Starting phenix.real_space_refine (version: dev) on Thu Dec 22 06:20:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnf_7533/12_2022/6cnf_7533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnf_7533/12_2022/6cnf_7533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnf_7533/12_2022/6cnf_7533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnf_7533/12_2022/6cnf_7533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnf_7533/12_2022/6cnf_7533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnf_7533/12_2022/6cnf_7533.pdb" } resolution = 4.5 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= 0.001 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 181": "OD1" <-> "OD2" Residue "P ARG 184": "NH1" <-> "NH2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "R ARG 14": "NH1" <-> "NH2" Residue "R ARG 294": "NH1" <-> "NH2" Residue "S ARG 413": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 47675 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11159 Classifications: {'peptide': 1428} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1361} Chain breaks: 2 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 43, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1484 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 12, 'TRANS': 171} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1338 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 1 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Chain: "O" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4329 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "P" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2242 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Chain: "Q" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 368 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 4131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4131 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1649 Classifications: {'peptide': 217} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 959 Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "Y" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1169 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" 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 492 SG CYS A 67 86.021 72.042 80.359 1.00 0.00 S ATOM 510 SG CYS A 70 89.448 72.607 77.483 1.00 0.00 S ATOM 557 SG CYS A 77 89.040 72.908 80.393 1.00 0.00 S ATOM 795 SG CYS A 107 71.376 115.744 88.650 1.00 0.00 S ATOM 818 SG CYS A 110 68.994 116.699 85.694 1.00 0.00 S ATOM 1184 SG CYS A 154 71.533 118.874 87.542 1.00 0.00 S ATOM 1208 SG CYS A 157 68.583 119.255 88.463 1.00 0.00 S ATOM 19520 SG CYS B1095 90.981 87.904 69.212 1.00 0.00 S ATOM 19543 SG CYS B1098 87.979 90.445 71.726 1.00 0.00 S ATOM 19609 SG CYS B1107 89.452 86.160 71.896 1.00 0.00 S ATOM 19629 SG CYS B1110 87.348 87.792 70.770 1.00 0.00 S ATOM 28652 SG CYS I 5 77.935 121.987 153.768 1.00 0.00 S ATOM 28671 SG CYS I 8 74.143 122.050 154.852 1.00 0.00 S ATOM 28799 SG CYS I 26 77.150 122.555 151.102 1.00 0.00 S ATOM 28822 SG CYS I 29 74.477 120.567 151.833 1.00 0.00 S ATOM 28988 SG CYS J 7 138.555 51.061 124.037 1.00 0.00 S ATOM 29011 SG CYS J 10 142.571 52.032 124.434 1.00 0.00 S ATOM 29291 SG CYS J 45 140.865 54.682 125.789 1.00 0.00 S ATOM 29297 SG CYS J 46 141.379 50.620 126.740 1.00 0.00 S ATOM 30330 SG CYS L 31 97.627 35.040 124.061 1.00 0.00 S ATOM 30350 SG CYS L 34 96.558 35.073 128.279 1.00 0.00 S ATOM 30454 SG CYS L 48 93.840 36.467 124.271 1.00 0.00 S ATOM 30477 SG CYS L 51 94.954 36.748 126.367 1.00 0.00 S ATOM 39788 SG CYS R 4 103.273 54.398 74.741 1.00 0.00 S ATOM 39811 SG CYS R 7 104.285 51.195 75.024 1.00 0.00 S ATOM 39952 SG CYS R 25 103.947 51.773 78.208 1.00 0.00 S ATOM 39972 SG CYS R 28 106.033 53.482 77.168 1.00 0.00 S Time building chain proxies: 25.23, per 1000 atoms: 0.53 Number of scatterers: 47675 At special positions: 0 Unit cell: (198.24, 169.92, 200.6, 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 7 29.99 S 242 16.00 P 102 15.00 O 9182 8.00 N 8248 7.00 C 29894 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: 22.36 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 29 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 31 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb=" ZN R1001 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 25 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 4 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 7 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 28 " Number of angles added : 39 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10898 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 56 sheets defined 42.5% alpha, 10.7% beta 41 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 15.21 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.616A pdb=" N ILE A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.870A pdb=" N ASP A 41 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.957A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.781A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 208 removed outlier: 3.535A pdb=" N LYS A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.553A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.709A pdb=" N GLU A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.513A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.574A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.605A pdb=" N GLY A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.970A pdb=" N VAL A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 423 removed outlier: 4.750A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.935A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.513A pdb=" N ARG A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 554 through 566 Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.610A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.527A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.275A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.914A pdb=" N VAL A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 746 removed outlier: 4.024A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 857 through 894 removed outlier: 3.889A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY A 868 " --> pdb=" O HIS A 864 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 934 through 947 removed outlier: 3.610A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 975 removed outlier: 4.419A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Proline residue: A 969 - end of helix removed outlier: 5.037A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 998 through 1026 Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 3.898A pdb=" N THR A1047 " --> pdb=" O PRO A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1050 No H-bonds generated for 'chain 'A' and resid 1049 through 1050' Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1081 Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.612A pdb=" N ILE A1092 " --> pdb=" O ALA A1088 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 4.009A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1202 through 1213 Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 4.029A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.785A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1346 removed outlier: 3.856A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 4.397A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1377 removed outlier: 3.642A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 removed outlier: 4.082A pdb=" N GLU A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1410 through 1417 removed outlier: 3.721A pdb=" N ILE A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 4.173A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.630A pdb=" N ASP A1440 " --> pdb=" O SER A1437 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1442 " --> pdb=" O LYS A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.510A pdb=" N LEU A1451 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A1452 " --> pdb=" O PHE A1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1447 through 1452' Processing helix chain 'A' and resid 1453 through 1456 removed outlier: 3.716A pdb=" N ALA A1456 " --> pdb=" O ASN A1453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1453 through 1456' Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.419A pdb=" N LYS B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.528A pdb=" N LYS B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 Processing helix chain 'B' and resid 71 through 80 removed outlier: 3.557A pdb=" N LYS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.990A pdb=" N MET B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 292 removed outlier: 3.651A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.723A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 4.127A pdb=" N ILE B 319 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.896A pdb=" N THR B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.650A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 removed outlier: 3.676A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.764A pdb=" N VAL B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.866A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 567 through 581 removed outlier: 3.608A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 650 through 657 Processing helix chain 'B' and resid 676 through 681 removed outlier: 4.199A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 707 removed outlier: 3.828A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'B' and resid 738 through 745 Processing helix chain 'B' and resid 746 through 749 Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.039A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 971 removed outlier: 3.948A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 993 removed outlier: 3.853A pdb=" N SER B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1035 Processing helix chain 'B' and resid 1063 through 1068 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1075 through 1084 removed outlier: 3.759A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1080 " --> pdb=" O SER B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1135 removed outlier: 3.569A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.601A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.944A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.729A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 179' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.525A pdb=" N GLN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.626A pdb=" N TYR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.661A pdb=" N ARG C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 27 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.691A pdb=" N THR D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 removed outlier: 4.169A pdb=" N ALA D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.580A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR D 135 " --> pdb=" O MET D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.597A pdb=" N MET D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 160 " --> pdb=" O ILE D 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.568A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.545A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.667A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.724A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'J' and resid 14 through 27 removed outlier: 3.539A pdb=" N TRP J 18 " --> pdb=" O VAL J 14 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.197A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.843A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.761A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 133 through 139 removed outlier: 3.884A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 195 removed outlier: 3.926A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 241 removed outlier: 4.269A pdb=" N VAL M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 261 removed outlier: 3.882A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 296 removed outlier: 3.588A pdb=" N GLU N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU N 283 " --> pdb=" O GLU N 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN N 284 " --> pdb=" O LEU N 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 Processing helix chain 'O' and resid 61 through 72 removed outlier: 4.152A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 81 removed outlier: 4.044A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 76 through 81' Processing helix chain 'O' and resid 89 through 101 Processing helix chain 'O' and resid 127 through 133 Processing helix chain 'O' and resid 133 through 144 removed outlier: 3.602A pdb=" N ILE O 140 " --> pdb=" O ILE O 136 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE O 141 " --> pdb=" O ILE O 137 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 167 removed outlier: 3.504A pdb=" N GLN O 154 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 178 Processing helix chain 'O' and resid 183 through 188 removed outlier: 3.743A pdb=" N SER O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.886A pdb=" N TYR O 208 " --> pdb=" O LYS O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 220 removed outlier: 3.815A pdb=" N GLN O 216 " --> pdb=" O GLU O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 258 removed outlier: 3.689A pdb=" N LYS O 237 " --> pdb=" O SER O 233 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 259 through 265 removed outlier: 4.224A pdb=" N VAL O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 304 Processing helix chain 'O' and resid 305 through 320 removed outlier: 4.049A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 356 removed outlier: 4.501A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU O 351 " --> pdb=" O ASP O 347 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR O 356 " --> pdb=" O VAL O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 361 Processing helix chain 'O' and resid 453 through 458 Processing helix chain 'O' and resid 459 through 463 Processing helix chain 'O' and resid 482 through 491 removed outlier: 3.624A pdb=" N SER O 490 " --> pdb=" O VAL O 486 " (cutoff:3.500A) Processing helix chain 'O' and resid 492 through 496 removed outlier: 4.321A pdb=" N ILE O 496 " --> pdb=" O GLU O 493 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 514 removed outlier: 4.314A pdb=" N ARG O 506 " --> pdb=" O PRO O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.843A pdb=" N SER O 535 " --> pdb=" O LYS O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 575 Processing helix chain 'O' and resid 576 through 582 removed outlier: 3.887A pdb=" N ASN O 580 " --> pdb=" O PHE O 576 " (cutoff:3.500A) Processing helix chain 'O' and resid 587 through 610 removed outlier: 3.761A pdb=" N GLN O 597 " --> pdb=" O GLU O 593 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU O 598 " --> pdb=" O LYS O 594 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN O 599 " --> pdb=" O LEU O 595 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N THR O 601 " --> pdb=" O GLN O 597 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU O 602 " --> pdb=" O GLU O 598 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG O 608 " --> pdb=" O LYS O 604 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP O 610 " --> pdb=" O ALA O 606 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 649 removed outlier: 4.177A pdb=" N LYS O 628 " --> pdb=" O LEU O 624 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU O 647 " --> pdb=" O ARG O 643 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 19 Processing helix chain 'P' and resid 19 through 25 Processing helix chain 'P' and resid 32 through 40 Processing helix chain 'P' and resid 44 through 58 Processing helix chain 'P' and resid 76 through 86 Processing helix chain 'P' and resid 87 through 98 removed outlier: 3.646A pdb=" N LEU P 92 " --> pdb=" O ALA P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 104 removed outlier: 3.884A pdb=" N GLU P 103 " --> pdb=" O SER P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 115 removed outlier: 3.553A pdb=" N ILE P 110 " --> pdb=" O TRP P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 132 removed outlier: 3.768A pdb=" N VAL P 121 " --> pdb=" O HIS P 117 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS P 124 " --> pdb=" O VAL P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 189 removed outlier: 3.813A pdb=" N LEU P 178 " --> pdb=" O PHE P 174 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE P 185 " --> pdb=" O ILE P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 213 Processing helix chain 'P' and resid 218 through 226 removed outlier: 4.234A pdb=" N LEU P 222 " --> pdb=" O THR P 218 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 250 removed outlier: 3.568A pdb=" N VAL P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 271 Processing helix chain 'Q' and resid 48 through 67 removed outlier: 3.906A pdb=" N LYS Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Q 66 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1084 through 1088 removed outlier: 3.564A pdb=" N UNK Q1088 " --> pdb=" O UNK Q1085 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 93 Processing helix chain 'R' and resid 97 through 114 removed outlier: 3.610A pdb=" N THR R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA R 104 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 137 Processing helix chain 'R' and resid 142 through 148 Processing helix chain 'R' and resid 154 through 168 removed outlier: 3.859A pdb=" N LYS R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 189 removed outlier: 4.003A pdb=" N PHE R 181 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 removed outlier: 3.901A pdb=" N LYS R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 204 " --> pdb=" O LYS R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 235 removed outlier: 3.899A pdb=" N ILE R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 249 removed outlier: 3.629A pdb=" N VAL R 247 " --> pdb=" O GLU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 264 removed outlier: 3.543A pdb=" N LEU R 255 " --> pdb=" O ALA R 251 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG R 258 " --> pdb=" O THR R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 272 Processing helix chain 'R' and resid 287 through 296 removed outlier: 3.889A pdb=" N VAL R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS R 296 " --> pdb=" O LYS R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 413 removed outlier: 3.510A pdb=" N VAL R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 472 removed outlier: 4.191A pdb=" N ALA R 466 " --> pdb=" O SER R 462 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE R 468 " --> pdb=" O LYS R 464 " (cutoff:3.500A) Processing helix chain 'R' and resid 497 through 506 Processing helix chain 'R' and resid 545 through 563 removed outlier: 3.966A pdb=" N ILE R 549 " --> pdb=" O GLN R 545 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR R 550 " --> pdb=" O ARG R 546 " (cutoff:3.500A) Proline residue: R 558 - end of helix Processing helix chain 'R' and resid 587 through 594 removed outlier: 3.783A pdb=" N TYR R 591 " --> pdb=" O THR R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 609 through 614 removed outlier: 3.612A pdb=" N LEU R 614 " --> pdb=" O LEU R 610 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 650 removed outlier: 3.525A pdb=" N SER R 620 " --> pdb=" O ASN R 616 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG R 625 " --> pdb=" O LYS R 621 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP R 633 " --> pdb=" O GLY R 629 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N PHE R 634 " --> pdb=" O LEU R 630 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU R 646 " --> pdb=" O ARG R 642 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 650 " --> pdb=" O GLU R 646 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 317 removed outlier: 4.006A pdb=" N UNK S 317 " --> pdb=" O UNK S 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 376 through 380 removed outlier: 3.942A pdb=" N VAL S 380 " --> pdb=" O GLU S 377 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 393 removed outlier: 3.627A pdb=" N ALA S 387 " --> pdb=" O ARG S 383 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE S 389 " --> pdb=" O LYS S 385 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR S 393 " --> pdb=" O ILE S 389 " (cutoff:3.500A) Processing helix chain 'S' and resid 421 through 434 removed outlier: 4.330A pdb=" N LYS S 427 " --> pdb=" O GLU S 423 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE S 428 " --> pdb=" O GLU S 424 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU S 432 " --> pdb=" O PHE S 428 " (cutoff:3.500A) Processing helix chain 'S' and resid 441 through 446 removed outlier: 3.571A pdb=" N LEU S 445 " --> pdb=" O LEU S 441 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR S 446 " --> pdb=" O ILE S 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 441 through 446' Processing helix chain 'S' and resid 450 through 465 Processing helix chain 'S' and resid 465 through 475 Processing helix chain 'S' and resid 481 through 488 Processing helix chain 'S' and resid 494 through 532 removed outlier: 3.609A pdb=" N ASN S 499 " --> pdb=" O VAL S 495 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU S 500 " --> pdb=" O ALA S 496 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG S 532 " --> pdb=" O GLN S 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 180 removed outlier: 4.745A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.733A pdb=" N VAL A 392 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 491 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 493 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 376 " --> pdb=" O ARG B1038 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B1038 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.210A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 626 through 628 removed outlier: 6.595A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 897 through 898 removed outlier: 3.538A pdb=" N GLN A 913 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1278 through 1286 removed outlier: 3.623A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1176 through 1178 Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.656A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 133 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.962A pdb=" N GLN B 197 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 196 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 510 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 205 through 207 removed outlier: 6.793A pdb=" N LYS B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.549A pdb=" N LEU B 444 " --> pdb=" O MET B 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AB8, first strand: chain 'B' and resid 555 through 556 Processing sheet with id=AB9, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AC1, first strand: chain 'B' and resid 724 through 725 removed outlier: 3.948A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 879 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 881 " --> pdb=" O MET B 834 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B 834 " --> pdb=" O ILE B 881 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 724 through 725 removed outlier: 3.948A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 884 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 58 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET B 886 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L 56 " --> pdb=" O MET B 886 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC4, first strand: chain 'B' and resid 919 through 921 removed outlier: 4.764A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 758 " --> pdb=" O ILE B 942 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 919 through 921 Processing sheet with id=AC6, first strand: chain 'B' and resid 841 through 843 removed outlier: 3.611A pdb=" N TYR B 842 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 871 " --> pdb=" O TYR B 842 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 846 through 848 removed outlier: 3.629A pdb=" N VAL B 847 " --> pdb=" O ARG B 867 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1091 through 1095 Processing sheet with id=AC9, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.776A pdb=" N ARG C 293 " --> pdb=" O VAL C 5 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 42 through 47 removed outlier: 7.047A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 76 through 80 Processing sheet with id=AD3, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AD4, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.559A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 162 removed outlier: 4.197A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AD7, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD8, first strand: chain 'D' and resid 2 through 5 removed outlier: 4.965A pdb=" N VAL D 3 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA G 8 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.373A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE E 135 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.097A pdb=" N SER E 202 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY E 206 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE E 178 " --> pdb=" O MET E 215 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 83 through 85 Processing sheet with id=AE3, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AE4, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.581A pdb=" N THR G 122 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA G 127 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE6, first strand: chain 'H' and resid 95 through 98 removed outlier: 3.813A pdb=" N LEU H 142 " --> pdb=" O MET H 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA H 28 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AE8, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.615A pdb=" N LYS K 48 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN K 64 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 76 through 77 removed outlier: 6.404A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 152 through 154 removed outlier: 3.847A pdb=" N VAL M 87 " --> pdb=" O ARG M 175 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA M 177 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU N 407 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA M 248 " --> pdb=" O LEU N 408 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 148 through 149 Processing sheet with id=AF3, first strand: chain 'O' and resid 74 through 75 removed outlier: 3.574A pdb=" N LEU O 74 " --> pdb=" O TYR O 120 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 168 through 169 Processing sheet with id=AF5, first strand: chain 'O' and resid 549 through 551 removed outlier: 3.978A pdb=" N VAL O 551 " --> pdb=" O VAL O 563 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL O 563 " --> pdb=" O VAL O 551 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 61 through 64 Processing sheet with id=AF7, first strand: chain 'P' and resid 134 through 137 removed outlier: 4.074A pdb=" N MET P 149 " --> pdb=" O LYS P 135 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 253 through 256 Processing sheet with id=AF9, first strand: chain 'R' and resid 13 through 15 removed outlier: 7.019A pdb=" N LEU R 23 " --> pdb=" O SER R 32 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 446 through 449 removed outlier: 5.863A pdb=" N LEU R 393 " --> pdb=" O SER R 489 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER R 489 " --> pdb=" O LEU R 393 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN R 395 " --> pdb=" O VAL R 487 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR R 399 " --> pdb=" O ILE R 483 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE R 483 " --> pdb=" O THR R 399 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR R 401 " --> pdb=" O PHE R 481 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE R 481 " --> pdb=" O THR R 401 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE R 486 " --> pdb=" O GLY R 542 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY R 542 " --> pdb=" O ILE R 486 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 418 through 421 removed outlier: 4.402A pdb=" N ASN R 421 " --> pdb=" O ALA R 427 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA R 427 " --> pdb=" O ASN R 421 " (cutoff:3.500A) 1713 hydrogen bonds defined for protein. 4803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 23.09 Time building geometry restraints manager: 23.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12929 1.33 - 1.46: 11054 1.46 - 1.58: 24148 1.58 - 1.71: 209 1.71 - 1.83: 393 Bond restraints: 48733 Sorted by residual: bond pdb=" CA GLN R 151 " pdb=" C GLN R 151 " ideal model delta sigma weight residual 1.522 1.627 -0.105 1.39e-02 5.18e+03 5.75e+01 bond pdb=" C LEU R 173 " pdb=" N PRO R 174 " ideal model delta sigma weight residual 1.334 1.501 -0.167 2.34e-02 1.83e+03 5.12e+01 bond pdb=" C TYR J 63 " pdb=" N ASN J 64 " ideal model delta sigma weight residual 1.329 1.252 0.077 1.21e-02 6.83e+03 4.05e+01 bond pdb=" CA HIS B 550 " pdb=" C HIS B 550 " ideal model delta sigma weight residual 1.522 1.604 -0.082 1.31e-02 5.83e+03 3.96e+01 bond pdb=" CA ASP A 829 " pdb=" C ASP A 829 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.70e+01 ... (remaining 48728 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.31: 1223 104.31 - 111.78: 22379 111.78 - 119.25: 17878 119.25 - 126.72: 23959 126.72 - 134.19: 801 Bond angle restraints: 66240 Sorted by residual: angle pdb=" N ASN O 587 " pdb=" CA ASN O 587 " pdb=" C ASN O 587 " ideal model delta sigma weight residual 111.03 124.44 -13.41 1.11e+00 8.12e-01 1.46e+02 angle pdb=" C LYS O 472 " pdb=" N PRO O 473 " pdb=" CA PRO O 473 " ideal model delta sigma weight residual 119.84 131.55 -11.71 1.25e+00 6.40e-01 8.78e+01 angle pdb=" N LEU B 824 " pdb=" CA LEU B 824 " pdb=" C LEU B 824 " ideal model delta sigma weight residual 108.49 119.21 -10.72 1.15e+00 7.56e-01 8.69e+01 angle pdb=" N LYS R 211 " pdb=" CA LYS R 211 " pdb=" C LYS R 211 " ideal model delta sigma weight residual 111.28 121.30 -10.02 1.09e+00 8.42e-01 8.45e+01 angle pdb=" N LYS C 35 " pdb=" CA LYS C 35 " pdb=" C LYS C 35 " ideal model delta sigma weight residual 111.28 101.45 9.83 1.09e+00 8.42e-01 8.14e+01 ... (remaining 66235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 28786 34.63 - 69.25: 678 69.25 - 103.88: 60 103.88 - 138.50: 1 138.50 - 173.13: 2 Dihedral angle restraints: 29527 sinusoidal: 12715 harmonic: 16812 Sorted by residual: dihedral pdb=" CA GLU A 210 " pdb=" C GLU A 210 " pdb=" N LEU A 211 " pdb=" CA LEU A 211 " ideal model delta harmonic sigma weight residual 180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA THR A 409 " pdb=" C THR A 409 " pdb=" N ARG A 410 " pdb=" CA ARG A 410 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ALA B 598 " pdb=" C ALA B 598 " pdb=" N VAL B 599 " pdb=" CA VAL B 599 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 29524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 6975 0.103 - 0.206: 444 0.206 - 0.309: 41 0.309 - 0.412: 31 0.412 - 0.515: 6 Chirality restraints: 7497 Sorted by residual: chirality pdb=" CA HIS B 550 " pdb=" N HIS B 550 " pdb=" C HIS B 550 " pdb=" CB HIS B 550 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CA TYR O 480 " pdb=" N TYR O 480 " pdb=" C TYR O 480 " pdb=" CB TYR O 480 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CA ARG A 573 " pdb=" N ARG A 573 " pdb=" C ARG A 573 " pdb=" CB ARG A 573 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 7494 not shown) Planarity restraints: 8156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN O 587 " 0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ASN O 587 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN O 587 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU O 588 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 567 " 0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO B 568 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 568 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 568 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 299 " 0.015 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C GLN B 299 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN B 299 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN B 300 " 0.018 2.00e-02 2.50e+03 ... (remaining 8153 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 639 2.50 - 3.10: 42614 3.10 - 3.70: 77627 3.70 - 4.30: 109688 4.30 - 4.90: 164799 Nonbonded interactions: 395367 Sorted by model distance: nonbonded pdb=" O GLY A 251 " pdb=" O ARG A 252 " model vdw 1.905 3.040 nonbonded pdb=" O ASP O 328 " pdb=" O PRO O 329 " model vdw 1.941 3.040 nonbonded pdb=" CG2 THR F 115 " pdb=" N ASP F 116 " model vdw 1.953 3.540 nonbonded pdb=" O PRO A 836 " pdb=" O LYS A 837 " model vdw 1.974 3.040 nonbonded pdb=" O HIS B 600 " pdb=" CD1 ILE B 601 " model vdw 1.984 3.460 ... (remaining 395362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 7 6.06 5 P 102 5.49 5 S 242 5.16 5 C 29894 2.51 5 N 8248 2.21 5 O 9182 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 9.320 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.380 Process input model: 145.780 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 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 : 0.006 0.167 48733 Z= 0.381 Angle : 1.160 13.410 66240 Z= 0.713 Chirality : 0.062 0.515 7497 Planarity : 0.006 0.082 8156 Dihedral : 13.860 173.127 18629 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 40.33 Ramachandran Plot: Outliers : 1.56 % Allowed : 17.94 % Favored : 80.50 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.66 % 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: -5.23 (0.08), residues: 5625 helix: -4.14 (0.07), residues: 1823 sheet: -2.36 (0.17), residues: 591 loop : -3.38 (0.09), residues: 3211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1148 time to evaluate : 5.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 11 residues processed: 1177 average time/residue: 0.6061 time to fit residues: 1162.6837 Evaluate side-chains 658 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 647 time to evaluate : 5.769 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4559 time to fit residues: 17.3631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 482 optimal weight: 0.0570 chunk 432 optimal weight: 30.0000 chunk 240 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 231 optimal weight: 0.2980 chunk 447 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 272 optimal weight: 0.3980 chunk 333 optimal weight: 10.0000 chunk 518 optimal weight: 10.0000 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 147 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN A 281 ASN A 386 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 477 GLN A 518 ASN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 423 ASN B 425 HIS B 456 HIS ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN C 207 HIS ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 126 GLN E 54 GLN E 101 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS E 174 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 133 ASN H 134 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN N 377 ASN ** N 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 ASN O 193 GLN O 244 ASN O 310 GLN O 337 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 189 ASN P 305 HIS R 118 GLN R 183 GLN R 184 HIS R 249 HIS R 394 GLN R 414 HIS S 367 ASN S 384 HIS S 499 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 48733 Z= 0.294 Angle : 0.887 14.553 66240 Z= 0.471 Chirality : 0.050 0.318 7497 Planarity : 0.006 0.108 8156 Dihedral : 16.231 172.376 7251 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.48 % Favored : 86.70 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.08 (0.09), residues: 5625 helix: -2.52 (0.09), residues: 1992 sheet: -1.96 (0.18), residues: 605 loop : -3.08 (0.10), residues: 3028 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 918 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 928 average time/residue: 0.5892 time to fit residues: 907.4194 Evaluate side-chains 616 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 613 time to evaluate : 5.741 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4030 time to fit residues: 9.8647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 288 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 431 optimal weight: 9.9990 chunk 353 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 519 optimal weight: 20.0000 chunk 561 optimal weight: 6.9990 chunk 462 optimal weight: 30.0000 chunk 515 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 416 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS B 116 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS D 64 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 112 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN M 104 HIS ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS O 295 GLN ** O 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 GLN S 528 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.076 48733 Z= 0.429 Angle : 0.885 13.444 66240 Z= 0.469 Chirality : 0.049 0.391 7497 Planarity : 0.006 0.115 8156 Dihedral : 16.100 168.920 7251 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 32.10 Ramachandran Plot: Outliers : 0.89 % Allowed : 14.20 % Favored : 84.91 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.79 (0.10), residues: 5625 helix: -2.00 (0.10), residues: 2047 sheet: -2.09 (0.18), residues: 617 loop : -3.06 (0.10), residues: 2961 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 746 time to evaluate : 5.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 751 average time/residue: 0.5854 time to fit residues: 740.6897 Evaluate side-chains 525 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 523 time to evaluate : 5.653 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4006 time to fit residues: 9.1685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 513 optimal weight: 20.0000 chunk 390 optimal weight: 8.9990 chunk 269 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 348 optimal weight: 8.9990 chunk 521 optimal weight: 30.0000 chunk 551 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 494 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 ASN A1385 GLN A1395 HIS ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 HIS B 902 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN M 92 ASN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 161 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 GLN ** O 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 183 GLN ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 48733 Z= 0.326 Angle : 0.812 11.399 66240 Z= 0.427 Chirality : 0.047 0.389 7497 Planarity : 0.006 0.092 8156 Dihedral : 15.966 171.323 7251 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.14 % Favored : 85.81 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.10), residues: 5625 helix: -1.57 (0.10), residues: 2051 sheet: -2.02 (0.18), residues: 618 loop : -2.97 (0.10), residues: 2956 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 744 time to evaluate : 5.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 746 average time/residue: 0.5820 time to fit residues: 735.2904 Evaluate side-chains 550 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 549 time to evaluate : 5.996 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4122 time to fit residues: 8.8946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 459 optimal weight: 30.0000 chunk 313 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 410 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 470 optimal weight: 2.9990 chunk 381 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 495 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 48733 Z= 0.283 Angle : 0.796 15.514 66240 Z= 0.414 Chirality : 0.047 0.314 7497 Planarity : 0.005 0.085 8156 Dihedral : 15.841 172.729 7251 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 1.01 % Allowed : 13.16 % Favored : 85.83 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.10), residues: 5625 helix: -1.33 (0.10), residues: 2040 sheet: -1.81 (0.19), residues: 587 loop : -2.93 (0.10), residues: 2998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 733 time to evaluate : 5.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 734 average time/residue: 0.5952 time to fit residues: 741.9266 Evaluate side-chains 537 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 536 time to evaluate : 5.959 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4082 time to fit residues: 8.5935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 185 optimal weight: 2.9990 chunk 497 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 324 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 552 optimal weight: 20.0000 chunk 458 optimal weight: 10.0000 chunk 255 optimal weight: 0.0970 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 290 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A1395 HIS ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 HIS ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 ASN B 902 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 283 ASN ** O 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 48733 Z= 0.229 Angle : 0.779 14.958 66240 Z= 0.399 Chirality : 0.047 0.351 7497 Planarity : 0.005 0.121 8156 Dihedral : 15.719 173.364 7251 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.93 % Favored : 87.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.07 (0.10), residues: 5625 helix: -1.15 (0.11), residues: 2065 sheet: -1.79 (0.19), residues: 611 loop : -2.82 (0.11), residues: 2949 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 765 time to evaluate : 7.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 765 average time/residue: 0.5971 time to fit residues: 779.2000 Evaluate side-chains 559 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 559 time to evaluate : 6.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 532 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 314 optimal weight: 1.9990 chunk 403 optimal weight: 6.9990 chunk 312 optimal weight: 6.9990 chunk 465 optimal weight: 8.9990 chunk 308 optimal weight: 6.9990 chunk 550 optimal weight: 20.0000 chunk 344 optimal weight: 5.9990 chunk 335 optimal weight: 50.0000 chunk 254 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 643 ASN ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN K 102 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 575 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 48733 Z= 0.414 Angle : 0.850 16.647 66240 Z= 0.444 Chirality : 0.048 0.466 7497 Planarity : 0.006 0.080 8156 Dihedral : 15.730 174.269 7251 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 30.06 Ramachandran Plot: Outliers : 1.01 % Allowed : 13.85 % Favored : 85.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.14 (0.10), residues: 5625 helix: -1.20 (0.10), residues: 2080 sheet: -1.80 (0.19), residues: 606 loop : -2.88 (0.11), residues: 2939 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 5.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.5615 time to fit residues: 643.0287 Evaluate side-chains 503 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 6.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 340 optimal weight: 6.9990 chunk 219 optimal weight: 0.0170 chunk 328 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 349 optimal weight: 8.9990 chunk 374 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 432 optimal weight: 30.0000 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 48733 Z= 0.227 Angle : 0.787 15.015 66240 Z= 0.400 Chirality : 0.047 0.382 7497 Planarity : 0.005 0.078 8156 Dihedral : 15.630 173.963 7251 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.77 % Favored : 87.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.90 (0.10), residues: 5625 helix: -0.97 (0.11), residues: 2068 sheet: -1.69 (0.19), residues: 605 loop : -2.77 (0.11), residues: 2952 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 6.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.5739 time to fit residues: 718.6905 Evaluate side-chains 540 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 6.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 500 optimal weight: 9.9990 chunk 527 optimal weight: 20.0000 chunk 481 optimal weight: 20.0000 chunk 512 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 223 optimal weight: 0.2980 chunk 402 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 463 optimal weight: 30.0000 chunk 485 optimal weight: 7.9990 chunk 511 optimal weight: 7.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 902 GLN E 54 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN ** O 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 GLN P 117 HIS ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 48733 Z= 0.318 Angle : 0.800 15.216 66240 Z= 0.414 Chirality : 0.047 0.343 7497 Planarity : 0.005 0.085 8156 Dihedral : 15.604 174.634 7251 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.92 % Allowed : 13.72 % Favored : 85.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.88 (0.10), residues: 5625 helix: -0.95 (0.11), residues: 2075 sheet: -1.64 (0.20), residues: 584 loop : -2.76 (0.11), residues: 2966 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 5.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.5567 time to fit residues: 640.9054 Evaluate side-chains 519 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 6.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 336 optimal weight: 4.9990 chunk 542 optimal weight: 30.0000 chunk 331 optimal weight: 40.0000 chunk 257 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 568 optimal weight: 10.0000 chunk 523 optimal weight: 50.0000 chunk 452 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 349 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS M 92 ASN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 48733 Z= 0.307 Angle : 0.805 13.726 66240 Z= 0.415 Chirality : 0.047 0.354 7497 Planarity : 0.005 0.073 8156 Dihedral : 15.581 174.832 7251 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.91 % Allowed : 13.28 % Favored : 85.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.87 (0.10), residues: 5625 helix: -0.94 (0.11), residues: 2080 sheet: -1.68 (0.20), residues: 598 loop : -2.76 (0.11), residues: 2947 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 5.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.5755 time to fit residues: 670.5966 Evaluate side-chains 510 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 6.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.3483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 571 random chunks: chunk 359 optimal weight: 10.0000 chunk 482 optimal weight: 9.9990 chunk 138 optimal weight: 0.0470 chunk 417 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 125 optimal weight: 0.0070 chunk 453 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 465 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN M 146 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.072614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052110 restraints weight = 236544.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.053937 restraints weight = 126669.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055154 restraints weight = 82050.457| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 48733 Z= 0.227 Angle : 0.786 19.919 66240 Z= 0.397 Chirality : 0.047 0.315 7497 Planarity : 0.005 0.074 8156 Dihedral : 15.480 174.854 7251 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.28 % Favored : 86.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.74 (0.11), residues: 5625 helix: -0.83 (0.11), residues: 2070 sheet: -1.46 (0.20), residues: 601 loop : -2.72 (0.11), residues: 2954 =============================================================================== Job complete usr+sys time: 11974.73 seconds wall clock time: 216 minutes 31.56 seconds (12991.56 seconds total)