": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I GLU 541": "OE1" <-> "OE2" Residue "I GLU 562": "OE1" <-> "OE2" Residue "I GLU 565": "OE1" <-> "OE2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I GLU 738": "OE1" <-> "OE2" Residue "I GLU 745": "OE1" <-> "OE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 1020": "OE1" <-> "OE2" Residue "I GLU 1026": "OE1" <-> "OE2" Residue "I GLU 1114": "OE1" <-> "OE2" Residue "I GLU 1168": "OE1" <-> "OE2" Residue "I GLU 1194": "OE1" <-> "OE2" Residue "I PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1321": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 207": "OE1" <-> "OE2" Residue "J GLU 375": "OE1" <-> "OE2" Residue "J GLU 443": "OE1" <-> "OE2" Residue "J GLU 562": "OE1" <-> "OE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J GLU 756": "OE1" <-> "OE2" Residue "J PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 925": "OE1" <-> "OE2" Residue "J GLU 1030": "OE1" <-> "OE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J GLU 1215": "OE1" <-> "OE2" Residue "J GLU 1254": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36079 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8951 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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 23160 SG CYS J 70 26.018 98.800 103.950 1.00156.22 S ATOM 23174 SG CYS J 72 25.542 102.314 102.985 1.00158.71 S ATOM 23282 SG CYS J 85 24.097 99.462 100.857 1.00148.19 S ATOM 23306 SG CYS J 88 27.680 99.944 100.646 1.00151.65 S ATOM 28982 SG CYS J 814 52.446 37.176 110.486 1.00114.64 S ATOM 29547 SG CYS J 888 52.836 39.793 109.324 1.00 90.94 S ATOM 29598 SG CYS J 895 52.659 39.553 112.068 1.00 91.36 S ATOM 29619 SG CYS J 898 54.816 37.963 111.582 1.00 92.44 S Time building chain proxies: 18.47, per 1000 atoms: 0.51 Number of scatterers: 36079 At special positions: 0 Unit cell: (137.8, 209.3, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 141 16.00 P 115 15.00 Mg 1 11.99 O 7110 8.00 N 6402 7.00 C 22308 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: 16.08 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " 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 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 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: 144 helices and 39 sheets defined 32.6% alpha, 11.2% beta 53 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 17.71 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 49 through 62 removed outlier: 3.706A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.753A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 257 through 260 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 291 through 305 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: 3.830A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.754A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (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 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' 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 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.555A pdb=" N ASP A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 648 removed outlier: 3.880A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.704A pdb=" N GLN A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 745 removed outlier: 4.963A pdb=" N ILE A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 766 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 821 through 832 removed outlier: 3.698A pdb=" N ARG A 828 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 831 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 858 Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 924 through 935 Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 972 through 989 removed outlier: 4.317A pdb=" N GLY A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 999 No H-bonds generated for 'chain 'A' and resid 996 through 999' Processing helix chain 'A' and resid 1020 through 1031 Processing helix chain 'A' and resid 1036 through 1050 Processing helix chain 'A' and resid 1055 through 1073 Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1128 through 1144 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 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 213 through 230 removed outlier: 4.868A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.768A pdb=" N ASN H 41 " --> pdb=" O HIS H 37 " (cutoff:3.500A) removed outlier: 3.580A 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 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 213 through 228 removed outlier: 3.624A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) 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 213 removed outlier: 3.695A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 223 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 289 through 292 Processing helix chain 'I' and resid 319 through 328 Processing helix chain 'I' and resid 346 through 353 removed outlier: 3.780A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.553A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) 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: 3.842A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 removed outlier: 4.189A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 526 Processing helix chain 'I' and resid 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 613 No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 677 through 688 removed outlier: 4.504A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 821 through 824 No H-bonds generated for 'chain 'I' and resid 821 through 824' Processing helix chain 'I' and resid 859 through 862 No H-bonds generated for 'chain 'I' and resid 859 through 862' Processing helix chain 'I' and resid 943 through 977 Processing helix chain 'I' and resid 988 through 991 No H-bonds generated for 'chain 'I' and resid 988 through 991' Processing helix chain 'I' and resid 1006 through 1036 removed outlier: 4.338A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1105 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1109 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1175 removed outlier: 3.529A pdb=" N ASN I1175 " --> pdb=" O ARG I1171 " (cutoff:3.500A) Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1280 removed outlier: 3.592A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 4.053A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 96 through 99 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 128 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.519A pdb=" N VAL J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 264 through 284 removed outlier: 3.723A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 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 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 408 through 415 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 483 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: 3.817A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 701 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: 3.916A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (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 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1069 through 1071 No H-bonds generated for 'chain 'J' and resid 1069 through 1071' Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1217 through 1224 removed outlier: 3.957A pdb=" N LEU J1221 " --> pdb=" O PRO J1217 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG J1222 " --> pdb=" O HIS J1218 " (cutoff:3.500A) Processing helix chain 'J' and resid 1226 through 1243 removed outlier: 4.216A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 removed outlier: 3.810A pdb=" N VAL J1255 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 Processing helix chain 'J' and resid 1311 through 1314 No H-bonds generated for 'chain 'J' and resid 1311 through 1314' Processing helix chain 'J' and resid 1328 through 1336 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 4.564A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 78 Processing sheet with id= A, first strand: chain 'A' and resid 350 through 352 removed outlier: 8.085A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG A 336 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU A 19 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN A 338 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN A 284 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL A 43 " --> pdb=" O VAL A 283 " (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 161 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 489 through 493 removed outlier: 3.962A pdb=" N GLN A 481 " --> pdb=" O TYR A 493 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 496 through 499 Processing sheet with id= G, first strand: chain 'A' and resid 623 through 625 removed outlier: 7.374A pdb=" N ILE A 751 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 707 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 787 through 792 removed outlier: 3.633A pdb=" N ILE A 883 " --> pdb=" O TYR A 911 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id= J, first strand: chain 'G' and resid 12 through 15 removed outlier: 6.579A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 97 through 104 removed outlier: 5.541A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.639A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 15 through 18 removed outlier: 3.686A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.966A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.680A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= Q, first strand: chain 'I' and resid 116 through 123 removed outlier: 3.881A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= S, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.933A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 332 through 336 removed outlier: 3.959A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 529 through 531 Processing sheet with id= V, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= W, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= X, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.569A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 798 through 803 Processing sheet with id= Z, first strand: chain 'I' and resid 830 through 838 removed outlier: 3.762A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.739A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.261A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.681A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL J 244 " --> pdb=" O GLY J 103 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AE, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AF, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AG, first strand: chain 'J' and resid 958 through 961 Processing sheet with id= AH, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AI, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.514A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.988A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AL, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.649A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 949 through 952 removed outlier: 4.170A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 134 hydrogen bonds 260 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 17.38 Time building geometry restraints manager: 17.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7627 1.32 - 1.45: 8548 1.45 - 1.57: 20252 1.57 - 1.70: 224 1.70 - 1.82: 247 Bond restraints: 36898 Sorted by residual: bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.39e+01 bond pdb=" C CYS J 898 " pdb=" N TYR J 899 " ideal model delta sigma weight residual 1.334 1.232 0.102 1.30e-02 5.92e+03 6.13e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" CA PHE J 116 " pdb=" C PHE J 116 " ideal model delta sigma weight residual 1.522 1.439 0.083 1.37e-02 5.33e+03 3.70e+01 bond pdb=" C5 ATP A2000 " pdb=" N7 ATP A2000 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.36e+01 ... (remaining 36893 not shown) Histogram of bond angle deviations from ideal: 93.29 - 102.10: 260 102.10 - 110.90: 13356 110.90 - 119.71: 19602 119.71 - 128.52: 16875 128.52 - 137.33: 297 Bond angle restraints: 50390 Sorted by residual: angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 119.06 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" O CYS J 898 " pdb=" C CYS J 898 " pdb=" N TYR J 899 " ideal model delta sigma weight residual 122.22 137.33 -15.11 1.17e+00 7.31e-01 1.67e+02 angle pdb=" CA CYS J 898 " pdb=" C CYS J 898 " pdb=" N TYR J 899 " ideal model delta sigma weight residual 117.63 101.84 15.79 1.25e+00 6.40e-01 1.59e+02 angle pdb=" C CYS J 898 " pdb=" N TYR J 899 " pdb=" CA TYR J 899 " ideal model delta sigma weight residual 120.88 104.06 16.82 1.62e+00 3.81e-01 1.08e+02 ... (remaining 50385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 21362 34.14 - 68.28: 910 68.28 - 102.42: 69 102.42 - 136.56: 4 136.56 - 170.70: 2 Dihedral angle restraints: 22347 sinusoidal: 9918 harmonic: 12429 Sorted by residual: dihedral pdb=" CA SER I 512 " pdb=" C SER I 512 " pdb=" N GLN I 513 " pdb=" CA GLN I 513 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO A 310 " pdb=" C PRO A 310 " pdb=" N MET A 311 " pdb=" CA MET A 311 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER J 263 " pdb=" C SER J 263 " pdb=" N ASP J 264 " pdb=" CA ASP J 264 " ideal model delta harmonic sigma weight residual -180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 22344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5150 0.103 - 0.206: 541 0.206 - 0.309: 42 0.309 - 0.413: 9 0.413 - 0.516: 3 Chirality restraints: 5745 Sorted by residual: chirality pdb=" CA GLN J 504 " pdb=" N GLN J 504 " pdb=" C GLN J 504 " pdb=" CB GLN J 504 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CG LEU G 83 " pdb=" CB LEU G 83 " pdb=" CD1 LEU G 83 " pdb=" CD2 LEU G 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA SER J 503 " pdb=" N SER J 503 " pdb=" C SER J 503 " pdb=" CB SER J 503 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 5742 not shown) Planarity restraints: 6199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS J 814 " -0.041 2.00e-02 2.50e+03 7.78e-02 6.05e+01 pdb=" C CYS J 814 " 0.135 2.00e-02 2.50e+03 pdb=" O CYS J 814 " -0.049 2.00e-02 2.50e+03 pdb=" N GLY J 815 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 898 " -0.017 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C CYS J 898 " 0.077 2.00e-02 2.50e+03 pdb=" O CYS J 898 " -0.032 2.00e-02 2.50e+03 pdb=" N TYR J 899 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 128 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C LEU A 128 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 128 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL A 129 " 0.021 2.00e-02 2.50e+03 ... (remaining 6196 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 504 2.60 - 3.17: 30387 3.17 - 3.75: 59973 3.75 - 4.32: 79576 4.32 - 4.90: 125976 Nonbonded interactions: 296416 Sorted by model distance: nonbonded pdb=" O THR A 464 " pdb=" CG PRO A 467 " model vdw 2.024 3.440 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 2.031 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.056 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.084 2.170 nonbonded pdb=" CD2 LEU I1101 " pdb=" O GLN J 504 " model vdw 2.179 3.460 ... (remaining 296411 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 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.860 Check model and map are aligned: 0.550 Set scattering table: 0.290 Process input model: 112.130 Find NCS groups from input model: 1.830 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.009 0.142 36898 Z= 0.596 Angle : 1.208 21.339 50390 Z= 0.689 Chirality : 0.066 0.516 5745 Planarity : 0.007 0.088 6199 Dihedral : 17.593 170.696 14335 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.15 % Favored : 91.57 % Rotamer: Outliers : 0.28 % Allowed : 0.69 % Favored : 99.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.11), residues: 4294 helix: -1.65 (0.12), residues: 1470 sheet: -1.68 (0.21), residues: 561 loop : -2.16 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 913 HIS 0.024 0.003 HIS I1023 PHE 0.044 0.004 PHE I 514 TYR 0.037 0.003 TYR I 584 ARG 0.041 0.002 ARG A 902 *********************** 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 473 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 463 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.5842 (tpp) cc_final: 0.5301 (tpp) REVERT: A 157 MET cc_start: 0.5961 (tpt) cc_final: 0.5759 (pmm) REVERT: A 873 THR cc_start: 0.8051 (p) cc_final: 0.7776 (p) REVERT: H 147 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7134 (tm-30) REVERT: H 185 TYR cc_start: 0.9406 (p90) cc_final: 0.9194 (p90) REVERT: I 102 LEU cc_start: 0.8845 (tp) cc_final: 0.8543 (pt) REVERT: I 195 PHE cc_start: 0.7808 (m-80) cc_final: 0.7039 (m-80) REVERT: I 654 ASP cc_start: 0.8119 (m-30) cc_final: 0.7737 (m-30) REVERT: I 741 MET cc_start: 0.8151 (tpp) cc_final: 0.7890 (tpp) REVERT: I 964 LEU cc_start: 0.8171 (tp) cc_final: 0.7869 (mt) REVERT: I 1079 ILE cc_start: 0.9093 (mm) cc_final: 0.8857 (mm) REVERT: I 1143 GLU cc_start: 0.8595 (pp20) cc_final: 0.8300 (pp20) REVERT: I 1296 ASP cc_start: 0.8089 (t70) cc_final: 0.7562 (t0) REVERT: J 29 MET cc_start: 0.8171 (tpp) cc_final: 0.7852 (tpt) REVERT: J 46 TYR cc_start: 0.7068 (m-10) cc_final: 0.6657 (m-80) REVERT: J 724 MET cc_start: 0.9048 (mtm) cc_final: 0.8699 (mtm) REVERT: J 868 TRP cc_start: 0.8174 (m100) cc_final: 0.7303 (m100) REVERT: J 1143 ASP cc_start: 0.8358 (t0) cc_final: 0.8056 (t0) REVERT: J 1281 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8355 (mt-10) REVERT: K 3 ARG cc_start: 0.7267 (mmp80) cc_final: 0.6408 (mmm160) REVERT: K 44 ASP cc_start: 0.7598 (m-30) cc_final: 0.6724 (m-30) outliers start: 10 outliers final: 3 residues processed: 470 average time/residue: 0.4739 time to fit residues: 363.0481 Evaluate side-chains 354 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 351 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 1090 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 369 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 342 optimal weight: 8.9990 chunk 132 optimal weight: 0.0770 chunk 208 optimal weight: 0.6980 chunk 254 optimal weight: 0.3980 chunk 396 optimal weight: 7.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS A 715 GLN H 18 GLN H 186 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN J 495 ASN J1019 ASN K 62 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36898 Z= 0.177 Angle : 0.649 10.451 50390 Z= 0.339 Chirality : 0.044 0.226 5745 Planarity : 0.005 0.068 6199 Dihedral : 16.680 169.849 6018 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 1.24 % Allowed : 8.34 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 4294 helix: -0.61 (0.13), residues: 1495 sheet: -1.36 (0.21), residues: 554 loop : -1.97 (0.12), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J1193 HIS 0.009 0.001 HIS A 84 PHE 0.026 0.001 PHE I 514 TYR 0.015 0.001 TYR G 177 ARG 0.008 0.000 ARG A 771 *********************** 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 464 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 419 time to evaluate : 3.535 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 114 MET cc_start: 0.6399 (tpp) cc_final: 0.6040 (tpp) REVERT: A 157 MET cc_start: 0.6112 (tpt) cc_final: 0.5637 (pmm) REVERT: I 102 LEU cc_start: 0.8715 (tp) cc_final: 0.8484 (pt) REVERT: I 195 PHE cc_start: 0.7253 (m-80) cc_final: 0.6543 (m-80) REVERT: I 472 GLU cc_start: 0.8297 (pp20) cc_final: 0.8084 (pp20) REVERT: I 542 ARG cc_start: 0.7593 (mmp80) cc_final: 0.7313 (mtt-85) REVERT: I 654 ASP cc_start: 0.7994 (m-30) cc_final: 0.7618 (m-30) REVERT: I 741 MET cc_start: 0.8050 (tpp) cc_final: 0.7759 (tpp) REVERT: I 964 LEU cc_start: 0.8123 (tp) cc_final: 0.7861 (mt) REVERT: I 1079 ILE cc_start: 0.9032 (mm) cc_final: 0.8811 (mm) REVERT: I 1220 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8535 (tp40) REVERT: I 1243 MET cc_start: 0.8428 (tmm) cc_final: 0.8206 (ttp) REVERT: I 1296 ASP cc_start: 0.8182 (t70) cc_final: 0.7655 (t0) REVERT: J 140 TYR cc_start: 0.8640 (m-10) cc_final: 0.8261 (m-10) REVERT: J 236 TRP cc_start: 0.8849 (m-10) cc_final: 0.7577 (m-90) REVERT: J 500 ILE cc_start: 0.9396 (mm) cc_final: 0.8993 (pt) REVERT: J 821 MET cc_start: 0.7874 (tpp) cc_final: 0.7575 (tpp) REVERT: J 1143 ASP cc_start: 0.8143 (t0) cc_final: 0.7760 (t0) REVERT: J 1189 MET cc_start: 0.8172 (tmm) cc_final: 0.7968 (tmm) REVERT: K 3 ARG cc_start: 0.7115 (mmp80) cc_final: 0.6729 (mmp-170) REVERT: K 44 ASP cc_start: 0.7446 (m-30) cc_final: 0.6926 (m-30) REVERT: K 68 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7114 (tm-30) outliers start: 45 outliers final: 21 residues processed: 447 average time/residue: 0.4519 time to fit residues: 341.2025 Evaluate side-chains 375 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 353 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 220 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 397 optimal weight: 20.0000 chunk 429 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 394 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN I 148 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 798 GLN I 808 ASN I1010 GLN I1134 GLN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 36898 Z= 0.425 Angle : 0.751 9.897 50390 Z= 0.392 Chirality : 0.046 0.232 5745 Planarity : 0.005 0.071 6199 Dihedral : 16.641 167.398 6012 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 2.29 % Allowed : 12.54 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4294 helix: -0.32 (0.13), residues: 1496 sheet: -1.28 (0.22), residues: 543 loop : -1.89 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1134 HIS 0.011 0.002 HIS A 84 PHE 0.023 0.002 PHE I 514 TYR 0.023 0.002 TYR G 185 ARG 0.007 0.001 ARG K 67 *********************** 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 426 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 343 time to evaluate : 4.057 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: A 114 MET cc_start: 0.6505 (tpp) cc_final: 0.6001 (tpp) REVERT: A 928 LYS cc_start: 0.9049 (pptt) cc_final: 0.8728 (pptt) REVERT: A 967 MET cc_start: 0.9011 (pmm) cc_final: 0.8806 (pmm) REVERT: A 1038 GLU cc_start: 0.8239 (pt0) cc_final: 0.7846 (pt0) REVERT: I 102 LEU cc_start: 0.8738 (tp) cc_final: 0.8446 (pt) REVERT: I 187 GLU cc_start: 0.7429 (pm20) cc_final: 0.7216 (pm20) REVERT: I 195 PHE cc_start: 0.7697 (m-80) cc_final: 0.7229 (m-80) REVERT: I 368 ARG cc_start: 0.8465 (tpp-160) cc_final: 0.8005 (tpt170) REVERT: I 542 ARG cc_start: 0.7705 (mmp80) cc_final: 0.7265 (mtt-85) REVERT: I 654 ASP cc_start: 0.8021 (m-30) cc_final: 0.7750 (m-30) REVERT: I 741 MET cc_start: 0.8114 (tpp) cc_final: 0.7829 (tpp) REVERT: I 1220 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8538 (tp40) REVERT: I 1296 ASP cc_start: 0.8006 (t70) cc_final: 0.7444 (t0) REVERT: J 199 GLU cc_start: 0.8471 (pm20) cc_final: 0.8254 (pm20) REVERT: J 747 MET cc_start: 0.7998 (mtp) cc_final: 0.7698 (mmt) REVERT: J 1143 ASP cc_start: 0.8336 (t0) cc_final: 0.8115 (t0) REVERT: J 1193 TRP cc_start: 0.6828 (p90) cc_final: 0.6282 (p90) REVERT: K 3 ARG cc_start: 0.7307 (mmp80) cc_final: 0.6861 (mmp-170) REVERT: K 43 ASN cc_start: 0.8417 (t0) cc_final: 0.8166 (t0) REVERT: K 44 ASP cc_start: 0.7487 (m-30) cc_final: 0.6814 (m-30) outliers start: 83 outliers final: 59 residues processed: 397 average time/residue: 0.4388 time to fit residues: 294.9338 Evaluate side-chains 380 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 320 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1279 GLU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL 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: 4.9990 chunk 206 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 398 optimal weight: 0.9980 chunk 422 optimal weight: 4.9990 chunk 208 optimal weight: 0.5980 chunk 378 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 367 GLN ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36898 Z= 0.184 Angle : 0.618 11.380 50390 Z= 0.318 Chirality : 0.043 0.214 5745 Planarity : 0.004 0.075 6199 Dihedral : 16.386 166.595 6012 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 1.88 % Allowed : 15.69 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 4294 helix: 0.12 (0.13), residues: 1483 sheet: -1.27 (0.21), residues: 578 loop : -1.75 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1134 HIS 0.006 0.001 HIS A 84 PHE 0.015 0.001 PHE I 514 TYR 0.021 0.001 TYR G 185 ARG 0.005 0.000 ARG K 67 *********************** 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 432 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 364 time to evaluate : 4.064 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: A 157 MET cc_start: 0.6016 (tpt) cc_final: 0.5154 (pmm) REVERT: A 765 MET cc_start: 0.6446 (ttt) cc_final: 0.4947 (ttt) REVERT: A 821 ASN cc_start: 0.7946 (t0) cc_final: 0.7581 (t0) REVERT: A 967 MET cc_start: 0.9041 (pmm) cc_final: 0.8688 (pmm) REVERT: G 35 PHE cc_start: 0.7505 (m-80) cc_final: 0.7161 (m-80) REVERT: I 102 LEU cc_start: 0.8698 (tp) cc_final: 0.8430 (pt) REVERT: I 187 GLU cc_start: 0.7370 (pm20) cc_final: 0.7115 (pm20) REVERT: I 195 PHE cc_start: 0.7307 (m-80) cc_final: 0.6554 (m-80) REVERT: I 542 ARG cc_start: 0.7724 (mmp80) cc_final: 0.7271 (mtt-85) REVERT: I 741 MET cc_start: 0.8025 (tpp) cc_final: 0.7733 (tpp) REVERT: I 1220 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8590 (tp40) REVERT: I 1296 ASP cc_start: 0.7909 (t70) cc_final: 0.7437 (t0) REVERT: I 1337 ILE cc_start: 0.9193 (tt) cc_final: 0.8908 (tt) REVERT: J 747 MET cc_start: 0.7959 (mtp) cc_final: 0.7713 (mmt) REVERT: J 821 MET cc_start: 0.7893 (tpp) cc_final: 0.7607 (tpp) REVERT: J 973 LEU cc_start: 0.7223 (tp) cc_final: 0.6921 (mp) REVERT: J 988 PHE cc_start: 0.6692 (t80) cc_final: 0.6392 (m-10) REVERT: J 1143 ASP cc_start: 0.8127 (t0) cc_final: 0.7804 (t0) REVERT: J 1188 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6744 (pm20) REVERT: J 1189 MET cc_start: 0.8528 (tmm) cc_final: 0.7982 (tmm) REVERT: J 1193 TRP cc_start: 0.6958 (p90) cc_final: 0.6448 (p90) REVERT: K 3 ARG cc_start: 0.7197 (mmp80) cc_final: 0.6765 (mmp-170) REVERT: K 44 ASP cc_start: 0.7540 (m-30) cc_final: 0.6886 (m-30) outliers start: 68 outliers final: 40 residues processed: 405 average time/residue: 0.4522 time to fit residues: 308.1682 Evaluate side-chains 382 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 341 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 0.0670 chunk 239 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1236 ASN I1257 GLN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 36898 Z= 0.355 Angle : 0.681 11.526 50390 Z= 0.352 Chirality : 0.044 0.236 5745 Planarity : 0.005 0.069 6199 Dihedral : 16.400 166.251 6012 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.04 % Rotamer: Outliers : 2.87 % Allowed : 16.74 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 4294 helix: 0.14 (0.13), residues: 1484 sheet: -1.08 (0.22), residues: 531 loop : -1.75 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 321 HIS 0.008 0.001 HIS A 84 PHE 0.014 0.002 PHE I 514 TYR 0.017 0.002 TYR G 177 ARG 0.009 0.001 ARG I 368 *********************** 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 452 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 348 time to evaluate : 4.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.6012 (tpt) cc_final: 0.5143 (pmm) REVERT: A 158 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: A 496 MET cc_start: 0.8553 (mmm) cc_final: 0.8353 (mmm) REVERT: A 765 MET cc_start: 0.6636 (ttt) cc_final: 0.6408 (ttt) REVERT: A 821 ASN cc_start: 0.8097 (t0) cc_final: 0.7711 (t0) REVERT: A 967 MET cc_start: 0.9060 (pmm) cc_final: 0.8446 (pmm) REVERT: A 1038 GLU cc_start: 0.8212 (pt0) cc_final: 0.7824 (pt0) REVERT: G 35 PHE cc_start: 0.7632 (m-80) cc_final: 0.7198 (m-80) REVERT: G 185 TYR cc_start: 0.8864 (p90) cc_final: 0.8448 (p90) REVERT: H 132 HIS cc_start: 0.7883 (m-70) cc_final: 0.7349 (m-70) REVERT: I 102 LEU cc_start: 0.8793 (tp) cc_final: 0.8469 (pt) REVERT: I 187 GLU cc_start: 0.7520 (pm20) cc_final: 0.7281 (pm20) REVERT: I 195 PHE cc_start: 0.7488 (m-80) cc_final: 0.6665 (m-80) REVERT: I 542 ARG cc_start: 0.7728 (mmp80) cc_final: 0.7276 (mtt-85) REVERT: I 741 MET cc_start: 0.8043 (tpp) cc_final: 0.7735 (tpp) REVERT: I 810 TYR cc_start: 0.8638 (m-80) cc_final: 0.8381 (m-80) REVERT: I 1296 ASP cc_start: 0.7901 (t70) cc_final: 0.7430 (t0) REVERT: J 697 MET cc_start: 0.9019 (ttp) cc_final: 0.8479 (ttp) REVERT: J 821 MET cc_start: 0.7980 (tpp) cc_final: 0.7694 (tpp) REVERT: J 973 LEU cc_start: 0.7456 (tp) cc_final: 0.7087 (mp) REVERT: J 1143 ASP cc_start: 0.8331 (t0) cc_final: 0.8103 (t0) REVERT: J 1193 TRP cc_start: 0.6965 (p90) cc_final: 0.6479 (p90) REVERT: J 1334 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7952 (tp30) REVERT: K 3 ARG cc_start: 0.7250 (mmp80) cc_final: 0.6819 (mmp-170) REVERT: K 43 ASN cc_start: 0.8699 (t0) cc_final: 0.8438 (t0) REVERT: K 44 ASP cc_start: 0.7532 (m-30) cc_final: 0.6829 (m-30) outliers start: 104 outliers final: 72 residues processed: 415 average time/residue: 0.4472 time to fit residues: 313.0423 Evaluate side-chains 403 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 330 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 142 optimal weight: 0.4980 chunk 380 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 422 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 HIS I 808 ASN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36898 Z= 0.330 Angle : 0.670 10.861 50390 Z= 0.346 Chirality : 0.044 0.224 5745 Planarity : 0.005 0.062 6199 Dihedral : 16.366 164.315 6012 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 3.12 % Allowed : 17.96 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 4294 helix: 0.19 (0.13), residues: 1485 sheet: -1.13 (0.22), residues: 537 loop : -1.74 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1134 HIS 0.008 0.001 HIS A 84 PHE 0.012 0.002 PHE A 789 TYR 0.017 0.001 TYR G 177 ARG 0.007 0.001 ARG I 368 *********************** 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 450 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 337 time to evaluate : 3.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.5470 (tpt) cc_final: 0.4858 (pmm) REVERT: A 616 MET cc_start: 0.6948 (ppp) cc_final: 0.6628 (ppp) REVERT: A 821 ASN cc_start: 0.8123 (t0) cc_final: 0.7704 (t0) REVERT: A 967 MET cc_start: 0.9110 (pmm) cc_final: 0.8204 (pmm) REVERT: G 35 PHE cc_start: 0.7623 (m-80) cc_final: 0.7155 (m-80) REVERT: G 185 TYR cc_start: 0.8871 (p90) cc_final: 0.8512 (p90) REVERT: H 132 HIS cc_start: 0.7928 (m-70) cc_final: 0.7358 (m-70) REVERT: I 102 LEU cc_start: 0.8797 (tp) cc_final: 0.8482 (pt) REVERT: I 187 GLU cc_start: 0.7612 (pm20) cc_final: 0.7331 (pm20) REVERT: I 195 PHE cc_start: 0.7603 (m-80) cc_final: 0.6808 (m-80) REVERT: I 542 ARG cc_start: 0.7801 (mmp80) cc_final: 0.7229 (mtt-85) REVERT: I 741 MET cc_start: 0.8031 (tpp) cc_final: 0.7654 (tpp) REVERT: I 781 ASP cc_start: 0.8110 (t0) cc_final: 0.7868 (t0) REVERT: I 810 TYR cc_start: 0.8594 (m-80) cc_final: 0.8320 (m-80) REVERT: I 1296 ASP cc_start: 0.7940 (t70) cc_final: 0.7463 (t0) REVERT: I 1304 MET cc_start: 0.8836 (tpp) cc_final: 0.8259 (ttm) REVERT: J 697 MET cc_start: 0.8805 (ttp) cc_final: 0.8374 (ttp) REVERT: J 973 LEU cc_start: 0.7513 (tp) cc_final: 0.7134 (mp) REVERT: J 1143 ASP cc_start: 0.8243 (t0) cc_final: 0.8039 (t0) REVERT: K 3 ARG cc_start: 0.7208 (mmp80) cc_final: 0.6779 (mmp-170) REVERT: K 43 ASN cc_start: 0.8659 (t0) cc_final: 0.8385 (t0) REVERT: K 44 ASP cc_start: 0.7511 (m-30) cc_final: 0.6805 (m-30) outliers start: 113 outliers final: 88 residues processed: 417 average time/residue: 0.4289 time to fit residues: 304.0281 Evaluate side-chains 422 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 334 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 821 ARG Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 407 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 355 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 421 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36898 Z= 0.253 Angle : 0.643 11.246 50390 Z= 0.328 Chirality : 0.043 0.231 5745 Planarity : 0.004 0.061 6199 Dihedral : 16.294 164.648 6012 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.43 % Favored : 92.52 % Rotamer: Outliers : 2.90 % Allowed : 19.31 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 4294 helix: 0.32 (0.14), residues: 1481 sheet: -1.11 (0.22), residues: 547 loop : -1.65 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1134 HIS 0.006 0.001 HIS A 215 PHE 0.013 0.001 PHE I1221 TYR 0.016 0.001 TYR G 177 ARG 0.006 0.000 ARG K 67 *********************** 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 453 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 348 time to evaluate : 4.492 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: A 157 MET cc_start: 0.5401 (tpt) cc_final: 0.4847 (pmm) REVERT: A 616 MET cc_start: 0.6839 (ppp) cc_final: 0.6635 (ppp) REVERT: A 821 ASN cc_start: 0.8121 (t0) cc_final: 0.7647 (t0) REVERT: A 967 MET cc_start: 0.9102 (pmm) cc_final: 0.8313 (pmm) REVERT: G 185 TYR cc_start: 0.8921 (p90) cc_final: 0.8508 (p90) REVERT: H 132 HIS cc_start: 0.7933 (m-70) cc_final: 0.7343 (m-70) REVERT: I 102 LEU cc_start: 0.8711 (tp) cc_final: 0.8398 (pt) REVERT: I 187 GLU cc_start: 0.7572 (pm20) cc_final: 0.7293 (pm20) REVERT: I 195 PHE cc_start: 0.7592 (m-80) cc_final: 0.6769 (m-80) REVERT: I 515 MET cc_start: 0.8552 (ttp) cc_final: 0.8166 (ttt) REVERT: I 542 ARG cc_start: 0.7788 (mmp80) cc_final: 0.7179 (mtt-85) REVERT: I 741 MET cc_start: 0.8023 (tpp) cc_final: 0.7653 (tpp) REVERT: I 781 ASP cc_start: 0.8035 (t0) cc_final: 0.7823 (t0) REVERT: I 810 TYR cc_start: 0.8558 (m-80) cc_final: 0.8259 (m-80) REVERT: I 1220 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8612 (tp40) REVERT: I 1296 ASP cc_start: 0.7907 (t70) cc_final: 0.7462 (t0) REVERT: J 821 MET cc_start: 0.7722 (tpp) cc_final: 0.7267 (tpp) REVERT: J 822 MET cc_start: 0.7655 (tpp) cc_final: 0.7205 (tpp) REVERT: J 973 LEU cc_start: 0.7546 (tp) cc_final: 0.7146 (mp) REVERT: J 1143 ASP cc_start: 0.8212 (t0) cc_final: 0.7989 (t0) REVERT: K 3 ARG cc_start: 0.7046 (mmp80) cc_final: 0.6660 (mmp-170) REVERT: K 43 ASN cc_start: 0.8642 (t0) cc_final: 0.8386 (t0) REVERT: K 44 ASP cc_start: 0.7532 (m-30) cc_final: 0.6887 (m-30) REVERT: K 71 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7830 (mm-30) REVERT: K 72 GLN cc_start: 0.7574 (pp30) cc_final: 0.6972 (pp30) outliers start: 105 outliers final: 75 residues processed: 424 average time/residue: 0.4452 time to fit residues: 318.4969 Evaluate side-chains 411 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 335 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 821 ARG Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 260 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 286 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 331 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36898 Z= 0.236 Angle : 0.643 13.118 50390 Z= 0.325 Chirality : 0.043 0.249 5745 Planarity : 0.004 0.061 6199 Dihedral : 16.222 165.325 6012 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.24 % Favored : 92.73 % Rotamer: Outliers : 2.98 % Allowed : 19.59 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 4294 helix: 0.38 (0.14), residues: 1490 sheet: -1.16 (0.22), residues: 556 loop : -1.60 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP J1020 HIS 0.005 0.001 HIS A 215 PHE 0.015 0.001 PHE H 8 TYR 0.015 0.001 TYR G 185 ARG 0.007 0.000 ARG K 67 *********************** 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 454 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 346 time to evaluate : 3.967 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: A 157 MET cc_start: 0.5380 (tpt) cc_final: 0.4877 (pmm) REVERT: A 765 MET cc_start: 0.7010 (ttt) cc_final: 0.6704 (ttt) REVERT: A 821 ASN cc_start: 0.8041 (t0) cc_final: 0.7510 (t0) REVERT: A 967 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8140 (pmm) REVERT: G 25 LYS cc_start: 0.8862 (tttp) cc_final: 0.8395 (tptp) REVERT: G 35 PHE cc_start: 0.7303 (m-80) cc_final: 0.6950 (m-80) REVERT: G 185 TYR cc_start: 0.8899 (p90) cc_final: 0.8505 (p90) REVERT: H 132 HIS cc_start: 0.7946 (m-70) cc_final: 0.7342 (m-70) REVERT: I 102 LEU cc_start: 0.8676 (tp) cc_final: 0.8404 (pt) REVERT: I 187 GLU cc_start: 0.7558 (pm20) cc_final: 0.7283 (pm20) REVERT: I 195 PHE cc_start: 0.7445 (m-80) cc_final: 0.6431 (m-80) REVERT: I 542 ARG cc_start: 0.7732 (mmp80) cc_final: 0.7196 (mtt-85) REVERT: I 741 MET cc_start: 0.8065 (tpp) cc_final: 0.7712 (tpp) REVERT: I 781 ASP cc_start: 0.8027 (t0) cc_final: 0.7771 (t0) REVERT: I 810 TYR cc_start: 0.8521 (m-80) cc_final: 0.8270 (m-80) REVERT: I 1220 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8655 (tp40) REVERT: I 1274 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: I 1296 ASP cc_start: 0.8061 (t70) cc_final: 0.7603 (t0) REVERT: J 821 MET cc_start: 0.7727 (tpp) cc_final: 0.7323 (tpp) REVERT: J 973 LEU cc_start: 0.7544 (tp) cc_final: 0.7133 (mp) REVERT: J 1143 ASP cc_start: 0.8178 (t0) cc_final: 0.7950 (t0) REVERT: K 3 ARG cc_start: 0.7102 (mmp80) cc_final: 0.6748 (mmp-170) REVERT: K 43 ASN cc_start: 0.8643 (t0) cc_final: 0.8419 (t0) REVERT: K 44 ASP cc_start: 0.7470 (m-30) cc_final: 0.6833 (m-30) outliers start: 108 outliers final: 87 residues processed: 429 average time/residue: 0.4394 time to fit residues: 319.5609 Evaluate side-chains 417 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 327 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 383 optimal weight: 8.9990 chunk 403 optimal weight: 0.8980 chunk 368 optimal weight: 2.9990 chunk 392 optimal weight: 9.9990 chunk 236 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 354 optimal weight: 4.9990 chunk 371 optimal weight: 6.9990 chunk 391 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36898 Z= 0.214 Angle : 0.638 12.170 50390 Z= 0.322 Chirality : 0.043 0.294 5745 Planarity : 0.004 0.058 6199 Dihedral : 16.163 165.868 6012 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.99 % Favored : 92.99 % Rotamer: Outliers : 2.68 % Allowed : 20.03 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 4294 helix: 0.44 (0.14), residues: 1488 sheet: -1.10 (0.22), residues: 553 loop : -1.56 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J1020 HIS 0.005 0.001 HIS A 215 PHE 0.018 0.001 PHE I 253 TYR 0.015 0.001 TYR G 185 ARG 0.004 0.000 ARG K 25 *********************** 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 437 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 340 time to evaluate : 4.381 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: A 157 MET cc_start: 0.5331 (tpt) cc_final: 0.4866 (pmm) REVERT: A 616 MET cc_start: 0.6632 (ppp) cc_final: 0.6410 (ppp) REVERT: A 765 MET cc_start: 0.7123 (ttt) cc_final: 0.6823 (ttt) REVERT: A 967 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8245 (pmm) REVERT: G 25 LYS cc_start: 0.8834 (tttp) cc_final: 0.8357 (tptp) REVERT: G 35 PHE cc_start: 0.7284 (m-80) cc_final: 0.6932 (m-80) REVERT: G 185 TYR cc_start: 0.8849 (p90) cc_final: 0.8397 (p90) REVERT: H 132 HIS cc_start: 0.7945 (m-70) cc_final: 0.7337 (m-70) REVERT: I 102 LEU cc_start: 0.8701 (tp) cc_final: 0.8405 (pt) REVERT: I 187 GLU cc_start: 0.7535 (pm20) cc_final: 0.7258 (pm20) REVERT: I 195 PHE cc_start: 0.7426 (m-80) cc_final: 0.6417 (m-80) REVERT: I 370 MET cc_start: 0.7994 (mmm) cc_final: 0.7724 (mmm) REVERT: I 429 MET cc_start: 0.8872 (mtm) cc_final: 0.8502 (mtm) REVERT: I 515 MET cc_start: 0.8551 (ttp) cc_final: 0.8228 (ttt) REVERT: I 542 ARG cc_start: 0.7707 (mmp80) cc_final: 0.7222 (mtt-85) REVERT: I 741 MET cc_start: 0.7992 (tpp) cc_final: 0.7621 (tpp) REVERT: I 781 ASP cc_start: 0.8006 (t0) cc_final: 0.7738 (t0) REVERT: I 1220 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8644 (tp40) REVERT: I 1274 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: I 1296 ASP cc_start: 0.8024 (t70) cc_final: 0.7595 (t0) REVERT: J 140 TYR cc_start: 0.8966 (m-10) cc_final: 0.8651 (m-10) REVERT: J 822 MET cc_start: 0.7396 (tpp) cc_final: 0.7067 (tpp) REVERT: J 973 LEU cc_start: 0.7538 (tp) cc_final: 0.7120 (mp) REVERT: J 1143 ASP cc_start: 0.8216 (t0) cc_final: 0.7994 (t0) REVERT: K 3 ARG cc_start: 0.7073 (mmp80) cc_final: 0.6715 (mmp-170) REVERT: K 43 ASN cc_start: 0.8612 (t0) cc_final: 0.8409 (t0) REVERT: K 44 ASP cc_start: 0.7487 (m-30) cc_final: 0.6887 (m-30) outliers start: 97 outliers final: 84 residues processed: 412 average time/residue: 0.4367 time to fit residues: 303.1734 Evaluate side-chains 424 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 337 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 821 ARG Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 257 optimal weight: 10.0000 chunk 415 optimal weight: 1.9990 chunk 253 optimal weight: 0.0470 chunk 196 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 435 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 227 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1313 HIS I1324 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36898 Z= 0.245 Angle : 0.659 13.845 50390 Z= 0.330 Chirality : 0.043 0.316 5745 Planarity : 0.004 0.059 6199 Dihedral : 16.148 166.051 6012 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.90 % Allowed : 20.28 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 4294 helix: 0.42 (0.14), residues: 1489 sheet: -1.11 (0.22), residues: 565 loop : -1.55 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 409 HIS 0.005 0.001 HIS J 80 PHE 0.010 0.001 PHE I1221 TYR 0.018 0.001 TYR I 810 ARG 0.011 0.000 ARG G 195 ********************** 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 440 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 335 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.5331 (tpt) cc_final: 0.4869 (pmm) REVERT: A 616 MET cc_start: 0.6532 (ppp) cc_final: 0.6293 (ppp) REVERT: A 765 MET cc_start: 0.7148 (ttt) cc_final: 0.6825 (ttt) REVERT: A 967 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8167 (pmm) REVERT: G 25 LYS cc_start: 0.8839 (tttp) cc_final: 0.8347 (tptp) REVERT: G 35 PHE cc_start: 0.7312 (m-80) cc_final: 0.6939 (m-80) REVERT: G 185 TYR cc_start: 0.8842 (p90) cc_final: 0.8320 (p90) REVERT: H 132 HIS cc_start: 0.7954 (m-70) cc_final: 0.7345 (m-70) REVERT: I 102 LEU cc_start: 0.8721 (tp) cc_final: 0.8420 (pt) REVERT: I 187 GLU cc_start: 0.7539 (pm20) cc_final: 0.7262 (pm20) REVERT: I 195 PHE cc_start: 0.7460 (m-80) cc_final: 0.6462 (m-80) REVERT: I 370 MET cc_start: 0.8003 (mmm) cc_final: 0.7749 (mmm) REVERT: I 429 MET cc_start: 0.8872 (mtm) cc_final: 0.8490 (mtm) REVERT: I 515 MET cc_start: 0.8534 (ttp) cc_final: 0.8199 (ttt) REVERT: I 542 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7211 (mtt-85) REVERT: I 741 MET cc_start: 0.7998 (tpp) cc_final: 0.7624 (tpp) REVERT: I 781 ASP cc_start: 0.8041 (t0) cc_final: 0.7770 (t0) REVERT: I 1220 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8639 (tp40) REVERT: I 1274 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: I 1296 ASP cc_start: 0.8049 (t70) cc_final: 0.7591 (t0) REVERT: J 140 TYR cc_start: 0.8910 (m-10) cc_final: 0.8618 (m-10) REVERT: J 725 MET cc_start: 0.8247 (ttt) cc_final: 0.7939 (ttm) REVERT: J 821 MET cc_start: 0.7727 (tpp) cc_final: 0.7343 (tpp) REVERT: J 822 MET cc_start: 0.7380 (tpp) cc_final: 0.7017 (tpp) REVERT: J 973 LEU cc_start: 0.7558 (tp) cc_final: 0.7145 (mp) REVERT: J 1143 ASP cc_start: 0.8174 (t0) cc_final: 0.7964 (t0) REVERT: J 1334 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8022 (tp30) REVERT: K 3 ARG cc_start: 0.7078 (mmp80) cc_final: 0.6714 (mmp-170) REVERT: K 44 ASP cc_start: 0.7524 (m-30) cc_final: 0.6884 (m-30) outliers start: 105 outliers final: 87 residues processed: 416 average time/residue: 0.4434 time to fit residues: 311.8862 Evaluate side-chains 417 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 327 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 821 ARG Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 275 optimal weight: 4.9990 chunk 369 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 319 optimal weight: 0.0000 chunk 51 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 overall best weight: 1.6108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.110303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088952 restraints weight = 132459.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089955 restraints weight = 81117.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090232 restraints weight = 52552.523| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36898 Z= 0.191 Angle : 0.647 14.030 50390 Z= 0.322 Chirality : 0.043 0.311 5745 Planarity : 0.004 0.058 6199 Dihedral : 16.084 166.353 6012 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.43 % Allowed : 20.83 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4294 helix: 0.46 (0.14), residues: 1483 sheet: -1.02 (0.22), residues: 558 loop : -1.48 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 409 HIS 0.004 0.001 HIS A 215 PHE 0.011 0.001 PHE I1221 TYR 0.014 0.001 TYR G 185 ARG 0.004 0.000 ARG I 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6709.86 seconds wall clock time: 122 minutes 34.28 seconds (7354.28 seconds total)