Starting phenix.real_space_refine on Fri Feb 23 00:58:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4w_22043/02_2024/6x4w_22043_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4w_22043/02_2024/6x4w_22043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4w_22043/02_2024/6x4w_22043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4w_22043/02_2024/6x4w_22043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4w_22043/02_2024/6x4w_22043_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4w_22043/02_2024/6x4w_22043_updated.pdb" } resolution = 3.8 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= 0.010 sd= 1.075 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 113 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 22279 2.51 5 N 6391 2.21 5 O 7093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 820": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H GLU 229": "OE1" <-> "OE2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I GLU 602": "OE1" <-> "OE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 985": "OE1" <-> "OE2" Residue "I GLU 1192": "OE1" <-> "OE2" Residue "I GLU 1194": "OE1" <-> "OE2" Residue "I GLU 1197": "OE1" <-> "OE2" Residue "I GLU 1272": "OE1" <-> "OE2" Residue "I GLU 1279": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J GLU 203": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 404": "OE1" <-> "OE2" Residue "J GLU 405": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J GLU 523": "OE1" <-> "OE2" Residue "J GLU 663": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J GLU 765": "OE1" <-> "OE2" Residue "J GLU 827": "OE1" <-> "OE2" Residue "J GLU 833": "OE1" <-> "OE2" Residue "J GLU 1030": "OE1" <-> "OE2" Residue "J GLU 1152": "OE1" <-> "OE2" Residue "J GLU 1168": "OE1" <-> "OE2" Residue "J GLU 1215": "OE1" <-> "OE2" Residue "J TYR 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36021 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8955 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1717 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} 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: 10348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10348 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 10373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10373 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 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: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 991 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23132 SG CYS J 70 20.856 92.418 99.987 1.00183.37 S ATOM 23146 SG CYS J 72 19.869 95.903 98.848 1.00177.89 S ATOM 23254 SG CYS J 85 18.184 92.799 97.433 1.00203.51 S ATOM 23278 SG CYS J 88 21.735 93.305 96.550 1.00199.09 S ATOM 28948 SG CYS J 814 53.426 35.649 101.612 1.00 96.96 S ATOM 29513 SG CYS J 888 53.987 38.864 100.479 1.00 78.85 S ATOM 29585 SG CYS J 898 55.902 35.910 103.171 1.00 85.60 S Time building chain proxies: 18.94, per 1000 atoms: 0.53 Number of scatterers: 36021 At special positions: 0 Unit cell: (140.4, 193.7, 191.1, 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 142 16.00 P 113 15.00 Mg 1 11.99 O 7093 8.00 N 6391 7.00 C 22279 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: 13.67 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " 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 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 6 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 147 helices and 41 sheets defined 32.7% alpha, 11.5% beta 53 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 16.51 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 49 through 62 removed outlier: 4.525A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.540A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (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 234 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 288 through 305 removed outlier: 4.969A pdb=" N GLU A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.825A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.649A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (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 449 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' 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 587 through 596 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 634 through 648 removed outlier: 3.579A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 672 removed outlier: 3.577A pdb=" N ASP A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.765A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 795 through 806 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.724A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 858 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 893 through 900 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 986 Processing helix chain 'A' and resid 994 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 87 removed outlier: 4.244A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) 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: 3.651A pdb=" N ALA G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 40 Processing helix chain 'H' and resid 42 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 228 removed outlier: 3.825A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 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: 3.798A pdb=" N ALA I 212 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.562A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.565A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 289 through 292' Processing helix chain 'I' and resid 319 through 327 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.687A 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 Processing helix chain 'I' and resid 484 through 486 No H-bonds generated for 'chain 'I' and resid 484 through 486' Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 521 through 526 Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 664 through 666 No H-bonds generated for 'chain 'I' and resid 664 through 666' 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 676 through 688 removed outlier: 4.016A 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 820 through 824 Processing helix chain 'I' and resid 861 through 864 No H-bonds generated for 'chain 'I' and resid 861 through 864' Processing helix chain 'I' and resid 943 through 980 removed outlier: 4.048A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 986 through 991 removed outlier: 3.712A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 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 1102 No H-bonds generated for 'chain 'I' and resid 1100 through 1102' Processing helix chain 'I' and resid 1109 through 1133 Processing helix chain 'I' and resid 1138 through 1149 removed outlier: 4.399A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) 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 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1298 through 1309 Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' 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 95 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 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 213 through 229 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 308 removed outlier: 3.604A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 333 through 335 No H-bonds generated for 'chain 'J' and resid 333 through 335' Processing helix chain 'J' and resid 339 through 342 No H-bonds generated for 'chain 'J' and resid 339 through 342' 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 407 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 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 582 removed outlier: 4.408A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (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 611 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 788 removed outlier: 4.261A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 792 through 803 Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 5.115A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) 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 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.966A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1260 removed outlier: 3.867A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 removed outlier: 3.646A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1314 removed outlier: 3.792A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1319 through 1322 No H-bonds generated for 'chain 'J' and resid 1319 through 1322' Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1349 through 1353 Processing helix chain 'J' and resid 1361 through 1372 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 76 Processing sheet with id= A, first strand: chain 'A' and resid 350 through 352 removed outlier: 8.498A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG A 336 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 19 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLN A 338 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASN A 284 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 285 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY A 104 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 44 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 106 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA A 46 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 108 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 128 through 131 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 410 through 412 removed outlier: 3.515A pdb=" N ILE A 412 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 434 through 436 Processing sheet with id= F, first strand: chain 'A' and resid 489 through 492 Processing sheet with id= G, first strand: chain 'A' and resid 496 through 500 Processing sheet with id= H, first strand: chain 'A' and resid 623 through 625 removed outlier: 7.283A pdb=" N ILE A 751 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG A 679 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU A 707 " --> pdb=" O ARG A 679 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU A 681 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY A 709 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 683 " --> pdb=" O GLY A 709 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 788 through 792 removed outlier: 6.832A pdb=" N ALA A 912 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ARG A 791 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A 914 " --> pdb=" O ARG A 791 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN A 811 " --> pdb=" O ASN A 881 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 883 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR A 813 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE A 885 " --> pdb=" O TYR A 813 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 815 " --> pdb=" O ILE A 885 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1118 through 1122 Processing sheet with id= K, first strand: chain 'G' and resid 23 through 28 Processing sheet with id= L, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.646A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.531A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.720A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 14 through 17 removed outlier: 3.660A pdb=" N VAL H 202 " --> pdb=" O ASN H 186 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.582A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 66 through 70 removed outlier: 3.761A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= S, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.507A pdb=" N ILE I 127 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= U, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= V, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.669A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 332 through 336 removed outlier: 4.552A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 589 through 592 Processing sheet with id= Y, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= Z, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.304A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.666A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.854A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.732A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.559A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 103 through 106 removed outlier: 4.206A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AG, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AH, first strand: chain 'J' and resid 820 through 822 Processing sheet with id= AI, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= AJ, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.569A pdb=" N ALA J1001 " --> pdb=" O ILE J 975 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= AL, first strand: chain 'J' and resid 1046 through 1048 Processing sheet with id= AM, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 4.641A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.446A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.219A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 15.28 Time building geometry restraints manager: 14.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10124 1.33 - 1.45: 6905 1.45 - 1.57: 19337 1.57 - 1.70: 222 1.70 - 1.82: 249 Bond restraints: 36837 Sorted by residual: bond pdb=" N PRO A 467 " pdb=" CD PRO A 467 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.89e+01 bond pdb=" O3' DT P 24 " pdb=" P DA P 25 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.62e+01 bond pdb=" CA LYS I1234 " pdb=" CB LYS I1234 " ideal model delta sigma weight residual 1.527 1.475 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" CA GLU I 672 " pdb=" C GLU I 672 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.38e-02 5.25e+03 1.57e+01 bond pdb=" CA THR A 762 " pdb=" C THR A 762 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.39e-02 5.18e+03 1.53e+01 ... (remaining 36832 not shown) Histogram of bond angle deviations from ideal: 90.75 - 99.70: 56 99.70 - 108.65: 3651 108.65 - 117.60: 24265 117.60 - 126.56: 21650 126.56 - 135.51: 683 Bond angle restraints: 50305 Sorted by residual: angle pdb=" CA ILE A 877 " pdb=" CB ILE A 877 " pdb=" CG2 ILE A 877 " ideal model delta sigma weight residual 110.50 120.31 -9.81 1.70e+00 3.46e-01 3.33e+01 angle pdb=" C ILE I1079 " pdb=" N ASN I1080 " pdb=" CA ASN I1080 " ideal model delta sigma weight residual 120.94 131.51 -10.57 1.90e+00 2.77e-01 3.09e+01 angle pdb=" N THR J 212 " pdb=" CA THR J 212 " pdb=" C THR J 212 " ideal model delta sigma weight residual 114.56 107.57 6.99 1.27e+00 6.20e-01 3.03e+01 angle pdb=" C GLY I 112 " pdb=" N THR I 113 " pdb=" CA THR I 113 " ideal model delta sigma weight residual 121.80 131.04 -9.24 1.71e+00 3.42e-01 2.92e+01 angle pdb=" N VAL A 156 " pdb=" CA VAL A 156 " pdb=" C VAL A 156 " ideal model delta sigma weight residual 109.30 116.35 -7.05 1.31e+00 5.83e-01 2.90e+01 ... (remaining 50300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 20306 23.60 - 47.19: 1579 47.19 - 70.79: 354 70.79 - 94.39: 50 94.39 - 117.98: 2 Dihedral angle restraints: 22291 sinusoidal: 9862 harmonic: 12429 Sorted by residual: dihedral pdb=" C5' ADP A2000 " pdb=" O5' ADP A2000 " pdb=" PA ADP A2000 " pdb=" O2A ADP A2000 " ideal model delta sinusoidal sigma weight residual -60.00 54.94 -114.94 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA ASN I 519 " pdb=" C ASN I 519 " pdb=" N PRO I 520 " pdb=" CA PRO I 520 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA VAL G 14 " pdb=" C VAL G 14 " pdb=" N ASP G 15 " pdb=" CA ASP G 15 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 22288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 5345 0.118 - 0.235: 375 0.235 - 0.353: 19 0.353 - 0.471: 1 0.471 - 0.589: 1 Chirality restraints: 5741 Sorted by residual: chirality pdb=" CG LEU J 527 " pdb=" CB LEU J 527 " pdb=" CD1 LEU J 527 " pdb=" CD2 LEU J 527 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.66e+00 chirality pdb=" CB ILE I 11 " pdb=" CA ILE I 11 " pdb=" CG1 ILE I 11 " pdb=" CG2 ILE I 11 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE J1248 " pdb=" CA ILE J1248 " pdb=" CG1 ILE J1248 " pdb=" CG2 ILE J1248 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5738 not shown) Planarity restraints: 6190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I1229 " -0.032 2.00e-02 2.50e+03 2.63e-02 1.39e+01 pdb=" CG TYR I1229 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR I1229 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR I1229 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I1229 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR I1229 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR I1229 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I1229 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 759 " -0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO A 760 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 876 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASP A 876 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP A 876 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 877 " -0.019 2.00e-02 2.50e+03 ... (remaining 6187 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 202 2.45 - 3.06: 22901 3.06 - 3.68: 58607 3.68 - 4.29: 81390 4.29 - 4.90: 130624 Nonbonded interactions: 293724 Sorted by model distance: nonbonded pdb=" O ARG J 709 " pdb=" OD1 ASP J 710 " model vdw 1.840 3.040 nonbonded pdb=" O ASN J 206 " pdb=" OE1 GLU J 207 " model vdw 1.967 3.040 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.035 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1501 " model vdw 2.138 2.170 ... (remaining 293719 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 187 or (resid 188 through 191 and (name N or nam \ e CA or name C or name O or name CB )) or resid 192 through 193 or (resid 194 an \ d (name N or name CA or name C or name O or name CB )) or resid 195 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: 1.230 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.000 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 104.010 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 0.107 36837 Z= 0.582 Angle : 1.198 13.967 50305 Z= 0.660 Chirality : 0.064 0.589 5741 Planarity : 0.007 0.087 6190 Dihedral : 17.227 117.983 14279 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.03 % Favored : 91.71 % Rotamer: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -2.71 (0.11), residues: 4294 helix: -1.66 (0.11), residues: 1456 sheet: -1.44 (0.20), residues: 605 loop : -1.97 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP I 997 HIS 0.012 0.002 HIS A 38 PHE 0.043 0.003 PHE I 80 TYR 0.062 0.003 TYR I1229 ARG 0.020 0.001 ARG I 371 *********************** 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 424 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 417 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 922 MET cc_start: 0.7667 (ptp) cc_final: 0.7143 (ptp) REVERT: G 8 PHE cc_start: 0.8172 (m-80) cc_final: 0.7947 (m-80) REVERT: I 85 CYS cc_start: 0.8767 (m) cc_final: 0.8517 (m) REVERT: I 642 SER cc_start: 0.8149 (t) cc_final: 0.7899 (p) REVERT: I 704 MET cc_start: 0.8403 (mmm) cc_final: 0.8075 (tpp) REVERT: I 1230 MET cc_start: 0.8259 (ttt) cc_final: 0.8006 (ttt) REVERT: J 118 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8399 (mtmt) REVERT: J 320 ASN cc_start: 0.5678 (t0) cc_final: 0.5419 (t0) REVERT: J 644 MET cc_start: 0.6526 (mpp) cc_final: 0.6311 (mtm) REVERT: J 822 MET cc_start: 0.7794 (mmt) cc_final: 0.7575 (mmp) REVERT: J 868 TRP cc_start: 0.7930 (m100) cc_final: 0.7725 (m100) REVERT: J 1371 ARG cc_start: 0.7857 (ppt170) cc_final: 0.7095 (tpm170) REVERT: K 26 ARG cc_start: 0.8421 (tmt-80) cc_final: 0.8163 (tpm170) REVERT: K 30 MET cc_start: 0.7896 (mmm) cc_final: 0.7575 (mmt) REVERT: K 31 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7773 (tm-30) outliers start: 7 outliers final: 2 residues processed: 423 average time/residue: 0.4703 time to fit residues: 326.5185 Evaluate side-chains 317 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 850 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 369 optimal weight: 5.9990 chunk 331 optimal weight: 0.9980 chunk 183 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 342 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 254 optimal weight: 7.9990 chunk 396 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** A 738 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN H 41 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN I 573 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 861 ASN J1049 GLN J1126 GLN ** J1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1326 GLN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36837 Z= 0.184 Angle : 0.647 11.753 50305 Z= 0.332 Chirality : 0.043 0.179 5741 Planarity : 0.005 0.068 6190 Dihedral : 16.103 123.976 5979 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 0.91 % Allowed : 9.10 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -1.99 (0.12), residues: 4294 helix: -0.74 (0.12), residues: 1497 sheet: -1.40 (0.20), residues: 623 loop : -1.69 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 73 HIS 0.005 0.001 HIS G 117 PHE 0.015 0.001 PHE J1319 TYR 0.023 0.001 TYR G 185 ARG 0.006 0.000 ARG J1330 *********************** 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 439 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 406 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8061 (tpp) cc_final: 0.7575 (tpp) REVERT: A 443 LEU cc_start: 0.8914 (tp) cc_final: 0.8644 (tt) REVERT: G 185 TYR cc_start: 0.8798 (p90) cc_final: 0.8585 (p90) REVERT: H 117 HIS cc_start: 0.8217 (t-90) cc_final: 0.7897 (t-90) REVERT: H 125 LYS cc_start: 0.7394 (tptt) cc_final: 0.6871 (tptt) REVERT: H 205 MET cc_start: 0.8752 (tpp) cc_final: 0.7955 (ttt) REVERT: I 85 CYS cc_start: 0.8763 (m) cc_final: 0.8460 (m) REVERT: I 315 MET cc_start: 0.8195 (mmm) cc_final: 0.7846 (tpt) REVERT: I 472 GLU cc_start: 0.8608 (pp20) cc_final: 0.8390 (pp20) REVERT: I 642 SER cc_start: 0.8148 (t) cc_final: 0.7894 (p) REVERT: I 704 MET cc_start: 0.8371 (mmm) cc_final: 0.8015 (tpp) REVERT: I 811 ASN cc_start: 0.8803 (p0) cc_final: 0.8521 (p0) REVERT: I 1236 ASN cc_start: 0.8849 (t0) cc_final: 0.8341 (t0) REVERT: I 1315 MET cc_start: 0.7561 (ptm) cc_final: 0.7344 (ppp) REVERT: J 180 MET cc_start: 0.7900 (tpp) cc_final: 0.7695 (tpp) REVERT: J 192 MET cc_start: 0.7125 (tpt) cc_final: 0.6850 (tpt) REVERT: J 320 ASN cc_start: 0.5572 (t0) cc_final: 0.5276 (t0) REVERT: J 707 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7555 (tp) REVERT: J 801 VAL cc_start: 0.9307 (p) cc_final: 0.9083 (p) REVERT: J 1124 ILE cc_start: 0.8272 (mt) cc_final: 0.7940 (mm) REVERT: J 1371 ARG cc_start: 0.7840 (ppt170) cc_final: 0.7021 (tpm170) REVERT: K 30 MET cc_start: 0.7651 (mmm) cc_final: 0.7359 (mmt) REVERT: K 31 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 33 outliers final: 14 residues processed: 425 average time/residue: 0.4537 time to fit residues: 321.8756 Evaluate side-chains 344 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 329 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 1209 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: 7.9990 chunk 330 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 397 optimal weight: 4.9990 chunk 429 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 394 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 338 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1299 ASN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 477 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 680 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 867 GLN ** J1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 36837 Z= 0.557 Angle : 0.836 10.590 50305 Z= 0.432 Chirality : 0.048 0.200 5741 Planarity : 0.006 0.078 6190 Dihedral : 16.185 126.014 5975 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.59 % Favored : 91.31 % Rotamer: Outliers : 2.30 % Allowed : 14.89 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -1.96 (0.12), residues: 4294 helix: -0.61 (0.12), residues: 1470 sheet: -1.52 (0.20), residues: 660 loop : -1.69 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 321 HIS 0.011 0.002 HIS I1070 PHE 0.021 0.003 PHE A1138 TYR 0.029 0.003 TYR A 96 ARG 0.007 0.001 ARG J 431 *********************** 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 400 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 317 time to evaluate : 5.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8075 (tpp) cc_final: 0.7674 (tpp) REVERT: A 443 LEU cc_start: 0.9045 (tp) cc_final: 0.8772 (tt) REVERT: A 636 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: A 845 MET cc_start: 0.8172 (ppp) cc_final: 0.7719 (ppp) REVERT: H 8 PHE cc_start: 0.8508 (m-80) cc_final: 0.8257 (m-80) REVERT: H 117 HIS cc_start: 0.8167 (t-90) cc_final: 0.7783 (t-90) REVERT: H 205 MET cc_start: 0.8854 (tpp) cc_final: 0.8112 (ttt) REVERT: I 85 CYS cc_start: 0.8896 (m) cc_final: 0.8502 (m) REVERT: I 472 GLU cc_start: 0.8711 (pp20) cc_final: 0.8407 (pp20) REVERT: I 488 MET cc_start: 0.8408 (mmt) cc_final: 0.7921 (mmm) REVERT: I 644 LEU cc_start: 0.8516 (tp) cc_final: 0.8245 (tp) REVERT: I 704 MET cc_start: 0.8854 (mmm) cc_final: 0.8450 (tpp) REVERT: J 180 MET cc_start: 0.7850 (tpp) cc_final: 0.7444 (tpp) REVERT: J 320 ASN cc_start: 0.5806 (t0) cc_final: 0.5489 (t0) REVERT: J 1040 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5343 (ttp) REVERT: J 1371 ARG cc_start: 0.7966 (ppt170) cc_final: 0.7285 (tpm170) REVERT: K 30 MET cc_start: 0.7776 (mmm) cc_final: 0.7463 (mmt) REVERT: K 31 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7506 (tm-30) outliers start: 83 outliers final: 55 residues processed: 380 average time/residue: 0.4674 time to fit residues: 297.1973 Evaluate side-chains 347 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 790 ASP Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain K residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 392 optimal weight: 40.0000 chunk 298 optimal weight: 0.7980 chunk 206 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 398 optimal weight: 1.9990 chunk 422 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 378 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN I1209 GLN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1019 ASN J1238 GLN K 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36837 Z= 0.176 Angle : 0.627 12.481 50305 Z= 0.316 Chirality : 0.042 0.206 5741 Planarity : 0.004 0.074 6190 Dihedral : 15.894 132.285 5975 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.01 % Rotamer: Outliers : 1.91 % Allowed : 17.10 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -0.05 (0.13), residues: 1493 sheet: -1.34 (0.20), residues: 640 loop : -1.51 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 580 HIS 0.004 0.001 HIS G 117 PHE 0.010 0.001 PHE J1319 TYR 0.025 0.001 TYR G 185 ARG 0.007 0.000 ARG J 81 *********************** 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 441 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 372 time to evaluate : 4.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7693 (mmm) cc_final: 0.7205 (mmt) REVERT: A 426 MET cc_start: 0.8202 (tpp) cc_final: 0.7677 (tpp) REVERT: A 443 LEU cc_start: 0.9079 (tp) cc_final: 0.8869 (tt) REVERT: A 845 MET cc_start: 0.8108 (ppp) cc_final: 0.7624 (ppp) REVERT: A 867 CYS cc_start: 0.7976 (p) cc_final: 0.7699 (p) REVERT: A 959 LEU cc_start: 0.8561 (tp) cc_final: 0.8283 (tp) REVERT: G 152 TYR cc_start: 0.9123 (t80) cc_final: 0.8915 (t80) REVERT: H 8 PHE cc_start: 0.8352 (m-80) cc_final: 0.8134 (m-80) REVERT: H 117 HIS cc_start: 0.8271 (t-90) cc_final: 0.7865 (t-90) REVERT: H 205 MET cc_start: 0.8734 (tpp) cc_final: 0.7933 (ttt) REVERT: I 85 CYS cc_start: 0.8783 (m) cc_final: 0.8414 (m) REVERT: I 221 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9033 (mm) REVERT: I 239 MET cc_start: 0.4323 (tmm) cc_final: 0.3662 (ptp) REVERT: I 315 MET cc_start: 0.7943 (tpp) cc_final: 0.7577 (tpt) REVERT: I 472 GLU cc_start: 0.8726 (pp20) cc_final: 0.8478 (pp20) REVERT: I 644 LEU cc_start: 0.8395 (tp) cc_final: 0.7984 (tp) REVERT: I 704 MET cc_start: 0.8688 (mmm) cc_final: 0.8226 (tpp) REVERT: I 918 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6789 (pt) REVERT: I 927 THR cc_start: 0.9290 (m) cc_final: 0.9043 (p) REVERT: I 1236 ASN cc_start: 0.8791 (t0) cc_final: 0.8432 (t0) REVERT: J 180 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7462 (tpp) REVERT: J 320 ASN cc_start: 0.5712 (t0) cc_final: 0.5397 (t0) REVERT: J 707 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7651 (tp) REVERT: J 1371 ARG cc_start: 0.7904 (ppt170) cc_final: 0.7181 (tpm170) REVERT: K 30 MET cc_start: 0.7713 (mmm) cc_final: 0.7288 (mmt) REVERT: K 31 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7355 (tm-30) outliers start: 69 outliers final: 41 residues processed: 421 average time/residue: 0.4409 time to fit residues: 314.3171 Evaluate side-chains 374 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 329 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 4.9990 chunk 239 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 314 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 360 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 379 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36837 Z= 0.282 Angle : 0.643 13.850 50305 Z= 0.327 Chirality : 0.043 0.225 5741 Planarity : 0.004 0.070 6190 Dihedral : 15.813 135.478 5975 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.50 % Favored : 92.43 % Rotamer: Outliers : 2.66 % Allowed : 18.32 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4294 helix: 0.08 (0.13), residues: 1495 sheet: -1.28 (0.21), residues: 632 loop : -1.50 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.005 0.001 HIS A 38 PHE 0.025 0.001 PHE I 828 TYR 0.036 0.002 TYR I1229 ARG 0.003 0.000 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 432 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 336 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8376 (mmm) cc_final: 0.7965 (mmm) REVERT: A 426 MET cc_start: 0.8188 (tpp) cc_final: 0.7840 (tpp) REVERT: A 845 MET cc_start: 0.8181 (ppp) cc_final: 0.7748 (ppp) REVERT: A 867 CYS cc_start: 0.7990 (p) cc_final: 0.7740 (p) REVERT: A 967 MET cc_start: 0.7621 (mmm) cc_final: 0.7413 (mmm) REVERT: H 8 PHE cc_start: 0.8534 (m-80) cc_final: 0.8235 (m-80) REVERT: H 117 HIS cc_start: 0.8307 (t-90) cc_final: 0.7966 (t-90) REVERT: H 205 MET cc_start: 0.8704 (tpp) cc_final: 0.8057 (ttt) REVERT: I 85 CYS cc_start: 0.8812 (m) cc_final: 0.8400 (m) REVERT: I 221 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9071 (mm) REVERT: I 239 MET cc_start: 0.4463 (tmm) cc_final: 0.3670 (ptp) REVERT: I 315 MET cc_start: 0.8039 (tpp) cc_final: 0.7678 (tpt) REVERT: I 369 MET cc_start: 0.8438 (ppp) cc_final: 0.7815 (ppp) REVERT: I 370 MET cc_start: 0.8898 (mmp) cc_final: 0.8666 (mmp) REVERT: I 700 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8954 (m) REVERT: I 704 MET cc_start: 0.8797 (mmm) cc_final: 0.8301 (tpp) REVERT: I 918 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6758 (pt) REVERT: I 927 THR cc_start: 0.9343 (m) cc_final: 0.9089 (p) REVERT: I 1229 TYR cc_start: 0.8353 (m-10) cc_final: 0.8011 (m-10) REVERT: I 1236 ASN cc_start: 0.8847 (t0) cc_final: 0.8541 (t0) REVERT: I 1274 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: J 77 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6642 (tpm170) REVERT: J 102 MET cc_start: 0.6504 (mmp) cc_final: 0.6190 (mmp) REVERT: J 180 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7750 (tpp) REVERT: J 320 ASN cc_start: 0.5794 (t0) cc_final: 0.5488 (t0) REVERT: J 746 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8441 (mt) REVERT: J 1371 ARG cc_start: 0.7958 (ppt170) cc_final: 0.7200 (tpm170) REVERT: K 26 ARG cc_start: 0.8474 (tmt-80) cc_final: 0.7484 (tpm170) REVERT: K 31 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7261 (tm-30) outliers start: 96 outliers final: 62 residues processed: 404 average time/residue: 0.4413 time to fit residues: 300.9311 Evaluate side-chains 388 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 984 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 142 optimal weight: 0.0670 chunk 380 optimal weight: 0.0570 chunk 83 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 422 optimal weight: 6.9990 chunk 350 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 overall best weight: 1.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36837 Z= 0.212 Angle : 0.613 13.434 50305 Z= 0.308 Chirality : 0.042 0.206 5741 Planarity : 0.004 0.069 6190 Dihedral : 15.730 137.532 5975 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 2.66 % Allowed : 18.82 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4294 helix: 0.26 (0.13), residues: 1500 sheet: -1.22 (0.21), residues: 630 loop : -1.42 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I1276 HIS 0.004 0.001 HIS A 38 PHE 0.011 0.001 PHE I 828 TYR 0.030 0.001 TYR I1229 ARG 0.003 0.000 ARG I 478 *********************** 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 446 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 350 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7875 (ppp) cc_final: 0.7572 (ppp) REVERT: A 174 MET cc_start: 0.8223 (mmm) cc_final: 0.7729 (mmm) REVERT: A 426 MET cc_start: 0.8187 (tpp) cc_final: 0.7886 (tpp) REVERT: A 867 CYS cc_start: 0.7950 (p) cc_final: 0.7745 (p) REVERT: G 71 LYS cc_start: 0.8766 (tppt) cc_final: 0.8513 (tppt) REVERT: H 8 PHE cc_start: 0.8527 (m-80) cc_final: 0.8246 (m-80) REVERT: H 117 HIS cc_start: 0.8263 (t-90) cc_final: 0.8016 (t-90) REVERT: H 205 MET cc_start: 0.8705 (tpp) cc_final: 0.8024 (ttt) REVERT: I 85 CYS cc_start: 0.8840 (m) cc_final: 0.8404 (m) REVERT: I 221 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9056 (mm) REVERT: I 239 MET cc_start: 0.4199 (tmm) cc_final: 0.3622 (ptp) REVERT: I 488 MET cc_start: 0.8477 (mmt) cc_final: 0.8222 (mmm) REVERT: I 700 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8736 (m) REVERT: I 704 MET cc_start: 0.8723 (mmm) cc_final: 0.8260 (tpp) REVERT: I 918 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6623 (pt) REVERT: I 927 THR cc_start: 0.9288 (m) cc_final: 0.9075 (p) REVERT: I 1236 ASN cc_start: 0.8743 (t0) cc_final: 0.8394 (t0) REVERT: I 1274 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: J 180 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7511 (tpp) REVERT: J 320 ASN cc_start: 0.5788 (t0) cc_final: 0.5540 (t0) REVERT: J 740 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8939 (tp) REVERT: J 1371 ARG cc_start: 0.7962 (ppt170) cc_final: 0.7159 (tpm170) REVERT: K 26 ARG cc_start: 0.8467 (tmt-80) cc_final: 0.7469 (tpm170) REVERT: K 31 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7242 (tm-30) outliers start: 96 outliers final: 68 residues processed: 421 average time/residue: 0.4511 time to fit residues: 323.0381 Evaluate side-chains 403 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 329 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 984 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1347 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 407 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 308 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 355 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 421 optimal weight: 5.9990 chunk 263 optimal weight: 0.0000 chunk 256 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1072 ASN I1209 GLN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 36837 Z= 0.251 Angle : 0.631 13.667 50305 Z= 0.317 Chirality : 0.042 0.198 5741 Planarity : 0.004 0.066 6190 Dihedral : 15.695 138.849 5975 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 3.18 % Allowed : 19.51 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -1.13 (0.13), residues: 4294 helix: 0.37 (0.13), residues: 1485 sheet: -1.16 (0.21), residues: 604 loop : -1.41 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I1276 HIS 0.005 0.001 HIS I1070 PHE 0.015 0.001 PHE I 224 TYR 0.030 0.001 TYR I1229 ARG 0.005 0.000 ARG J 278 *********************** 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 444 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 329 time to evaluate : 4.120 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 174 MET cc_start: 0.8449 (mmm) cc_final: 0.8024 (mmm) REVERT: A 545 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8005 (tp) REVERT: A 759 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8715 (mm) REVERT: G 71 LYS cc_start: 0.8781 (tppt) cc_final: 0.8527 (tppt) REVERT: H 8 PHE cc_start: 0.8552 (m-80) cc_final: 0.8267 (m-80) REVERT: H 49 SER cc_start: 0.9107 (t) cc_final: 0.8874 (t) REVERT: H 79 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8416 (pp) REVERT: H 117 HIS cc_start: 0.8354 (t-90) cc_final: 0.8135 (t-90) REVERT: H 205 MET cc_start: 0.8718 (tpp) cc_final: 0.7967 (ttt) REVERT: I 85 CYS cc_start: 0.8848 (m) cc_final: 0.8396 (m) REVERT: I 221 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9067 (mm) REVERT: I 239 MET cc_start: 0.3993 (tmm) cc_final: 0.3348 (ptp) REVERT: I 700 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8785 (m) REVERT: I 704 MET cc_start: 0.8807 (mmm) cc_final: 0.8319 (tpp) REVERT: I 813 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: I 918 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6500 (pt) REVERT: I 1229 TYR cc_start: 0.8283 (m-10) cc_final: 0.7978 (m-10) REVERT: I 1236 ASN cc_start: 0.8792 (t0) cc_final: 0.8471 (t0) REVERT: I 1254 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7213 (t) REVERT: I 1274 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: J 77 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6740 (tpm170) REVERT: J 164 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8931 (tm-30) REVERT: J 180 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7853 (tpp) REVERT: J 320 ASN cc_start: 0.5690 (t0) cc_final: 0.5486 (t0) REVERT: J 582 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8983 (tt) REVERT: J 644 MET cc_start: 0.6442 (mpp) cc_final: 0.6020 (mtm) REVERT: J 740 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8956 (tp) REVERT: J 746 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8444 (mt) REVERT: J 1371 ARG cc_start: 0.7964 (ppt170) cc_final: 0.7176 (tpm170) REVERT: K 26 ARG cc_start: 0.8478 (tmt-80) cc_final: 0.7506 (tpm170) REVERT: K 31 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7253 (tm-30) REVERT: K 73 GLN cc_start: 0.7081 (tt0) cc_final: 0.6663 (pt0) outliers start: 115 outliers final: 86 residues processed: 416 average time/residue: 0.4452 time to fit residues: 314.2381 Evaluate side-chains 421 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 321 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 997 TRP Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 984 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1351 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: 0.9990 chunk 251 optimal weight: 10.0000 chunk 126 optimal weight: 0.2980 chunk 82 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 208 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 331 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36837 Z= 0.158 Angle : 0.617 15.016 50305 Z= 0.304 Chirality : 0.042 0.184 5741 Planarity : 0.004 0.065 6190 Dihedral : 15.555 140.212 5975 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 2.35 % Allowed : 20.59 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4294 helix: 0.57 (0.14), residues: 1478 sheet: -1.00 (0.21), residues: 629 loop : -1.35 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 580 HIS 0.003 0.001 HIS I1070 PHE 0.018 0.001 PHE I 225 TYR 0.026 0.001 TYR I1229 ARG 0.004 0.000 ARG I 200 *********************** 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 468 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 383 time to evaluate : 4.023 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 49 MET cc_start: 0.7715 (mmm) cc_final: 0.7248 (mmt) REVERT: A 174 MET cc_start: 0.8472 (mmm) cc_final: 0.8079 (mmm) REVERT: A 759 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8699 (mm) REVERT: A 959 LEU cc_start: 0.8581 (tp) cc_final: 0.8378 (tp) REVERT: H 8 PHE cc_start: 0.8482 (m-80) cc_final: 0.8177 (m-80) REVERT: H 205 MET cc_start: 0.8728 (tpp) cc_final: 0.7750 (ttt) REVERT: I 36 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7961 (mm110) REVERT: I 85 CYS cc_start: 0.8805 (m) cc_final: 0.8347 (m) REVERT: I 239 MET cc_start: 0.3927 (tmm) cc_final: 0.3300 (ptp) REVERT: I 347 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8297 (mp) REVERT: I 488 MET cc_start: 0.8447 (mmm) cc_final: 0.8119 (mmt) REVERT: I 492 MET cc_start: 0.7728 (mmm) cc_final: 0.7528 (mmm) REVERT: I 700 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8637 (m) REVERT: I 704 MET cc_start: 0.8613 (mmm) cc_final: 0.8155 (tpp) REVERT: I 811 ASN cc_start: 0.8674 (p0) cc_final: 0.8412 (p0) REVERT: I 813 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: I 1236 ASN cc_start: 0.8629 (t0) cc_final: 0.8265 (t0) REVERT: I 1243 MET cc_start: 0.8156 (tmm) cc_final: 0.7469 (tmm) REVERT: J 77 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6836 (tpm170) REVERT: J 164 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8903 (tm-30) REVERT: J 180 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7564 (tpp) REVERT: J 330 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8032 (pmm) REVERT: J 582 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8987 (tt) REVERT: J 644 MET cc_start: 0.6263 (mpp) cc_final: 0.5842 (mtm) REVERT: J 725 MET cc_start: 0.7636 (mtp) cc_final: 0.7310 (mtp) REVERT: J 740 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8809 (tp) REVERT: J 746 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8359 (mt) REVERT: J 1040 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.4897 (ttp) REVERT: J 1371 ARG cc_start: 0.7943 (ppt170) cc_final: 0.7126 (tpm170) REVERT: K 26 ARG cc_start: 0.8458 (tmt-80) cc_final: 0.7470 (tpm170) REVERT: K 31 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7169 (tm-30) REVERT: K 73 GLN cc_start: 0.7173 (tt0) cc_final: 0.6646 (pt0) outliers start: 85 outliers final: 59 residues processed: 448 average time/residue: 0.4423 time to fit residues: 333.4629 Evaluate side-chains 412 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 342 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 997 TRP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 984 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 383 optimal weight: 10.0000 chunk 403 optimal weight: 8.9990 chunk 368 optimal weight: 3.9990 chunk 392 optimal weight: 30.0000 chunk 236 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 120 optimal weight: 0.1980 chunk 354 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 391 optimal weight: 5.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1098 GLN K 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 36837 Z= 0.416 Angle : 0.734 13.800 50305 Z= 0.371 Chirality : 0.045 0.239 5741 Planarity : 0.005 0.065 6190 Dihedral : 15.708 139.755 5975 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.94 % Favored : 91.99 % Rotamer: Outliers : 2.66 % Allowed : 21.11 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -1.16 (0.13), residues: 4294 helix: 0.35 (0.13), residues: 1470 sheet: -1.08 (0.21), residues: 608 loop : -1.45 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I1276 HIS 0.008 0.001 HIS A 38 PHE 0.027 0.002 PHE I 224 TYR 0.041 0.002 TYR H 177 ARG 0.004 0.001 ARG I 678 *********************** 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 417 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 321 time to evaluate : 4.029 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 174 MET cc_start: 0.8615 (mmm) cc_final: 0.8226 (mmm) REVERT: A 527 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8457 (p90) REVERT: A 759 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8709 (mm) REVERT: G 8 PHE cc_start: 0.8597 (m-80) cc_final: 0.8367 (m-80) REVERT: H 8 PHE cc_start: 0.8623 (m-80) cc_final: 0.8318 (m-80) REVERT: H 49 SER cc_start: 0.9144 (t) cc_final: 0.8905 (t) REVERT: I 85 CYS cc_start: 0.8852 (m) cc_final: 0.8388 (m) REVERT: I 239 MET cc_start: 0.4151 (tmm) cc_final: 0.3878 (tmm) REVERT: I 492 MET cc_start: 0.7826 (mmm) cc_final: 0.7622 (mmm) REVERT: I 700 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8940 (m) REVERT: I 704 MET cc_start: 0.8873 (mmm) cc_final: 0.8472 (tpp) REVERT: I 813 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: I 1229 TYR cc_start: 0.8405 (m-10) cc_final: 0.7968 (m-10) REVERT: I 1236 ASN cc_start: 0.8885 (t0) cc_final: 0.8600 (t0) REVERT: I 1274 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: J 77 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6776 (tpm170) REVERT: J 180 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7828 (tpp) REVERT: J 330 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8153 (pmm) REVERT: J 582 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9220 (tt) REVERT: J 644 MET cc_start: 0.6503 (mpp) cc_final: 0.6192 (mtm) REVERT: J 740 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8996 (tp) REVERT: J 746 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8433 (mt) REVERT: J 1040 MET cc_start: 0.6445 (ttt) cc_final: 0.5074 (ttp) REVERT: J 1371 ARG cc_start: 0.7937 (ppt170) cc_final: 0.7180 (tpm170) REVERT: K 31 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7225 (tm-30) outliers start: 96 outliers final: 72 residues processed: 398 average time/residue: 0.4392 time to fit residues: 295.1343 Evaluate side-chains 392 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 309 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 997 TRP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 257 optimal weight: 9.9990 chunk 415 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 288 optimal weight: 8.9990 chunk 435 optimal weight: 6.9990 chunk 400 optimal weight: 0.0570 chunk 346 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 267 optimal weight: 0.3980 chunk 212 optimal weight: 0.0070 overall best weight: 0.8518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN I1072 ASN ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 36837 Z= 0.179 Angle : 0.650 15.511 50305 Z= 0.320 Chirality : 0.043 0.229 5741 Planarity : 0.004 0.064 6190 Dihedral : 15.577 141.250 5975 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 2.10 % Allowed : 21.64 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -0.97 (0.13), residues: 4294 helix: 0.55 (0.14), residues: 1473 sheet: -0.96 (0.21), residues: 632 loop : -1.38 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I1276 HIS 0.003 0.001 HIS G 117 PHE 0.036 0.001 PHE I 224 TYR 0.037 0.001 TYR H 177 ARG 0.004 0.000 ARG A1029 ********************** 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 417 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 341 time to evaluate : 3.909 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 174 MET cc_start: 0.8575 (mmm) cc_final: 0.8195 (mmm) REVERT: A 759 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8662 (mm) REVERT: A 945 LEU cc_start: 0.9318 (tp) cc_final: 0.8940 (tp) REVERT: H 8 PHE cc_start: 0.8553 (m-80) cc_final: 0.8224 (m-80) REVERT: H 177 TYR cc_start: 0.8784 (m-10) cc_final: 0.8580 (m-10) REVERT: H 205 MET cc_start: 0.8730 (tpp) cc_final: 0.7750 (ttt) REVERT: I 36 GLN cc_start: 0.8267 (mm-40) cc_final: 0.8038 (mm110) REVERT: I 81 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.6975 (p0) REVERT: I 85 CYS cc_start: 0.8792 (m) cc_final: 0.8352 (m) REVERT: I 239 MET cc_start: 0.4050 (tmm) cc_final: 0.3362 (ptp) REVERT: I 488 MET cc_start: 0.8358 (mmm) cc_final: 0.8064 (mmt) REVERT: I 700 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8725 (m) REVERT: I 704 MET cc_start: 0.8722 (mmm) cc_final: 0.8221 (tpp) REVERT: I 813 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: I 1180 MET cc_start: 0.8431 (ttm) cc_final: 0.7949 (mtp) REVERT: I 1229 TYR cc_start: 0.8044 (m-10) cc_final: 0.7788 (m-10) REVERT: I 1236 ASN cc_start: 0.8659 (t0) cc_final: 0.8293 (t0) REVERT: I 1274 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: J 77 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6757 (tpm170) REVERT: J 115 TRP cc_start: 0.8809 (m-10) cc_final: 0.8455 (m-10) REVERT: J 180 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7603 (tpp) REVERT: J 227 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: J 330 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7767 (pmm) REVERT: J 644 MET cc_start: 0.6365 (mpp) cc_final: 0.6029 (mtm) REVERT: J 740 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8871 (tp) REVERT: J 746 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8353 (mt) REVERT: J 1040 MET cc_start: 0.6355 (ttt) cc_final: 0.5049 (ttp) REVERT: J 1371 ARG cc_start: 0.7939 (ppt170) cc_final: 0.7157 (tpm170) REVERT: K 26 ARG cc_start: 0.8418 (tmt-80) cc_final: 0.7547 (tpm170) REVERT: K 30 MET cc_start: 0.7852 (mmt) cc_final: 0.7406 (mmt) REVERT: K 31 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7407 (tm-30) REVERT: K 73 GLN cc_start: 0.7179 (tt0) cc_final: 0.6673 (pt0) outliers start: 76 outliers final: 60 residues processed: 398 average time/residue: 0.4548 time to fit residues: 304.5759 Evaluate side-chains 403 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 332 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 997 TRP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 275 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 319 optimal weight: 0.0670 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 347 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.6522 ------------------------------------------------------------------------------- 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** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.108211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083473 restraints weight = 118740.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085970 restraints weight = 58445.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086609 restraints weight = 33110.566| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 36837 Z= 0.290 Angle : 0.744 59.200 50305 Z= 0.393 Chirality : 0.044 0.796 5741 Planarity : 0.004 0.063 6190 Dihedral : 15.574 141.239 5975 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 2.16 % Allowed : 21.91 % Favored : 75.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % 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: -0.97 (0.13), residues: 4294 helix: 0.55 (0.14), residues: 1473 sheet: -0.96 (0.21), residues: 632 loop : -1.37 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I1276 HIS 0.006 0.001 HIS A 488 PHE 0.021 0.001 PHE I 224 TYR 0.027 0.001 TYR H 177 ARG 0.047 0.000 ARG K 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6798.88 seconds wall clock time: 125 minutes 12.52 seconds (7512.52 seconds total)