Starting phenix.real_space_refine on Sat Mar 23 07:40:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x50_22045/03_2024/6x50_22045_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x50_22045/03_2024/6x50_22045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x50_22045/03_2024/6x50_22045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x50_22045/03_2024/6x50_22045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x50_22045/03_2024/6x50_22045_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x50_22045/03_2024/6x50_22045_updated.pdb" } resolution = 3.3 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= 0.004 sd= 1.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 115 5.49 5 Mg 2 5.21 5 S 142 5.16 5 C 22305 2.51 5 N 6408 2.21 5 O 7103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A GLU 1045": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 631": "OE1" <-> "OE2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I GLU 745": "OE1" <-> "OE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 848": "OE1" <-> "OE2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I GLU 949": "OE1" <-> "OE2" Residue "I GLU 950": "OE1" <-> "OE2" Residue "I GLU 1005": "OE1" <-> "OE2" Residue "I GLU 1026": "OE1" <-> "OE2" Residue "I GLU 1083": "OE1" <-> "OE2" Residue "I GLU 1089": "OE1" <-> "OE2" Residue "I GLU 1338": "OE1" <-> "OE2" Residue "I GLU 1340": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 207": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J GLU 562": "OE1" <-> "OE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J GLU 652": "OE1" <-> "OE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 663": "OE1" <-> "OE2" Residue "J GLU 677": "OE1" <-> "OE2" Residue "J GLU 833": "OE1" <-> "OE2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J GLU 1030": "OE1" <-> "OE2" Residue "J GLU 1152": "OE1" <-> "OE2" Residue "J GLU 1200": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J GLU 1215": "OE1" <-> "OE2" Residue "J GLU 1276": "OE1" <-> "OE2" Residue "J GLU 1293": "OE1" <-> "OE2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36077 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1143, 8946 Classifications: {'peptide': 1143} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 55, 'TRANS': 1087} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10368 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 10383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10383 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 201 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1013 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 23155 SG CYS J 70 25.156 95.249 98.546 1.00 77.00 S ATOM 23169 SG CYS J 72 24.857 98.898 97.662 1.00 82.84 S ATOM 23277 SG CYS J 85 22.759 96.182 95.875 1.00 81.53 S ATOM 23301 SG CYS J 88 26.460 96.310 95.208 1.00 82.01 S ATOM 28977 SG CYS J 814 52.283 34.270 101.823 1.00 62.67 S ATOM 29542 SG CYS J 888 53.584 37.655 101.640 1.00 54.70 S ATOM 29593 SG CYS J 895 52.232 35.964 105.185 1.00 51.27 S ATOM 29614 SG CYS J 898 55.563 35.193 103.372 1.00 46.47 S Time building chain proxies: 17.53, per 1000 atoms: 0.49 Number of scatterers: 36077 At special positions: 0 Unit cell: (139.1, 193.7, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 142 16.00 P 115 15.00 Mg 2 11.99 O 7103 8.00 N 6408 7.00 C 22305 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: 14.93 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 43 sheets defined 31.6% alpha, 11.3% beta 54 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 17.58 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.662A pdb=" N GLU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 62 removed outlier: 4.006A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.557A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 324 through 333 removed outlier: 4.126A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASN A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 4.710A pdb=" N ALA A 373 " --> pdb=" O PRO A 370 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 374 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' 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 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 587 through 595 removed outlier: 4.082A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 removed outlier: 4.115A pdb=" N ASN A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 648 removed outlier: 3.547A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 689 through 701 removed outlier: 4.136A pdb=" N THR A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 714 Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 736 through 740 Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.735A pdb=" N ALA A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.507A pdb=" N GLU A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 858 removed outlier: 4.183A pdb=" N ARG A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A 858 " --> pdb=" O MET A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 893 through 902 removed outlier: 3.531A pdb=" N ARG A 902 " --> pdb=" O GLN A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 933 Processing helix chain 'A' and resid 941 through 952 removed outlier: 3.535A pdb=" N ALA A 946 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 994 through 1000 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 removed outlier: 3.672A pdb=" N LYS A1072 " --> pdb=" O GLN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1128 through 1145 removed outlier: 3.865A pdb=" N ASN A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 228 removed outlier: 3.614A pdb=" N ILE G 217 " --> pdb=" O PRO G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 4.161A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 removed outlier: 3.935A pdb=" N ASN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) 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 227 removed outlier: 3.577A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.765A pdb=" N LEU I 213 " --> 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 Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 289 through 291 No H-bonds generated for 'chain 'I' and resid 289 through 291' Processing helix chain 'I' and resid 319 through 328 Processing helix chain 'I' and resid 348 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 379 through 389 removed outlier: 3.837A pdb=" N LEU I 384 " --> pdb=" O ALA I 380 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 4.002A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 removed outlier: 3.826A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 528 removed outlier: 4.115A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 677 through 688 removed outlier: 4.286A 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 859 through 862 No H-bonds generated for 'chain 'I' and resid 859 through 862' Processing helix chain 'I' and resid 943 through 980 removed outlier: 3.682A pdb=" N LEU I 979 " --> pdb=" O ILE I 975 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 990 removed outlier: 3.650A pdb=" N ASP I 990 " --> pdb=" O GLU I 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 987 through 990' Processing helix chain 'I' and resid 1006 through 1036 removed outlier: 3.597A pdb=" N GLU I1016 " --> pdb=" O GLU I1012 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS I1027 " --> pdb=" O HIS I1023 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I1029 " --> pdb=" O PHE I1025 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 3.772A pdb=" N LEU I1113 " --> pdb=" O GLY I1110 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU I1114 " --> pdb=" O GLN I1111 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I1117 " --> pdb=" O GLU I1114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE I1128 " --> pdb=" O GLY I1125 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN I1129 " --> pdb=" O ASP I1126 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS I1133 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1148 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 1172 through 1175 No H-bonds generated for 'chain 'I' and resid 1172 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 1279 removed outlier: 3.506A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1289 Processing helix chain 'I' and resid 1298 through 1308 removed outlier: 3.923A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1330 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.711A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) 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 205 Processing helix chain 'J' and resid 212 through 229 removed outlier: 3.600A pdb=" N VAL J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 through 330' Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 408 through 416 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 454 through 457 No H-bonds generated for 'chain 'J' and resid 454 through 457' Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.838A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 803 removed outlier: 3.939A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1069 through 1071 No H-bonds generated for 'chain 'J' and resid 1069 through 1071' Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 removed outlier: 3.576A pdb=" N LEU J1221 " --> pdb=" O PRO J1217 " (cutoff:3.500A) Processing helix chain 'J' and resid 1226 through 1236 removed outlier: 4.025A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) Processing helix chain 'J' and resid 1238 through 1244 removed outlier: 3.648A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 removed outlier: 3.794A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 removed outlier: 3.745A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1311 through 1314 No H-bonds generated for 'chain 'J' and resid 1311 through 1314' Processing helix chain 'J' and resid 1328 through 1336 removed outlier: 3.606A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1353 removed outlier: 3.665A pdb=" N VAL J1353 " --> pdb=" O GLU J1349 " (cutoff:3.500A) Processing helix chain 'J' and resid 1363 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 55 Processing helix chain 'K' and resid 61 through 78 Processing sheet with id= A, first strand: chain 'A' and resid 350 through 352 removed outlier: 8.277A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 336 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU A 19 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN A 338 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASN A 284 " --> pdb=" O LEU A 339 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.359A pdb=" N GLY A 104 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 44 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 106 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 46 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 108 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 127 through 130 Processing sheet with id= D, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.445A pdb=" N THR A 164 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 179 through 181 removed outlier: 4.132A pdb=" N GLU A 204 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 423 through 427 removed outlier: 6.593A pdb=" N VAL A 385 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N MET A 426 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE A 387 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 489 through 492 Processing sheet with id= H, first strand: chain 'A' and resid 496 through 500 Processing sheet with id= I, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.945A pdb=" N ILE A 751 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 787 through 789 removed outlier: 3.602A pdb=" N ILE A 883 " --> pdb=" O TYR A 911 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN A 811 " --> pdb=" O ASN A 881 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 883 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR A 813 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE A 885 " --> pdb=" O TYR A 813 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 815 " --> pdb=" O ILE A 885 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1118 through 1122 Processing sheet with id= L, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.503A pdb=" N GLU G 29 " --> pdb=" O ARG G 12 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.587A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 151 through 153 Processing sheet with id= O, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.698A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 23 through 28 Processing sheet with id= Q, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.742A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.645A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 93 through 95 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: 3.566A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= X, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= Y, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= Z, first strand: chain 'I' and resid 634 through 637 Processing sheet with id= AA, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.258A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.489A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.880A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 68 through 75 removed outlier: 6.798A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.662A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.505A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.659A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 244 " --> pdb=" O GLY J 103 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AI, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AJ, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AK, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= AL, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AM, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id= AN, first strand: chain 'J' and resid 1059 through 1061 removed outlier: 3.733A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AP, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.559A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.502A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ 1024 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 16.71 Time building geometry restraints manager: 16.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5986 1.28 - 1.41: 8734 1.41 - 1.54: 21603 1.54 - 1.68: 324 1.68 - 1.81: 249 Bond restraints: 36896 Sorted by residual: bond pdb=" C ARG A 782 " pdb=" O ARG A 782 " ideal model delta sigma weight residual 1.236 1.144 0.092 9.80e-03 1.04e+04 8.87e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.92e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.47e+01 bond pdb=" C ALA A 785 " pdb=" O ALA A 785 " ideal model delta sigma weight residual 1.234 1.166 0.068 1.20e-02 6.94e+03 3.23e+01 bond pdb=" CA ALA A 785 " pdb=" C ALA A 785 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.32e-02 5.74e+03 3.06e+01 ... (remaining 36891 not shown) Histogram of bond angle deviations from ideal: 94.73 - 103.01: 455 103.01 - 111.28: 15524 111.28 - 119.55: 16184 119.55 - 127.83: 17844 127.83 - 136.10: 378 Bond angle restraints: 50385 Sorted by residual: angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" N ILE A 952 " pdb=" CA ILE A 952 " pdb=" C ILE A 952 " ideal model delta sigma weight residual 110.62 98.42 12.20 1.02e+00 9.61e-01 1.43e+02 angle pdb=" C5 ATP A2000 " pdb=" C4 ATP A2000 " pdb=" N3 ATP A2000 " ideal model delta sigma weight residual 126.80 118.65 8.15 1.00e+00 1.00e+00 6.64e+01 angle pdb=" N3 ATP A2000 " pdb=" C4 ATP A2000 " pdb=" N9 ATP A2000 " ideal model delta sigma weight residual 127.04 134.97 -7.93 1.15e+00 7.59e-01 4.77e+01 ... (remaining 50380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 21497 35.40 - 70.80: 792 70.80 - 106.20: 55 106.20 - 141.60: 1 141.60 - 176.99: 2 Dihedral angle restraints: 22347 sinusoidal: 9922 harmonic: 12425 Sorted by residual: dihedral pdb=" CA THR J1169 " pdb=" C THR J1169 " pdb=" N LYS J1170 " pdb=" CA LYS J1170 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN I 235 " pdb=" C ASN I 235 " pdb=" N LYS I 236 " pdb=" CA LYS I 236 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 22344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 5600 0.120 - 0.241: 134 0.241 - 0.361: 5 0.361 - 0.482: 4 0.482 - 0.602: 1 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CB ILE I 117 " pdb=" CA ILE I 117 " pdb=" CG1 ILE I 117 " pdb=" CG2 ILE I 117 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" CA ALA A 781 " pdb=" N ALA A 781 " pdb=" C ALA A 781 " pdb=" CB ALA A 781 " both_signs ideal model delta sigma weight residual False 2.48 2.03 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA GLU A 951 " pdb=" N GLU A 951 " pdb=" C GLU A 951 " pdb=" CB GLU A 951 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 5741 not shown) Planarity restraints: 6196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 208 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C THR J 208 " 0.064 2.00e-02 2.50e+03 pdb=" O THR J 208 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN J 209 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 759 " -0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO A 760 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 783 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ARG A 783 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG A 783 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 784 " -0.017 2.00e-02 2.50e+03 ... (remaining 6193 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 304 2.57 - 3.15: 27838 3.15 - 3.73: 56039 3.73 - 4.32: 78531 4.32 - 4.90: 129837 Nonbonded interactions: 292549 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 1.985 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 1.991 2.170 nonbonded pdb=" O3G ATP A2000 " pdb="MG MG A2001 " model vdw 2.062 2.170 nonbonded pdb=" O VAL A 117 " pdb=" O CYS A 118 " model vdw 2.069 3.040 nonbonded pdb=" CB ASP A 604 " pdb=" CG2 THR A 778 " model vdw 2.070 3.860 ... (remaining 292544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.990 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 109.200 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.005 0.092 36896 Z= 0.346 Angle : 0.834 18.935 50385 Z= 0.489 Chirality : 0.052 0.602 5744 Planarity : 0.006 0.075 6196 Dihedral : 17.106 176.994 14337 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.78 % Favored : 91.94 % Rotamer: Outliers : 0.19 % Allowed : 0.28 % Favored : 99.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.12), residues: 4293 helix: -1.11 (0.13), residues: 1472 sheet: -1.75 (0.20), residues: 627 loop : -2.14 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 183 HIS 0.017 0.001 HIS A 124 PHE 0.028 0.002 PHE A 172 TYR 0.034 0.002 TYR H 177 ARG 0.016 0.001 ARG I1211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 483 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7787 (pm20) cc_final: 0.7575 (pm20) REVERT: A 298 ASP cc_start: 0.7653 (t70) cc_final: 0.7381 (t0) REVERT: A 311 MET cc_start: 0.7524 (mtm) cc_final: 0.7213 (mtp) REVERT: A 1067 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8050 (tmm-80) REVERT: I 39 ILE cc_start: 0.8869 (pt) cc_final: 0.8636 (pt) REVERT: I 210 LEU cc_start: 0.7599 (mt) cc_final: 0.7396 (mt) REVERT: I 337 PHE cc_start: 0.8457 (t80) cc_final: 0.8099 (t80) REVERT: I 550 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8606 (p) REVERT: I 1080 ASN cc_start: 0.8062 (t0) cc_final: 0.7854 (t0) REVERT: J 129 ASP cc_start: 0.7874 (t0) cc_final: 0.7538 (t0) REVERT: J 295 GLU cc_start: 0.7640 (tp30) cc_final: 0.7152 (tp30) REVERT: J 634 ARG cc_start: 0.7867 (ttt90) cc_final: 0.7525 (ttm-80) REVERT: J 709 ARG cc_start: 0.6807 (ppt170) cc_final: 0.6467 (ppt170) REVERT: J 725 MET cc_start: 0.8291 (mtp) cc_final: 0.7906 (mtp) REVERT: J 892 PHE cc_start: 0.8414 (m-10) cc_final: 0.8014 (m-10) REVERT: J 1019 ASN cc_start: 0.6190 (m-40) cc_final: 0.5803 (m-40) REVERT: J 1174 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.6956 (ttp80) REVERT: J 1189 MET cc_start: 0.7358 (mmm) cc_final: 0.6830 (mmm) REVERT: J 1334 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 7 outliers final: 4 residues processed: 490 average time/residue: 0.5267 time to fit residues: 416.1298 Evaluate side-chains 387 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 382 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 207 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 369 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 113 optimal weight: 4.9990 chunk 223 optimal weight: 0.0670 chunk 176 optimal weight: 0.8980 chunk 342 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 396 optimal weight: 0.0870 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 909 GLN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 834 GLN I1061 GLN J 320 ASN J 365 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36896 Z= 0.173 Angle : 0.558 13.405 50385 Z= 0.294 Chirality : 0.042 0.200 5744 Planarity : 0.005 0.060 6196 Dihedral : 15.420 176.096 6018 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 0.88 % Allowed : 6.77 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.12), residues: 4293 helix: -0.41 (0.13), residues: 1477 sheet: -1.49 (0.21), residues: 598 loop : -1.94 (0.12), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1099 HIS 0.009 0.001 HIS A 84 PHE 0.011 0.001 PHE A 643 TYR 0.014 0.001 TYR G 177 ARG 0.007 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 413 time to evaluate : 4.778 Fit side-chains REVERT: A 298 ASP cc_start: 0.7594 (t70) cc_final: 0.7318 (t0) REVERT: A 950 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 1067 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7924 (tmm-80) REVERT: G 62 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: H 177 TYR cc_start: 0.8954 (m-10) cc_final: 0.8676 (m-10) REVERT: I 210 LEU cc_start: 0.7493 (mt) cc_final: 0.7132 (mt) REVERT: I 337 PHE cc_start: 0.8303 (t80) cc_final: 0.8034 (t80) REVERT: I 618 GLN cc_start: 0.7670 (tt0) cc_final: 0.7441 (tt0) REVERT: I 1297 ASP cc_start: 0.8147 (t70) cc_final: 0.7801 (t0) REVERT: J 129 ASP cc_start: 0.7875 (t0) cc_final: 0.7325 (t0) REVERT: J 198 CYS cc_start: 0.7449 (t) cc_final: 0.7118 (t) REVERT: J 245 LEU cc_start: 0.9040 (tp) cc_final: 0.8832 (tp) REVERT: J 709 ARG cc_start: 0.6928 (ppt170) cc_final: 0.6360 (ptm-80) REVERT: J 725 MET cc_start: 0.8230 (mtp) cc_final: 0.7896 (mtp) REVERT: J 1019 ASN cc_start: 0.6188 (m-40) cc_final: 0.5769 (m-40) REVERT: J 1174 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6823 (ttm170) REVERT: J 1189 MET cc_start: 0.7105 (mmm) cc_final: 0.6754 (mmm) REVERT: J 1235 ASN cc_start: 0.7600 (m-40) cc_final: 0.7006 (m-40) REVERT: J 1334 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7291 (tm-30) outliers start: 32 outliers final: 22 residues processed: 434 average time/residue: 0.5099 time to fit residues: 354.4864 Evaluate side-chains 388 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 364 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 891 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 220 optimal weight: 0.0870 chunk 123 optimal weight: 6.9990 chunk 330 optimal weight: 0.6980 chunk 270 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 397 optimal weight: 0.0370 chunk 429 optimal weight: 2.9990 chunk 354 optimal weight: 10.0000 chunk 394 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 356 GLN A 543 HIS A 863 ASN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 320 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 865 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36896 Z= 0.166 Angle : 0.518 11.341 50385 Z= 0.273 Chirality : 0.041 0.162 5744 Planarity : 0.004 0.057 6196 Dihedral : 15.302 174.921 6017 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 1.35 % Allowed : 9.67 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4293 helix: -0.01 (0.14), residues: 1483 sheet: -1.40 (0.21), residues: 616 loop : -1.75 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.009 0.001 HIS A 84 PHE 0.016 0.001 PHE A1121 TYR 0.023 0.001 TYR I 367 ARG 0.010 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 408 time to evaluate : 3.764 Fit side-chains REVERT: A 298 ASP cc_start: 0.7641 (t70) cc_final: 0.7350 (t0) REVERT: A 356 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: A 1067 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7961 (tmm-80) REVERT: G 62 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: G 141 SER cc_start: 0.8789 (p) cc_final: 0.8385 (p) REVERT: H 177 TYR cc_start: 0.8879 (m-10) cc_final: 0.8596 (m-10) REVERT: I 210 LEU cc_start: 0.7415 (mt) cc_final: 0.6934 (mt) REVERT: I 337 PHE cc_start: 0.8286 (t80) cc_final: 0.8049 (t80) REVERT: I 618 GLN cc_start: 0.7525 (tt0) cc_final: 0.7308 (tt0) REVERT: I 685 MET cc_start: 0.8500 (mtm) cc_final: 0.8232 (mtp) REVERT: J 129 ASP cc_start: 0.7810 (t0) cc_final: 0.7194 (t0) REVERT: J 294 ASN cc_start: 0.7645 (m-40) cc_final: 0.6960 (m110) REVERT: J 372 MET cc_start: 0.8880 (ttp) cc_final: 0.8678 (ttp) REVERT: J 1019 ASN cc_start: 0.6359 (m-40) cc_final: 0.5929 (m-40) REVERT: J 1174 ARG cc_start: 0.7224 (ttp-170) cc_final: 0.6932 (ttp80) REVERT: J 1189 MET cc_start: 0.7177 (mmm) cc_final: 0.6872 (mmm) REVERT: J 1235 ASN cc_start: 0.7609 (m-40) cc_final: 0.6983 (m-40) REVERT: J 1334 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7228 (tm-30) outliers start: 49 outliers final: 31 residues processed: 441 average time/residue: 0.5300 time to fit residues: 374.2875 Evaluate side-chains 408 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 375 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER 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: 0.0670 chunk 206 optimal weight: 3.9990 chunk 44 optimal weight: 0.0050 chunk 189 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 398 optimal weight: 0.8980 chunk 422 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 378 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 overall best weight: 1.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 543 HIS G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 320 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1114 GLN J1326 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36896 Z= 0.212 Angle : 0.522 11.960 50385 Z= 0.273 Chirality : 0.041 0.152 5744 Planarity : 0.004 0.053 6196 Dihedral : 15.314 174.591 6015 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 1.52 % Allowed : 11.60 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4293 helix: 0.19 (0.14), residues: 1479 sheet: -1.28 (0.21), residues: 612 loop : -1.71 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 183 HIS 0.008 0.001 HIS A 84 PHE 0.021 0.001 PHE A 355 TYR 0.019 0.001 TYR I 367 ARG 0.007 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 385 time to evaluate : 3.675 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.7682 (t70) cc_final: 0.7384 (t0) REVERT: A 1067 ARG cc_start: 0.8410 (ttp80) cc_final: 0.7987 (tmm-80) REVERT: G 62 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: G 141 SER cc_start: 0.8668 (p) cc_final: 0.8239 (p) REVERT: H 177 TYR cc_start: 0.8908 (m-10) cc_final: 0.8634 (m-10) REVERT: H 199 ASP cc_start: 0.8086 (m-30) cc_final: 0.7671 (t0) REVERT: I 210 LEU cc_start: 0.7606 (mt) cc_final: 0.7110 (mt) REVERT: I 337 PHE cc_start: 0.8304 (t80) cc_final: 0.8020 (t80) REVERT: I 386 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7214 (tm-30) REVERT: I 618 GLN cc_start: 0.7535 (tt0) cc_final: 0.7333 (tt0) REVERT: I 685 MET cc_start: 0.8488 (mtm) cc_final: 0.8180 (mtp) REVERT: I 1297 ASP cc_start: 0.8160 (t70) cc_final: 0.7904 (t0) REVERT: J 129 ASP cc_start: 0.7869 (t0) cc_final: 0.7199 (t0) REVERT: J 571 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7633 (p0) REVERT: J 634 ARG cc_start: 0.7405 (ttt90) cc_final: 0.7114 (ttm-80) REVERT: J 835 LEU cc_start: 0.8108 (tp) cc_final: 0.7752 (tp) REVERT: J 1019 ASN cc_start: 0.6228 (m-40) cc_final: 0.5777 (m-40) REVERT: J 1174 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6937 (ttp80) REVERT: J 1189 MET cc_start: 0.7118 (mmm) cc_final: 0.6839 (mmm) REVERT: J 1235 ASN cc_start: 0.7708 (m-40) cc_final: 0.7024 (m-40) REVERT: J 1334 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7254 (tm-30) outliers start: 55 outliers final: 33 residues processed: 425 average time/residue: 0.5233 time to fit residues: 354.0832 Evaluate side-chains 399 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 364 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 360 optimal weight: 0.6980 chunk 291 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN J 294 ASN J 320 ASN J 365 GLN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 36896 Z= 0.382 Angle : 0.598 12.147 50385 Z= 0.311 Chirality : 0.044 0.188 5744 Planarity : 0.004 0.059 6196 Dihedral : 15.419 176.380 6012 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.38 % Favored : 92.55 % Rotamer: Outliers : 1.93 % Allowed : 12.57 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4293 helix: 0.02 (0.14), residues: 1502 sheet: -1.44 (0.20), residues: 633 loop : -1.75 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 183 HIS 0.010 0.001 HIS A 84 PHE 0.018 0.001 PHE A 355 TYR 0.015 0.001 TYR I 367 ARG 0.008 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 367 time to evaluate : 3.384 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.7764 (t70) cc_final: 0.7437 (t0) REVERT: A 1067 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8035 (tmm-80) REVERT: G 62 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: G 75 GLN cc_start: 0.8684 (pt0) cc_final: 0.8358 (tt0) REVERT: H 177 TYR cc_start: 0.9023 (m-10) cc_final: 0.8752 (m-10) REVERT: I 210 LEU cc_start: 0.7597 (mt) cc_final: 0.6956 (mt) REVERT: I 337 PHE cc_start: 0.8404 (t80) cc_final: 0.8094 (t80) REVERT: I 386 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7201 (tm-30) REVERT: I 685 MET cc_start: 0.8645 (mtm) cc_final: 0.8328 (mtp) REVERT: I 1297 ASP cc_start: 0.8429 (t70) cc_final: 0.8158 (t0) REVERT: J 129 ASP cc_start: 0.7924 (t0) cc_final: 0.7304 (t0) REVERT: J 289 ASP cc_start: 0.7963 (m-30) cc_final: 0.7674 (t0) REVERT: J 295 GLU cc_start: 0.7243 (tp30) cc_final: 0.6947 (tp30) REVERT: J 548 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8723 (t) REVERT: J 571 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7613 (p0) REVERT: J 709 ARG cc_start: 0.6805 (ppt170) cc_final: 0.6125 (ptm-80) REVERT: J 997 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7185 (m) REVERT: J 1019 ASN cc_start: 0.6395 (m-40) cc_final: 0.5819 (m-40) REVERT: J 1174 ARG cc_start: 0.7093 (ttp-170) cc_final: 0.6856 (ttp80) REVERT: J 1189 MET cc_start: 0.7188 (mmm) cc_final: 0.6810 (mmm) REVERT: J 1235 ASN cc_start: 0.7780 (m-40) cc_final: 0.7048 (m-40) REVERT: J 1266 ILE cc_start: 0.7969 (mm) cc_final: 0.7745 (mm) REVERT: J 1334 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7466 (tm-30) outliers start: 70 outliers final: 50 residues processed: 415 average time/residue: 0.5142 time to fit residues: 343.7369 Evaluate side-chains 406 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 352 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 142 optimal weight: 9.9990 chunk 380 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 104 optimal weight: 0.0570 chunk 422 optimal weight: 2.9990 chunk 350 optimal weight: 0.0370 chunk 195 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN J 365 GLN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36896 Z= 0.240 Angle : 0.539 12.090 50385 Z= 0.282 Chirality : 0.042 0.160 5744 Planarity : 0.004 0.051 6196 Dihedral : 15.363 175.494 6012 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 1.93 % Allowed : 13.40 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 4293 helix: 0.20 (0.14), residues: 1495 sheet: -1.43 (0.20), residues: 637 loop : -1.67 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 183 HIS 0.009 0.001 HIS A 84 PHE 0.013 0.001 PHE J 172 TYR 0.016 0.001 TYR I 367 ARG 0.008 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 365 time to evaluate : 4.063 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.7697 (t70) cc_final: 0.7375 (t0) REVERT: A 1067 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8028 (tmm-80) REVERT: G 62 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: G 141 SER cc_start: 0.8768 (p) cc_final: 0.8466 (p) REVERT: H 177 TYR cc_start: 0.8977 (m-10) cc_final: 0.8755 (m-10) REVERT: I 210 LEU cc_start: 0.7545 (mt) cc_final: 0.6881 (mt) REVERT: I 337 PHE cc_start: 0.8463 (t80) cc_final: 0.8170 (t80) REVERT: I 1297 ASP cc_start: 0.8363 (t70) cc_final: 0.8089 (t0) REVERT: J 129 ASP cc_start: 0.7837 (t0) cc_final: 0.7136 (t0) REVERT: J 289 ASP cc_start: 0.7932 (m-30) cc_final: 0.7636 (t0) REVERT: J 295 GLU cc_start: 0.7161 (tp30) cc_final: 0.6905 (tp30) REVERT: J 709 ARG cc_start: 0.6742 (ppt170) cc_final: 0.6063 (ptm-80) REVERT: J 835 LEU cc_start: 0.8107 (tp) cc_final: 0.7836 (tp) REVERT: J 997 VAL cc_start: 0.7363 (OUTLIER) cc_final: 0.7159 (m) REVERT: J 1019 ASN cc_start: 0.6322 (m-40) cc_final: 0.5831 (m-40) REVERT: J 1174 ARG cc_start: 0.7082 (ttp-170) cc_final: 0.6676 (ttp80) REVERT: J 1189 MET cc_start: 0.7156 (mmm) cc_final: 0.6799 (mmm) REVERT: J 1235 ASN cc_start: 0.7750 (m-40) cc_final: 0.7005 (m110) REVERT: J 1266 ILE cc_start: 0.7832 (mm) cc_final: 0.7599 (mm) REVERT: J 1334 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7311 (tm-30) outliers start: 70 outliers final: 52 residues processed: 416 average time/residue: 0.4922 time to fit residues: 329.6121 Evaluate side-chains 403 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 349 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 407 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 355 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 421 optimal weight: 7.9990 chunk 263 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 821 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36896 Z= 0.205 Angle : 0.523 12.088 50385 Z= 0.273 Chirality : 0.041 0.162 5744 Planarity : 0.004 0.052 6196 Dihedral : 15.288 174.342 6012 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 1.71 % Allowed : 14.42 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 4293 helix: 0.35 (0.14), residues: 1499 sheet: -1.36 (0.20), residues: 646 loop : -1.62 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 183 HIS 0.009 0.001 HIS A 84 PHE 0.013 0.001 PHE J 172 TYR 0.015 0.001 TYR I 367 ARG 0.008 0.000 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 380 time to evaluate : 3.915 Fit side-chains REVERT: A 298 ASP cc_start: 0.7672 (t70) cc_final: 0.7353 (t0) REVERT: A 1067 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7987 (tmm-80) REVERT: G 62 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: G 141 SER cc_start: 0.8750 (p) cc_final: 0.8440 (p) REVERT: H 199 ASP cc_start: 0.8151 (m-30) cc_final: 0.7694 (t0) REVERT: I 210 LEU cc_start: 0.7539 (mt) cc_final: 0.6885 (mt) REVERT: I 337 PHE cc_start: 0.8427 (t80) cc_final: 0.8143 (t80) REVERT: I 386 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7329 (tm-30) REVERT: J 129 ASP cc_start: 0.7830 (t0) cc_final: 0.7134 (t0) REVERT: J 289 ASP cc_start: 0.7923 (m-30) cc_final: 0.7624 (t0) REVERT: J 295 GLU cc_start: 0.7162 (tp30) cc_final: 0.6928 (tp30) REVERT: J 709 ARG cc_start: 0.6728 (ppt170) cc_final: 0.6029 (ptm-80) REVERT: J 835 LEU cc_start: 0.8084 (tp) cc_final: 0.7809 (tp) REVERT: J 997 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7158 (m) REVERT: J 1019 ASN cc_start: 0.6322 (m-40) cc_final: 0.5824 (m-40) REVERT: J 1174 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6672 (ttp80) REVERT: J 1189 MET cc_start: 0.7184 (mmm) cc_final: 0.6855 (mmm) REVERT: J 1235 ASN cc_start: 0.7785 (m-40) cc_final: 0.7275 (m110) REVERT: J 1266 ILE cc_start: 0.7832 (mm) cc_final: 0.7591 (mm) REVERT: J 1334 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7262 (tm-30) outliers start: 62 outliers final: 49 residues processed: 424 average time/residue: 0.5058 time to fit residues: 345.0308 Evaluate side-chains 414 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 363 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 260 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 251 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 chunk 286 optimal weight: 0.0970 chunk 208 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN I 955 GLN J 320 ASN J 594 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 36896 Z= 0.153 Angle : 0.507 12.068 50385 Z= 0.264 Chirality : 0.040 0.162 5744 Planarity : 0.004 0.053 6196 Dihedral : 15.175 172.954 6012 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 1.60 % Allowed : 14.78 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4293 helix: 0.57 (0.14), residues: 1497 sheet: -1.22 (0.20), residues: 631 loop : -1.51 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 183 HIS 0.006 0.001 HIS A 84 PHE 0.013 0.001 PHE J 172 TYR 0.049 0.001 TYR H 177 ARG 0.009 0.000 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 404 time to evaluate : 4.178 Fit side-chains revert: symmetry clash REVERT: A 84 HIS cc_start: 0.7102 (t70) cc_final: 0.6759 (t70) REVERT: A 298 ASP cc_start: 0.7634 (t70) cc_final: 0.7324 (t0) REVERT: A 1067 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7983 (tmm-80) REVERT: G 62 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: G 141 SER cc_start: 0.8717 (p) cc_final: 0.8396 (p) REVERT: H 199 ASP cc_start: 0.8064 (m-30) cc_final: 0.7546 (t0) REVERT: I 7 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6087 (mt-10) REVERT: I 18 ARG cc_start: 0.8021 (mmt90) cc_final: 0.7440 (mmt90) REVERT: I 337 PHE cc_start: 0.8370 (t80) cc_final: 0.8079 (t80) REVERT: I 386 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7302 (tm-30) REVERT: I 685 MET cc_start: 0.8433 (mtm) cc_final: 0.8231 (mtp) REVERT: J 129 ASP cc_start: 0.7733 (t0) cc_final: 0.7020 (t0) REVERT: J 294 ASN cc_start: 0.7598 (m-40) cc_final: 0.6893 (m110) REVERT: J 626 TYR cc_start: 0.8731 (m-80) cc_final: 0.8343 (m-80) REVERT: J 835 LEU cc_start: 0.8063 (tp) cc_final: 0.7777 (tp) REVERT: J 1019 ASN cc_start: 0.6289 (m-40) cc_final: 0.5789 (m-40) REVERT: J 1174 ARG cc_start: 0.7136 (ttp-170) cc_final: 0.6771 (ttp80) REVERT: J 1189 MET cc_start: 0.7158 (mmm) cc_final: 0.6914 (mmm) REVERT: J 1235 ASN cc_start: 0.7750 (m-40) cc_final: 0.7291 (m110) REVERT: J 1266 ILE cc_start: 0.7794 (mm) cc_final: 0.7560 (mm) REVERT: J 1334 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7200 (tm-30) REVERT: K 53 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8581 (mt-10) outliers start: 58 outliers final: 47 residues processed: 446 average time/residue: 0.4921 time to fit residues: 353.5470 Evaluate side-chains 428 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 379 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1287 ILE Chi-restraints excluded: chain J residue 1326 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 383 optimal weight: 8.9990 chunk 403 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 392 optimal weight: 0.0040 chunk 236 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 308 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 354 optimal weight: 7.9990 chunk 371 optimal weight: 3.9990 chunk 391 optimal weight: 5.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36896 Z= 0.305 Angle : 0.562 12.878 50385 Z= 0.291 Chirality : 0.043 0.207 5744 Planarity : 0.004 0.052 6196 Dihedral : 15.258 174.463 6012 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.76 % Favored : 93.17 % Rotamer: Outliers : 1.66 % Allowed : 15.14 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 4293 helix: 0.48 (0.14), residues: 1498 sheet: -1.29 (0.20), residues: 626 loop : -1.56 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 183 HIS 0.011 0.001 HIS A 84 PHE 0.012 0.001 PHE A 434 TYR 0.047 0.001 TYR H 177 ARG 0.009 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 370 time to evaluate : 4.212 Fit side-chains REVERT: A 84 HIS cc_start: 0.7321 (t70) cc_final: 0.7024 (t70) REVERT: A 298 ASP cc_start: 0.7712 (t70) cc_final: 0.7382 (t0) REVERT: G 62 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: G 141 SER cc_start: 0.8637 (p) cc_final: 0.8246 (p) REVERT: I 81 ASP cc_start: 0.8233 (p0) cc_final: 0.7934 (p0) REVERT: I 210 LEU cc_start: 0.7595 (mt) cc_final: 0.6858 (mt) REVERT: I 337 PHE cc_start: 0.8430 (t80) cc_final: 0.8116 (t80) REVERT: I 386 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7377 (tm-30) REVERT: I 685 MET cc_start: 0.8563 (mtm) cc_final: 0.8290 (mtp) REVERT: I 1297 ASP cc_start: 0.8367 (t70) cc_final: 0.8143 (t0) REVERT: J 129 ASP cc_start: 0.7877 (t0) cc_final: 0.7210 (t0) REVERT: J 289 ASP cc_start: 0.7884 (m-30) cc_final: 0.7578 (t0) REVERT: J 294 ASN cc_start: 0.7646 (m-40) cc_final: 0.6885 (m110) REVERT: J 295 GLU cc_start: 0.7226 (tp30) cc_final: 0.6906 (tp30) REVERT: J 709 ARG cc_start: 0.6732 (ppt170) cc_final: 0.6007 (ptm-80) REVERT: J 835 LEU cc_start: 0.8060 (tp) cc_final: 0.7791 (tp) REVERT: J 1019 ASN cc_start: 0.6359 (m-40) cc_final: 0.5833 (m-40) REVERT: J 1149 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7549 (mtp85) REVERT: J 1174 ARG cc_start: 0.7145 (ttp-170) cc_final: 0.6762 (ttp80) REVERT: J 1189 MET cc_start: 0.7180 (mmm) cc_final: 0.6866 (mmm) REVERT: J 1235 ASN cc_start: 0.7759 (m-40) cc_final: 0.7148 (m110) REVERT: J 1266 ILE cc_start: 0.7913 (mm) cc_final: 0.7681 (mm) REVERT: J 1334 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7286 (tm-30) REVERT: K 53 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8607 (mt-10) outliers start: 60 outliers final: 51 residues processed: 414 average time/residue: 0.4891 time to fit residues: 327.2831 Evaluate side-chains 410 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 358 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1287 ILE Chi-restraints excluded: chain J residue 1326 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 257 optimal weight: 10.0000 chunk 415 optimal weight: 4.9990 chunk 253 optimal weight: 0.0270 chunk 196 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 435 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 346 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 267 optimal weight: 0.0670 chunk 212 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 320 ASN J 594 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36896 Z= 0.159 Angle : 0.514 11.910 50385 Z= 0.268 Chirality : 0.041 0.179 5744 Planarity : 0.004 0.054 6196 Dihedral : 15.160 173.412 6012 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 1.63 % Allowed : 15.11 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4293 helix: 0.62 (0.14), residues: 1499 sheet: -1.22 (0.20), residues: 636 loop : -1.48 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 183 HIS 0.006 0.001 HIS A 84 PHE 0.012 0.001 PHE A 355 TYR 0.035 0.001 TYR H 177 ARG 0.010 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8586 Ramachandran restraints generated. 4293 Oldfield, 0 Emsley, 4293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 386 time to evaluate : 3.988 Fit side-chains revert: symmetry clash REVERT: A 84 HIS cc_start: 0.7139 (t70) cc_final: 0.6770 (t70) REVERT: A 298 ASP cc_start: 0.7640 (t70) cc_final: 0.7327 (t0) REVERT: A 740 GLU cc_start: 0.7744 (mp0) cc_final: 0.7395 (mp0) REVERT: G 141 SER cc_start: 0.8705 (p) cc_final: 0.8383 (p) REVERT: H 199 ASP cc_start: 0.8059 (m-30) cc_final: 0.7625 (t0) REVERT: I 7 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5804 (mp0) REVERT: I 18 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7396 (mmt90) REVERT: I 183 TRP cc_start: 0.8533 (m-10) cc_final: 0.7861 (m-10) REVERT: I 337 PHE cc_start: 0.8382 (t80) cc_final: 0.8122 (t80) REVERT: I 386 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7368 (tm-30) REVERT: I 685 MET cc_start: 0.8435 (mtm) cc_final: 0.8153 (mtp) REVERT: J 129 ASP cc_start: 0.7757 (t0) cc_final: 0.7051 (t0) REVERT: J 289 ASP cc_start: 0.7872 (m-30) cc_final: 0.7549 (t0) REVERT: J 709 ARG cc_start: 0.6681 (ppt170) cc_final: 0.6405 (ppt170) REVERT: J 835 LEU cc_start: 0.7992 (tp) cc_final: 0.7732 (tp) REVERT: J 1019 ASN cc_start: 0.6305 (m-40) cc_final: 0.5787 (m-40) REVERT: J 1174 ARG cc_start: 0.7127 (ttp-170) cc_final: 0.6178 (ttt-90) REVERT: J 1189 MET cc_start: 0.7064 (mmm) cc_final: 0.6823 (mmm) REVERT: J 1235 ASN cc_start: 0.7791 (m-40) cc_final: 0.7393 (m110) REVERT: J 1266 ILE cc_start: 0.7890 (mm) cc_final: 0.7644 (mm) REVERT: J 1334 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7205 (tm-30) outliers start: 59 outliers final: 48 residues processed: 426 average time/residue: 0.5082 time to fit residues: 347.3625 Evaluate side-chains 426 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 377 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 496 LYS Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1287 ILE Chi-restraints excluded: chain J residue 1326 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 275 optimal weight: 3.9990 chunk 369 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 319 optimal weight: 0.0270 chunk 51 optimal weight: 0.0470 chunk 96 optimal weight: 0.3980 chunk 347 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 356 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 320 ASN J1295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112247 restraints weight = 48588.138| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.41 r_work: 0.3180 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 36896 Z= 0.137 Angle : 0.504 16.690 50385 Z= 0.261 Chirality : 0.040 0.202 5744 Planarity : 0.004 0.055 6196 Dihedral : 15.028 171.536 6012 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 1.30 % Allowed : 15.55 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4293 helix: 0.84 (0.14), residues: 1499 sheet: -1.10 (0.20), residues: 637 loop : -1.37 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 260 HIS 0.004 0.000 HIS A 84 PHE 0.011 0.001 PHE J 172 TYR 0.032 0.001 TYR H 177 ARG 0.010 0.000 ARG I 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8627.09 seconds wall clock time: 154 minutes 57.15 seconds (9297.15 seconds total)