Starting phenix.real_space_refine (version: dev) on Thu Feb 23 13:52:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2023/6o7i_0642_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2023/6o7i_0642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2023/6o7i_0642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2023/6o7i_0642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2023/6o7i_0642_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7i_0642/02_2023/6o7i_0642_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "J ARG 74": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "K ARG 4": "NH1" <-> "NH2" Residue "K ARG 58": "NH1" <-> "NH2" Residue "K ARG 90": "NH1" <-> "NH2" Residue "K ARG 107": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "K ARG 173": "NH1" <-> "NH2" Residue "K ARG 181": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 231": "NH1" <-> "NH2" Residue "K PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 383": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20276 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5935 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 6 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1065 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2191 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2178 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 2 Chain: "E" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2207 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 20, 'TRANS': 258} Chain breaks: 1 Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 907 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 569 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 12, 'rna3p': 13} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "K" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2198 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "F" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2536 Classifications: {'peptide': 361} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 93, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3000 SG CYS A 389 61.945 108.426 107.521 1.00 26.96 S ATOM 3020 SG CYS A 392 57.962 106.580 107.991 1.00 25.58 S ATOM 3175 SG CYS A 413 59.672 108.840 110.942 1.00 33.04 S ATOM 3195 SG CYS A 416 60.786 105.552 110.270 1.00 32.70 S ATOM 7804 SG CYS C 113 78.649 118.893 83.547 1.00 26.80 S ATOM 7871 SG CYS C 122 80.218 118.407 80.144 1.00 17.37 S ATOM 7891 SG CYS C 125 76.481 116.361 82.122 1.00 21.96 S ATOM 10000 SG CYS D 113 95.191 89.112 86.916 1.00 29.12 S ATOM 10067 SG CYS D 122 97.096 88.689 83.714 1.00 23.66 S ATOM 10087 SG CYS D 125 93.080 88.859 83.641 1.00 23.54 S ATOM 16261 SG CYS K 113 95.575 55.229 83.185 1.00 56.33 S ATOM 16328 SG CYS K 122 98.462 54.545 81.147 1.00 52.56 S ATOM 16348 SG CYS K 125 94.722 56.298 79.316 1.00 44.05 S Time building chain proxies: 11.24, per 1000 atoms: 0.55 Number of scatterers: 20276 At special positions: 0 Unit cell: (129.591, 143.748, 168.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 60 16.00 P 48 15.00 O 3860 8.00 N 3555 7.00 C 12749 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: 7.85 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 111 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 122 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 125 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 113 " Number of angles added : 15 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 32 sheets defined 39.0% alpha, 14.9% beta 10 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 5.71 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.378A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 31 through 44 removed outlier: 5.210A pdb=" N PHE A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.793A pdb=" N LEU A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.823A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 106 removed outlier: 3.779A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.675A pdb=" N GLU A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.511A pdb=" N LEU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.715A pdb=" N LYS A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.564A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.619A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.951A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.874A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.653A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.517A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 598 through 614 removed outlier: 3.848A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.996A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.772A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.524A pdb=" N TRP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 removed outlier: 3.934A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 719' Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.547A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 removed outlier: 4.421A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.373A pdb=" N TRP B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 72 through 84 removed outlier: 3.736A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.695A pdb=" N LEU B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 removed outlier: 4.056A pdb=" N ARG B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.990A pdb=" N ARG B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 183 removed outlier: 3.863A pdb=" N GLN B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.595A pdb=" N LEU C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 3.631A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 205 through 220 removed outlier: 3.532A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.792A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.614A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 70 removed outlier: 4.052A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.714A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 223 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.728A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.895A pdb=" N VAL E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.602A pdb=" N ILE E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 81' Processing helix chain 'E' and resid 90 through 99 removed outlier: 3.599A pdb=" N ALA E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 164 through 171 removed outlier: 4.003A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'J' and resid 51 through 63 Processing helix chain 'J' and resid 72 through 83 removed outlier: 3.676A pdb=" N THR J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 100 through 108 removed outlier: 3.822A pdb=" N THR J 104 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS J 108 " --> pdb=" O THR J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 100 through 108' Processing helix chain 'J' and resid 117 through 132 removed outlier: 4.311A pdb=" N VAL J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR J 130 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL J 131 " --> pdb=" O LEU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 4.257A pdb=" N VAL J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 178 removed outlier: 3.874A pdb=" N VAL J 176 " --> pdb=" O LEU J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.702A pdb=" N ARG K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 115 through 120 Processing helix chain 'K' and resid 149 through 157 removed outlier: 4.197A pdb=" N LYS K 155 " --> pdb=" O GLU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 223 Processing helix chain 'K' and resid 249 through 254 Processing helix chain 'K' and resid 267 through 272 removed outlier: 3.572A pdb=" N ILE K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 280 Processing helix chain 'K' and resid 280 through 287 Processing helix chain 'F' and resid 36 through 44 removed outlier: 4.420A pdb=" N UNK F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 60 removed outlier: 3.572A pdb=" N UNK F 55 " --> pdb=" O UNK F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.785A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.716A pdb=" N UNK F 166 " --> pdb=" O UNK F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 185 removed outlier: 3.785A pdb=" N UNK F 183 " --> pdb=" O UNK F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 256 through 262 removed outlier: 3.505A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.654A pdb=" N ALA F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 304 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.666A pdb=" N ALA F 343 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET F 344 " --> pdb=" O TRP F 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 344' Processing helix chain 'F' and resid 345 through 352 removed outlier: 4.099A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 351 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.025A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.622A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.622A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.639A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.585A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 594 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA8, first strand: chain 'C' and resid 49 through 50 removed outlier: 4.398A pdb=" N GLU C 195 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA C 146 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU C 193 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 148 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU C 191 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 190 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 243 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 261 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88 removed outlier: 7.316A pdb=" N SER C 85 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB2, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AB3, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.702A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.589A pdb=" N PHE D 194 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 88 removed outlier: 5.247A pdb=" N SER D 85 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE D 101 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY D 87 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB7, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AB8, first strand: chain 'E' and resid 58 through 61 removed outlier: 8.185A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 68 Processing sheet with id=AC1, first strand: chain 'E' and resid 124 through 132 Processing sheet with id=AC2, first strand: chain 'E' and resid 251 through 254 removed outlier: 4.022A pdb=" N SER E 251 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 229 through 232 Processing sheet with id=AC4, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC5, first strand: chain 'E' and resid 261 through 263 removed outlier: 3.806A pdb=" N VAL E 271 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.963A pdb=" N GLY K 7 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE K 147 " --> pdb=" O GLU K 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.963A pdb=" N GLY K 7 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL K 10 " --> pdb=" O PHE K 243 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE K 243 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS K 12 " --> pdb=" O ASP K 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP K 241 " --> pdb=" O LYS K 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE K 243 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 85 through 88 removed outlier: 7.057A pdb=" N SER K 85 " --> pdb=" O PHE K 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AD1, first strand: chain 'K' and resid 163 through 168 removed outlier: 3.721A pdb=" N ARG K 181 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.668A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AD5, first strand: chain 'F' and resid 237 through 243 removed outlier: 3.723A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 8.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4689 1.33 - 1.45: 4929 1.45 - 1.57: 10990 1.57 - 1.69: 93 1.69 - 1.82: 97 Bond restraints: 20798 Sorted by residual: bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.82e+01 bond pdb=" CG LEU E 134 " pdb=" CD1 LEU E 134 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.56e+01 bond pdb=" CG1 ILE D 40 " pdb=" CD1 ILE D 40 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.20e+01 bond pdb=" CB PRO C 51 " pdb=" CG PRO C 51 " ideal model delta sigma weight residual 1.492 1.323 0.169 5.00e-02 4.00e+02 1.15e+01 bond pdb=" CB ILE E 143 " pdb=" CG2 ILE E 143 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.12e+01 ... (remaining 20793 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.41: 658 105.41 - 112.60: 10221 112.60 - 119.79: 7712 119.79 - 126.97: 9365 126.97 - 134.16: 360 Bond angle restraints: 28316 Sorted by residual: angle pdb=" C4' C G 14 " pdb=" C3' C G 14 " pdb=" O3' C G 14 " ideal model delta sigma weight residual 109.40 100.83 8.57 1.50e+00 4.44e-01 3.26e+01 angle pdb=" N ASP D 2 " pdb=" CA ASP D 2 " pdb=" C ASP D 2 " ideal model delta sigma weight residual 110.91 117.26 -6.35 1.17e+00 7.31e-01 2.94e+01 angle pdb=" C4' G G 9 " pdb=" C3' G G 9 " pdb=" O3' G G 9 " ideal model delta sigma weight residual 109.40 101.48 7.92 1.50e+00 4.44e-01 2.78e+01 angle pdb=" N VAL A 753 " pdb=" CA VAL A 753 " pdb=" C VAL A 753 " ideal model delta sigma weight residual 112.29 107.40 4.89 9.40e-01 1.13e+00 2.70e+01 angle pdb=" C GLY A 376 " pdb=" N LEU A 377 " pdb=" CA LEU A 377 " ideal model delta sigma weight residual 120.28 127.24 -6.96 1.34e+00 5.57e-01 2.70e+01 ... (remaining 28311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 12115 33.33 - 66.65: 172 66.65 - 99.98: 15 99.98 - 133.31: 0 133.31 - 166.64: 1 Dihedral angle restraints: 12303 sinusoidal: 5247 harmonic: 7056 Sorted by residual: dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 38.64 -166.64 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' U H 29 " pdb=" C1' U H 29 " pdb=" N1 U H 29 " pdb=" C2 U H 29 " ideal model delta sinusoidal sigma weight residual -160.00 -79.30 -80.70 1 1.50e+01 4.44e-03 3.58e+01 dihedral pdb=" CA LYS A 369 " pdb=" C LYS A 369 " pdb=" N ARG A 370 " pdb=" CA ARG A 370 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 12300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2350 0.073 - 0.147: 624 0.147 - 0.220: 116 0.220 - 0.293: 24 0.293 - 0.367: 7 Chirality restraints: 3121 Sorted by residual: chirality pdb=" CB VAL E 157 " pdb=" CA VAL E 157 " pdb=" CG1 VAL E 157 " pdb=" CG2 VAL E 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB VAL E 132 " pdb=" CA VAL E 132 " pdb=" CG1 VAL E 132 " pdb=" CG2 VAL E 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB VAL C 236 " pdb=" CA VAL C 236 " pdb=" CG1 VAL C 236 " pdb=" CG2 VAL C 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 3118 not shown) Planarity restraints: 3463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 13 " -0.048 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" N9 G G 13 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G G 13 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G G 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G G 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G G 13 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G G 13 " -0.019 2.00e-02 2.50e+03 pdb=" N1 G G 13 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G G 13 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G G 13 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G G 13 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G G 13 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 389 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 390 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 13 " -0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO E 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.045 5.00e-02 4.00e+02 ... (remaining 3460 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 700 2.68 - 3.24: 18183 3.24 - 3.79: 31834 3.79 - 4.35: 42391 4.35 - 4.90: 71150 Nonbonded interactions: 164258 Sorted by model distance: nonbonded pdb=" O2' G G 9 " pdb=" C5 C G 10 " model vdw 2.131 3.340 nonbonded pdb=" O2' C G 10 " pdb=" O5' G G 11 " model vdw 2.203 2.440 nonbonded pdb=" O THR A 435 " pdb=" OG SER A 449 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU C 168 " pdb=" OH TYR C 233 " model vdw 2.244 2.440 nonbonded pdb=" O ARG B 124 " pdb=" OH TYR J 178 " model vdw 2.251 2.440 ... (remaining 164253 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 'C' and (resid 4 through 24 or resid 38 through 272 or resid 276 through \ 287 or resid 301)) selection = (chain 'D' and (resid 4 through 24 or resid 38 through 287 or resid 301)) selection = (chain 'K' and (resid 4 through 24 or resid 38 through 272 or resid 276 through \ 287 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 48 5.49 5 S 60 5.16 5 C 12749 2.51 5 N 3555 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.490 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: 0.010 Extract box with map and model: 5.270 Check model and map are aligned: 0.290 Process input model: 59.260 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.012 0.169 20798 Z= 0.761 Angle : 1.170 10.493 28316 Z= 0.649 Chirality : 0.070 0.367 3121 Planarity : 0.008 0.087 3463 Dihedral : 12.130 166.637 7779 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.17 % Favored : 91.78 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.50 (0.14), residues: 2325 helix: -3.32 (0.12), residues: 803 sheet: -2.58 (0.24), residues: 359 loop : -2.84 (0.15), residues: 1163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 422 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 434 average time/residue: 0.4152 time to fit residues: 254.0028 Evaluate side-chains 283 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 276 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1977 time to fit residues: 5.7760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 382 HIS B 72 ASN C 22 HIS C 179 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 106 ASN E 200 HIS J 173 GLN K 22 HIS K 179 ASN F 18 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20798 Z= 0.186 Angle : 0.600 8.778 28316 Z= 0.310 Chirality : 0.043 0.218 3121 Planarity : 0.005 0.060 3463 Dihedral : 10.366 169.742 3280 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.36 (0.15), residues: 2325 helix: -1.92 (0.15), residues: 859 sheet: -2.11 (0.25), residues: 335 loop : -2.47 (0.16), residues: 1131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 350 average time/residue: 0.3874 time to fit residues: 197.4521 Evaluate side-chains 272 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 257 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1808 time to fit residues: 8.1621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 190 optimal weight: 0.0030 chunk 65 optimal weight: 0.6980 chunk 153 optimal weight: 0.4980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 20798 Z= 0.160 Angle : 0.557 10.116 28316 Z= 0.283 Chirality : 0.042 0.179 3121 Planarity : 0.005 0.052 3463 Dihedral : 10.032 170.252 3280 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.65 (0.16), residues: 2325 helix: -1.15 (0.17), residues: 872 sheet: -1.83 (0.26), residues: 339 loop : -2.21 (0.17), residues: 1114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 288 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 307 average time/residue: 0.3897 time to fit residues: 174.9589 Evaluate side-chains 259 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 246 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1996 time to fit residues: 7.7911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 203 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 20798 Z= 0.150 Angle : 0.539 19.134 28316 Z= 0.270 Chirality : 0.042 0.230 3121 Planarity : 0.004 0.047 3463 Dihedral : 9.845 171.357 3280 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.16), residues: 2325 helix: -0.61 (0.17), residues: 876 sheet: -1.56 (0.27), residues: 327 loop : -2.04 (0.17), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 287 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 305 average time/residue: 0.3821 time to fit residues: 172.6934 Evaluate side-chains 257 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1946 time to fit residues: 9.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 30.0000 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 20798 Z= 0.368 Angle : 0.643 15.269 28316 Z= 0.326 Chirality : 0.046 0.274 3121 Planarity : 0.005 0.049 3463 Dihedral : 10.020 157.932 3280 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.17), residues: 2325 helix: -0.55 (0.17), residues: 874 sheet: -1.42 (0.27), residues: 342 loop : -2.02 (0.17), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 254 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 277 average time/residue: 0.3684 time to fit residues: 152.1781 Evaluate side-chains 257 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 239 time to evaluate : 2.282 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2121 time to fit residues: 9.9239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 169 optimal weight: 0.0870 chunk 94 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 20798 Z= 0.140 Angle : 0.529 12.608 28316 Z= 0.266 Chirality : 0.041 0.258 3121 Planarity : 0.004 0.046 3463 Dihedral : 9.753 166.280 3280 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.17), residues: 2325 helix: -0.13 (0.18), residues: 885 sheet: -1.26 (0.27), residues: 323 loop : -1.85 (0.17), residues: 1117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 264 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 273 average time/residue: 0.3968 time to fit residues: 158.6781 Evaluate side-chains 249 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1920 time to fit residues: 6.3126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20798 Z= 0.222 Angle : 0.567 13.061 28316 Z= 0.285 Chirality : 0.043 0.239 3121 Planarity : 0.004 0.046 3463 Dihedral : 9.756 164.481 3280 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.17), residues: 2325 helix: 0.04 (0.18), residues: 880 sheet: -1.23 (0.27), residues: 323 loop : -1.77 (0.18), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 260 average time/residue: 0.3963 time to fit residues: 152.0318 Evaluate side-chains 242 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 234 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1981 time to fit residues: 6.0514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 20798 Z= 0.188 Angle : 0.553 14.914 28316 Z= 0.276 Chirality : 0.042 0.214 3121 Planarity : 0.004 0.046 3463 Dihedral : 9.693 165.320 3280 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.35 (0.17), residues: 2325 helix: 0.18 (0.18), residues: 882 sheet: -1.13 (0.28), residues: 323 loop : -1.71 (0.18), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 254 average time/residue: 0.3759 time to fit residues: 142.0106 Evaluate side-chains 246 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 241 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2027 time to fit residues: 5.2886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 189 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 171 optimal weight: 0.3980 chunk 179 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN C 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20798 Z= 0.158 Angle : 0.539 14.648 28316 Z= 0.267 Chirality : 0.042 0.249 3121 Planarity : 0.004 0.046 3463 Dihedral : 9.621 168.596 3280 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2325 helix: 0.27 (0.18), residues: 895 sheet: -0.99 (0.28), residues: 314 loop : -1.61 (0.18), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 254 average time/residue: 0.3656 time to fit residues: 139.9370 Evaluate side-chains 237 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1925 time to fit residues: 3.9186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 193 optimal weight: 0.0970 chunk 167 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20798 Z= 0.217 Angle : 0.577 14.610 28316 Z= 0.287 Chirality : 0.043 0.210 3121 Planarity : 0.004 0.046 3463 Dihedral : 9.662 165.799 3280 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2325 helix: 0.22 (0.18), residues: 900 sheet: -0.96 (0.29), residues: 318 loop : -1.59 (0.18), residues: 1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 240 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 249 average time/residue: 0.3776 time to fit residues: 140.8429 Evaluate side-chains 232 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1912 time to fit residues: 4.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 154 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN C 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.202892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155042 restraints weight = 25210.334| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 4.10 r_work: 0.3252 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 20798 Z= 0.133 Angle : 0.554 21.357 28316 Z= 0.269 Chirality : 0.041 0.216 3121 Planarity : 0.004 0.045 3463 Dihedral : 9.567 172.003 3280 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.18), residues: 2325 helix: 0.49 (0.18), residues: 893 sheet: -0.86 (0.29), residues: 316 loop : -1.53 (0.18), residues: 1116 =============================================================================== Job complete usr+sys time: 4343.45 seconds wall clock time: 79 minutes 8.18 seconds (4748.18 seconds total)