Starting phenix.real_space_refine on Wed Dec 13 01:59:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/12_2023/6bwi_7299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/12_2023/6bwi_7299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/12_2023/6bwi_7299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/12_2023/6bwi_7299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/12_2023/6bwi_7299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/12_2023/6bwi_7299.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 92 5.16 5 Na 5 4.78 5 C 15310 2.51 5 N 4064 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 882": "NH1" <-> "NH2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A ARG 1166": "NH1" <-> "NH2" Residue "A GLU 1169": "OE1" <-> "OE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 601": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 955": "NH1" <-> "NH2" Residue "B ARG 964": "NH1" <-> "NH2" Residue "B ARG 1062": "NH1" <-> "NH2" Residue "B ARG 1166": "NH1" <-> "NH2" Residue "B GLU 1169": "OE1" <-> "OE2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C ARG 601": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 882": "NH1" <-> "NH2" Residue "C ARG 892": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C ARG 1062": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "C ARG 1166": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D ARG 597": "NH1" <-> "NH2" Residue "D ARG 601": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 706": "NH1" <-> "NH2" Residue "D PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 882": "NH1" <-> "NH2" Residue "D ARG 892": "NH1" <-> "NH2" Residue "D ARG 905": "NH1" <-> "NH2" Residue "D ARG 964": "NH1" <-> "NH2" Residue "D ARG 1062": "NH1" <-> "NH2" Residue "D ARG 1166": "NH1" <-> "NH2" Residue "D GLU 1169": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23491 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5649 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 435 Chain: "B" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5644 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 440 Chain: "C" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5644 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 440 Chain: "D" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5649 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 435 Chain: "A" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 228 Unusual residues: {' NA': 3, 'NAG': 1, 'Y01': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 227 Unusual residues: {' NA': 2, 'NAG': 1, 'Y01': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 260 Unusual residues: {'NAG': 1, 'Y01': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 13.78, per 1000 atoms: 0.59 Number of scatterers: 23491 At special positions: 0 Unit cell: (131.61, 131.61, 153.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 Na 5 11.00 O 4020 8.00 N 4064 7.00 C 15310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.18 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=1.89 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=1.51 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=1.54 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=4, symmetry=0 Links applied NAG-ASN " NAG A1210 " - " ASN A 992 " " NAG B1209 " - " ASN B 992 " " NAG D1208 " - " ASN D 992 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.25 Conformation dependent library (CDL) restraints added in 3.5 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6280 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 8 sheets defined 83.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 removed outlier: 3.860A pdb=" N UNK A 9 " --> pdb=" O UNK A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 32 through 44 removed outlier: 3.973A pdb=" N UNK A 44 " --> pdb=" O UNK A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 4.042A pdb=" N UNK A 58 " --> pdb=" O UNK A 54 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK A 59 " --> pdb=" O UNK A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK A 232 " --> pdb=" O UNK A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.744A pdb=" N UNK A 241 " --> pdb=" O UNK A 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK A 242 " --> pdb=" O UNK A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 242' Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.519A pdb=" N TRP A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 3.766A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 removed outlier: 3.532A pdb=" N GLU A 439 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.526A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.673A pdb=" N SER A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 Processing helix chain 'A' and resid 610 through 634 removed outlier: 4.728A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 703 " --> pdb=" O CYS A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 698 through 703' Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 780 through 803 removed outlier: 3.962A pdb=" N VAL A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 832 removed outlier: 3.792A pdb=" N TYR A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 830 " --> pdb=" O CYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 removed outlier: 3.565A pdb=" N VAL A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 926 removed outlier: 3.900A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 952 removed outlier: 3.949A pdb=" N VAL A 930 " --> pdb=" O MET A 926 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 951 " --> pdb=" O ALA A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 1017 through 1031 removed outlier: 3.674A pdb=" N VAL A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1068 removed outlier: 4.285A pdb=" N ALA A1041 " --> pdb=" O ASN A1037 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A1049 " --> pdb=" O TYR A1045 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1090 removed outlier: 4.193A pdb=" N LEU A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1137 removed outlier: 4.000A pdb=" N ALA A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU A1172 " --> pdb=" O TYR A1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.862A pdb=" N UNK B 9 " --> pdb=" O UNK B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.973A pdb=" N UNK B 44 " --> pdb=" O UNK B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 4.043A pdb=" N UNK B 58 " --> pdb=" O UNK B 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N UNK B 59 " --> pdb=" O UNK B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK B 232 " --> pdb=" O UNK B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.744A pdb=" N UNK B 241 " --> pdb=" O UNK B 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK B 242 " --> pdb=" O UNK B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 261 through 276 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.519A pdb=" N TRP B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 3.765A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.531A pdb=" N GLU B 439 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.526A pdb=" N LEU B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 585 through 591 Processing helix chain 'B' and resid 595 through 602 Processing helix chain 'B' and resid 610 through 634 removed outlier: 4.728A pdb=" N ALA B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU B 657 " --> pdb=" O THR B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 668' Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU B 702 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 703 " --> pdb=" O CYS B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 698 through 703' Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 771 through 776 Processing helix chain 'B' and resid 780 through 803 removed outlier: 3.961A pdb=" N VAL B 803 " --> pdb=" O ARG B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 832 removed outlier: 3.792A pdb=" N TYR B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 830 " --> pdb=" O CYS B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 860 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 removed outlier: 3.565A pdb=" N VAL B 894 " --> pdb=" O LEU B 890 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 926 removed outlier: 3.901A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 952 removed outlier: 3.948A pdb=" N VAL B 930 " --> pdb=" O MET B 926 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 942 " --> pdb=" O GLY B 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 949 " --> pdb=" O GLY B 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY B 950 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 951 " --> pdb=" O ALA B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 1017 through 1034 removed outlier: 3.675A pdb=" N VAL B1021 " --> pdb=" O ASN B1017 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1069 removed outlier: 4.285A pdb=" N ALA B1041 " --> pdb=" O ASN B1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B1049 " --> pdb=" O TYR B1045 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1090 removed outlier: 4.192A pdb=" N LEU B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1137 removed outlier: 3.999A pdb=" N ALA B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU B1172 " --> pdb=" O TYR B1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.861A pdb=" N UNK C 9 " --> pdb=" O UNK C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 32 through 44 removed outlier: 3.972A pdb=" N UNK C 44 " --> pdb=" O UNK C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 4.043A pdb=" N UNK C 58 " --> pdb=" O UNK C 54 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK C 59 " --> pdb=" O UNK C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK C 232 " --> pdb=" O UNK C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.743A pdb=" N UNK C 241 " --> pdb=" O UNK C 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK C 242 " --> pdb=" O UNK C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 261 through 276 Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.518A pdb=" N TRP C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 3.765A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 440 removed outlier: 3.532A pdb=" N GLU C 439 " --> pdb=" O ASP C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 560 through 568 removed outlier: 3.526A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 585 through 591 Processing helix chain 'C' and resid 595 through 602 Processing helix chain 'C' and resid 610 through 634 removed outlier: 4.727A pdb=" N ALA C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU C 657 " --> pdb=" O THR C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 663 through 668' Processing helix chain 'C' and resid 672 through 681 Processing helix chain 'C' and resid 689 through 695 Processing helix chain 'C' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU C 702 " --> pdb=" O PHE C 698 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE C 703 " --> pdb=" O CYS C 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 698 through 703' Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 780 through 803 removed outlier: 3.961A pdb=" N VAL C 803 " --> pdb=" O ARG C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 832 removed outlier: 3.792A pdb=" N TYR C 818 " --> pdb=" O GLU C 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 830 " --> pdb=" O CYS C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 860 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU C 877 " --> pdb=" O THR C 873 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 910 removed outlier: 3.565A pdb=" N VAL C 894 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 926 removed outlier: 3.900A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 952 removed outlier: 3.949A pdb=" N VAL C 930 " --> pdb=" O MET C 926 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL C 942 " --> pdb=" O GLY C 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 949 " --> pdb=" O GLY C 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 951 " --> pdb=" O ALA C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 1017 through 1034 removed outlier: 3.675A pdb=" N VAL C1021 " --> pdb=" O ASN C1017 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C1032 " --> pdb=" O LEU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1068 removed outlier: 4.286A pdb=" N ALA C1041 " --> pdb=" O ASN C1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS C1049 " --> pdb=" O TYR C1045 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 4.193A pdb=" N LEU C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1137 removed outlier: 4.000A pdb=" N ALA C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU C1172 " --> pdb=" O TYR C1168 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.861A pdb=" N UNK D 9 " --> pdb=" O UNK D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.974A pdb=" N UNK D 44 " --> pdb=" O UNK D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 62 removed outlier: 4.042A pdb=" N UNK D 58 " --> pdb=" O UNK D 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N UNK D 59 " --> pdb=" O UNK D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK D 232 " --> pdb=" O UNK D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.743A pdb=" N UNK D 241 " --> pdb=" O UNK D 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK D 242 " --> pdb=" O UNK D 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 237 through 242' Processing helix chain 'D' and resid 261 through 276 Processing helix chain 'D' and resid 396 through 403 removed outlier: 3.518A pdb=" N TRP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.765A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 440 removed outlier: 3.531A pdb=" N GLU D 439 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 465 Processing helix chain 'D' and resid 473 through 479 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 560 through 568 removed outlier: 3.525A pdb=" N LEU D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP D 565 " --> pdb=" O ASP D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 585 through 591 Processing helix chain 'D' and resid 595 through 602 Processing helix chain 'D' and resid 610 through 634 removed outlier: 4.728A pdb=" N ALA D 616 " --> pdb=" O ARG D 612 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 634 " --> pdb=" O CYS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU D 657 " --> pdb=" O THR D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 663 through 668' Processing helix chain 'D' and resid 672 through 681 Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU D 702 " --> pdb=" O PHE D 698 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE D 703 " --> pdb=" O CYS D 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 698 through 703' Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 771 through 776 Processing helix chain 'D' and resid 780 through 803 removed outlier: 3.961A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 832 removed outlier: 3.791A pdb=" N TYR D 818 " --> pdb=" O GLU D 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 830 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 860 Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU D 877 " --> pdb=" O THR D 873 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 890 through 910 removed outlier: 3.564A pdb=" N VAL D 894 " --> pdb=" O LEU D 890 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 926 removed outlier: 3.901A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 952 removed outlier: 3.949A pdb=" N VAL D 930 " --> pdb=" O MET D 926 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 942 " --> pdb=" O GLY D 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY D 950 " --> pdb=" O VAL D 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU D 951 " --> pdb=" O ALA D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 966 Processing helix chain 'D' and resid 1017 through 1034 removed outlier: 3.675A pdb=" N VAL D1021 " --> pdb=" O ASN D1017 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D1032 " --> pdb=" O LEU D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1035 through 1068 removed outlier: 4.286A pdb=" N ALA D1041 " --> pdb=" O ASN D1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS D1049 " --> pdb=" O TYR D1045 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1090 removed outlier: 4.193A pdb=" N LEU D1085 " --> pdb=" O VAL D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1137 removed outlier: 4.000A pdb=" N ALA D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU D1172 " --> pdb=" O TYR D1168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA2, first strand: chain 'A' and resid 999 through 1000 removed outlier: 3.925A pdb=" N PHE A 999 " --> pdb=" O GLN A1014 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'B' and resid 999 through 1000 removed outlier: 3.925A pdb=" N PHE B 999 " --> pdb=" O GLN B1014 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA6, first strand: chain 'C' and resid 999 through 1000 removed outlier: 3.925A pdb=" N PHE C 999 " --> pdb=" O GLN C1014 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 101 through 103 Processing sheet with id=AA8, first strand: chain 'D' and resid 999 through 1000 removed outlier: 3.924A pdb=" N PHE D 999 " --> pdb=" O GLN D1014 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.60 Time building geometry restraints manager: 9.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6784 1.33 - 1.45: 4014 1.45 - 1.57: 13032 1.57 - 1.69: 2 1.69 - 1.81: 136 Bond restraints: 23968 Sorted by residual: bond pdb=" C GLU B1169 " pdb=" N GLN B1170 " ideal model delta sigma weight residual 1.334 1.590 -0.256 1.33e-02 5.65e+03 3.70e+02 bond pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 1.334 1.588 -0.254 1.32e-02 5.74e+03 3.70e+02 bond pdb=" C LEU B1162 " pdb=" N GLY B1163 " ideal model delta sigma weight residual 1.334 1.560 -0.226 1.32e-02 5.74e+03 2.92e+02 bond pdb=" C GLU A1169 " pdb=" N GLN A1170 " ideal model delta sigma weight residual 1.334 1.542 -0.208 1.33e-02 5.65e+03 2.43e+02 bond pdb=" C GLU D1169 " pdb=" N GLN D1170 " ideal model delta sigma weight residual 1.334 1.527 -0.192 1.33e-02 5.65e+03 2.09e+02 ... (remaining 23963 not shown) Histogram of bond angle deviations from ideal: 94.95 - 103.58: 308 103.58 - 112.20: 12479 112.20 - 120.83: 13057 120.83 - 129.45: 6810 129.45 - 138.07: 206 Bond angle restraints: 32860 Sorted by residual: angle pdb=" C LEU A1162 " pdb=" N GLY A1163 " pdb=" CA GLY A1163 " ideal model delta sigma weight residual 119.98 137.85 -17.87 1.11e+00 8.12e-01 2.59e+02 angle pdb=" O LEU A1162 " pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 122.12 108.93 13.19 1.06e+00 8.90e-01 1.55e+02 angle pdb=" CA LEU A1162 " pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 117.22 130.77 -13.55 1.17e+00 7.31e-01 1.34e+02 angle pdb=" C LEU B1162 " pdb=" N GLY B1163 " pdb=" CA GLY B1163 " ideal model delta sigma weight residual 119.98 132.24 -12.26 1.11e+00 8.12e-01 1.22e+02 angle pdb=" N PRO C 701 " pdb=" CA PRO C 701 " pdb=" CB PRO C 701 " ideal model delta sigma weight residual 103.25 113.65 -10.40 1.05e+00 9.07e-01 9.82e+01 ... (remaining 32855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 14677 21.68 - 43.35: 529 43.35 - 65.03: 84 65.03 - 86.71: 15 86.71 - 108.38: 3 Dihedral angle restraints: 15308 sinusoidal: 5764 harmonic: 9544 Sorted by residual: dihedral pdb=" CA UNK A 93 " pdb=" C UNK A 93 " pdb=" N UNK A 94 " pdb=" CA UNK A 94 " ideal model delta harmonic sigma weight residual -180.00 -138.03 -41.97 0 5.00e+00 4.00e-02 7.05e+01 dihedral pdb=" CA UNK D 93 " pdb=" C UNK D 93 " pdb=" N UNK D 94 " pdb=" CA UNK D 94 " ideal model delta harmonic sigma weight residual -180.00 -138.05 -41.95 0 5.00e+00 4.00e-02 7.04e+01 dihedral pdb=" CA UNK B 93 " pdb=" C UNK B 93 " pdb=" N UNK B 94 " pdb=" CA UNK B 94 " ideal model delta harmonic sigma weight residual -180.00 -138.11 -41.89 0 5.00e+00 4.00e-02 7.02e+01 ... (remaining 15305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 3921 0.224 - 0.447: 75 0.447 - 0.671: 16 0.671 - 0.894: 2 0.894 - 1.118: 1 Chirality restraints: 4015 Sorted by residual: chirality pdb=" C1 NAG D1208 " pdb=" ND2 ASN D 992 " pdb=" C2 NAG D1208 " pdb=" O5 NAG D1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" C1 NAG B1209 " pdb=" ND2 ASN B 992 " pdb=" C2 NAG B1209 " pdb=" O5 NAG B1209 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" C1 NAG A1210 " pdb=" ND2 ASN A 992 " pdb=" C2 NAG A1210 " pdb=" O5 NAG A1210 " both_signs ideal model delta sigma weight residual False -2.40 -3.07 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 4012 not shown) Planarity restraints: 4065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 992 " 0.561 2.00e-02 2.50e+03 5.54e-01 3.84e+03 pdb=" CG ASN A 992 " -0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN A 992 " 0.135 2.00e-02 2.50e+03 pdb=" ND2 ASN A 992 " -1.003 2.00e-02 2.50e+03 pdb=" C1 NAG A1210 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 992 " 0.490 2.00e-02 2.50e+03 4.96e-01 3.07e+03 pdb=" CG ASN D 992 " -0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN D 992 " 0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN D 992 " -0.890 2.00e-02 2.50e+03 pdb=" C1 NAG D1208 " 0.414 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 992 " -0.422 2.00e-02 2.50e+03 4.71e-01 2.77e+03 pdb=" CG ASN B 992 " 0.126 2.00e-02 2.50e+03 pdb=" OD1 ASN B 992 " -0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN B 992 " 0.831 2.00e-02 2.50e+03 pdb=" C1 NAG B1209 " -0.466 2.00e-02 2.50e+03 ... (remaining 4062 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 53 2.38 - 3.01: 11974 3.01 - 3.64: 34640 3.64 - 4.27: 49452 4.27 - 4.90: 78950 Nonbonded interactions: 175069 Sorted by model distance: nonbonded pdb=" CG ASN B 992 " pdb=" O1 NAG B1209 " model vdw 1.745 2.616 nonbonded pdb=" OD1 ASN B 992 " pdb=" O1 NAG B1209 " model vdw 1.857 2.440 nonbonded pdb=" O PHE D 975 " pdb=" N GLN D 977 " model vdw 1.917 2.520 nonbonded pdb=" CE3 TRP B 864 " pdb=" CAR Y01 B1207 " model vdw 1.975 2.992 nonbonded pdb=" CG ASN A 992 " pdb=" O1 NAG A1210 " model vdw 2.091 2.616 ... (remaining 175064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 989 or (resid 990 and (name N or name CA or name \ C or name O or name CB )) or resid 991 through 1174 or resid 1204 through 1205) \ ) selection = (chain 'B' and (resid 1 through 1174 or resid 1204 through 1205)) selection = (chain 'C' and (resid 1 through 1174 or resid 1204 through 1205)) selection = (chain 'D' and (resid 1 through 989 or (resid 990 and (name N or name CA or name \ C or name O or name CB )) or resid 991 through 1174 or resid 1204 through 1205) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.650 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 61.760 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.011 0.256 23968 Z= 0.694 Angle : 1.388 17.867 32860 Z= 0.728 Chirality : 0.085 1.118 4015 Planarity : 0.012 0.288 4062 Dihedral : 12.184 108.383 9016 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.11 % Favored : 91.52 % Rotamer: Outliers : 1.36 % Allowed : 6.02 % Favored : 92.62 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -5.08 (0.14), residues: 2428 helix: -3.41 (0.08), residues: 1572 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 565 HIS 0.006 0.002 HIS B1128 PHE 0.032 0.004 PHE D 710 TYR 0.020 0.002 TYR B 888 ARG 0.012 0.001 ARG C 644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 661 time to evaluate : 2.461 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 677 average time/residue: 0.4126 time to fit residues: 408.1362 Evaluate side-chains 367 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 357 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3795 time to fit residues: 8.7044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN A 990 HIS ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 ASN ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS C1164 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 977 GLN D1032 ASN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.8306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.089 0.508 23968 Z= 5.674 Angle : 5.010 48.116 32860 Z= 2.384 Chirality : 0.270 1.787 4015 Planarity : 0.030 0.263 4062 Dihedral : 19.447 142.394 5220 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 102.51 Ramachandran Plot: Outliers : 10.42 % Allowed : 25.62 % Favored : 63.96 % Rotamer: Outliers : 21.17 % Allowed : 20.37 % Favored : 58.46 % Cbeta Deviations : 4.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 6.36 % 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: -8.01 (0.08), residues: 2428 helix: -4.87 (0.06), residues: 1712 sheet: None (None), residues: 0 loop : -5.88 (0.14), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.017 TRP D 680 HIS 0.044 0.013 HIS B 453 PHE 0.194 0.021 PHE A 710 TYR 0.084 0.017 TYR D 944 ARG 0.036 0.005 ARG C 965 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 204 time to evaluate : 2.430 Fit side-chains outliers start: 373 outliers final: 254 residues processed: 543 average time/residue: 0.3309 time to fit residues: 284.1895 Evaluate side-chains 451 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 197 time to evaluate : 2.264 Switching outliers to nearest non-outliers outliers start: 254 outliers final: 5 residues processed: 254 average time/residue: 0.2299 time to fit residues: 108.0144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 866 GLN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.8781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 0.498 23968 Z= 5.626 Angle : 4.943 45.595 32860 Z= 2.359 Chirality : 0.265 1.688 4015 Planarity : 0.030 0.268 4062 Dihedral : 20.170 131.220 5220 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 108.51 Ramachandran Plot: Outliers : 7.83 % Allowed : 36.57 % Favored : 55.60 % Rotamer: Outliers : 27.81 % Allowed : 24.52 % Favored : 47.67 % Cbeta Deviations : 3.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 7.46 % 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: -8.49 (0.07), residues: 2428 helix: -5.08 (0.05), residues: 1664 sheet: None (None), residues: 0 loop : -6.50 (0.11), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.017 TRP A 680 HIS 0.045 0.013 HIS D 453 PHE 0.154 0.020 PHE A 710 TYR 0.094 0.017 TYR A 971 ARG 0.038 0.005 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 490 poor density : 185 time to evaluate : 2.390 Fit side-chains outliers start: 490 outliers final: 312 residues processed: 624 average time/residue: 0.3400 time to fit residues: 330.7636 Evaluate side-chains 488 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 176 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 312 outliers final: 13 residues processed: 312 average time/residue: 0.2198 time to fit residues: 129.2062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.9041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.089 0.501 23968 Z= 5.637 Angle : 4.945 45.214 32860 Z= 2.357 Chirality : 0.266 1.638 4015 Planarity : 0.031 0.285 4062 Dihedral : 20.357 137.647 5220 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 110.48 Ramachandran Plot: Outliers : 7.74 % Allowed : 39.37 % Favored : 52.88 % Rotamer: Outliers : 27.01 % Allowed : 29.00 % Favored : 43.98 % Cbeta Deviations : 3.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 8.14 % 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: -8.54 (0.07), residues: 2428 helix: -5.11 (0.05), residues: 1680 sheet: None (None), residues: 0 loop : -6.54 (0.11), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.017 TRP D 776 HIS 0.048 0.012 HIS B 453 PHE 0.137 0.018 PHE C 710 TYR 0.099 0.017 TYR A 971 ARG 0.052 0.005 ARG D1138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 476 poor density : 173 time to evaluate : 2.252 Fit side-chains outliers start: 476 outliers final: 327 residues processed: 615 average time/residue: 0.3577 time to fit residues: 336.4011 Evaluate side-chains 511 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 184 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 327 outliers final: 16 residues processed: 327 average time/residue: 0.2392 time to fit residues: 141.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.9210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 0.499 23968 Z= 5.626 Angle : 4.946 45.810 32860 Z= 2.356 Chirality : 0.267 1.666 4015 Planarity : 0.030 0.265 4062 Dihedral : 20.471 145.850 5220 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 111.75 Ramachandran Plot: Outliers : 7.13 % Allowed : 41.10 % Favored : 51.77 % Rotamer: Outliers : 24.40 % Allowed : 32.63 % Favored : 42.96 % Cbeta Deviations : 3.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 8.31 % 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: -8.51 (0.07), residues: 2428 helix: -5.12 (0.05), residues: 1728 sheet: None (None), residues: 0 loop : -6.44 (0.12), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.017 TRP D 680 HIS 0.056 0.013 HIS A 453 PHE 0.119 0.018 PHE D 933 TYR 0.101 0.017 TYR D 971 ARG 0.054 0.005 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 430 poor density : 161 time to evaluate : 2.521 Fit side-chains outliers start: 430 outliers final: 292 residues processed: 567 average time/residue: 0.3497 time to fit residues: 308.8173 Evaluate side-chains 466 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 174 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 292 outliers final: 16 residues processed: 292 average time/residue: 0.2477 time to fit residues: 130.0886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.9281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 0.500 23968 Z= 5.625 Angle : 4.937 45.514 32860 Z= 2.352 Chirality : 0.268 1.663 4015 Planarity : 0.030 0.275 4062 Dihedral : 20.618 146.304 5220 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 110.51 Ramachandran Plot: Outliers : 7.00 % Allowed : 42.59 % Favored : 50.41 % Rotamer: Outliers : 21.40 % Allowed : 35.53 % Favored : 43.08 % Cbeta Deviations : 3.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 13.54 % Twisted General : 8.64 % 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: -8.51 (0.07), residues: 2428 helix: -5.14 (0.05), residues: 1700 sheet: None (None), residues: 0 loop : -6.39 (0.12), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.017 TRP A 680 HIS 0.063 0.013 HIS D1164 PHE 0.125 0.018 PHE D 933 TYR 0.101 0.017 TYR D 971 ARG 0.050 0.005 ARG D1138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 170 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 377 outliers final: 232 residues processed: 515 average time/residue: 0.3712 time to fit residues: 292.0946 Evaluate side-chains 406 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 174 time to evaluate : 2.301 Switching outliers to nearest non-outliers outliers start: 232 outliers final: 14 residues processed: 232 average time/residue: 0.2443 time to fit residues: 104.2540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.9323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.088 0.499 23968 Z= 5.635 Angle : 4.950 45.488 32860 Z= 2.359 Chirality : 0.270 1.583 4015 Planarity : 0.031 0.295 4062 Dihedral : 20.652 147.381 5220 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 110.61 Ramachandran Plot: Outliers : 6.59 % Allowed : 43.33 % Favored : 50.08 % Rotamer: Outliers : 16.74 % Allowed : 39.10 % Favored : 44.15 % Cbeta Deviations : 3.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 13.54 % Twisted General : 8.64 % 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: -8.53 (0.07), residues: 2428 helix: -5.13 (0.05), residues: 1728 sheet: None (None), residues: 0 loop : -6.44 (0.12), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.017 TRP A 680 HIS 0.063 0.013 HIS C1164 PHE 0.127 0.019 PHE C 710 TYR 0.101 0.017 TYR B 971 ARG 0.050 0.005 ARG D1138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 175 time to evaluate : 2.447 Fit side-chains outliers start: 295 outliers final: 202 residues processed: 443 average time/residue: 0.3850 time to fit residues: 268.0599 Evaluate side-chains 372 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 170 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 202 outliers final: 12 residues processed: 202 average time/residue: 0.2684 time to fit residues: 100.2155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.9351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.089 0.497 23968 Z= 5.647 Angle : 4.955 45.411 32860 Z= 2.364 Chirality : 0.270 1.485 4015 Planarity : 0.030 0.281 4062 Dihedral : 20.703 147.195 5220 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 111.23 Ramachandran Plot: Outliers : 6.80 % Allowed : 43.86 % Favored : 49.34 % Rotamer: Outliers : 12.43 % Allowed : 42.28 % Favored : 45.29 % Cbeta Deviations : 3.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 13.54 % Twisted General : 8.86 % 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: -8.55 (0.07), residues: 2428 helix: -5.15 (0.05), residues: 1712 sheet: None (None), residues: 0 loop : -6.46 (0.12), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.017 TRP A 649 HIS 0.061 0.014 HIS D1164 PHE 0.125 0.019 PHE D 933 TYR 0.101 0.017 TYR C 971 ARG 0.053 0.005 ARG B1147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 170 time to evaluate : 2.174 Fit side-chains outliers start: 219 outliers final: 124 residues processed: 375 average time/residue: 0.3514 time to fit residues: 206.2050 Evaluate side-chains 292 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 168 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 12 residues processed: 124 average time/residue: 0.2355 time to fit residues: 58.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 866 GLN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.9364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.089 0.499 23968 Z= 5.653 Angle : 4.961 45.636 32860 Z= 2.367 Chirality : 0.272 1.458 4015 Planarity : 0.030 0.283 4062 Dihedral : 20.732 147.150 5220 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 112.17 Ramachandran Plot: Outliers : 6.51 % Allowed : 43.86 % Favored : 49.63 % Rotamer: Outliers : 9.99 % Allowed : 43.53 % Favored : 46.48 % Cbeta Deviations : 3.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.58 % Twisted General : 9.03 % 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: -8.60 (0.07), residues: 2428 helix: -5.16 (0.05), residues: 1704 sheet: None (None), residues: 0 loop : -6.55 (0.11), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.017 TRP C 559 HIS 0.060 0.013 HIS B1164 PHE 0.128 0.019 PHE D 710 TYR 0.101 0.017 TYR D 971 ARG 0.048 0.006 ARG D1138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 167 time to evaluate : 2.360 Fit side-chains outliers start: 176 outliers final: 99 residues processed: 329 average time/residue: 0.3632 time to fit residues: 184.7748 Evaluate side-chains 266 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 167 time to evaluate : 2.513 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 12 residues processed: 99 average time/residue: 0.2401 time to fit residues: 46.6055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN A 866 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 866 GLN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.9372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.089 0.499 23968 Z= 5.653 Angle : 4.958 45.391 32860 Z= 2.370 Chirality : 0.272 1.425 4015 Planarity : 0.031 0.287 4062 Dihedral : 20.807 146.929 5220 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 112.40 Ramachandran Plot: Outliers : 6.67 % Allowed : 43.95 % Favored : 49.38 % Rotamer: Outliers : 4.94 % Allowed : 47.05 % Favored : 48.01 % Cbeta Deviations : 3.89 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 15.62 % Twisted General : 8.94 % 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: -8.60 (0.07), residues: 2428 helix: -5.18 (0.05), residues: 1720 sheet: None (None), residues: 0 loop : -6.50 (0.11), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.017 TRP C 649 HIS 0.063 0.013 HIS C 453 PHE 0.125 0.019 PHE C 710 TYR 0.101 0.017 TYR B 971 ARG 0.048 0.005 ARG C1138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 167 time to evaluate : 2.284 Fit side-chains outliers start: 87 outliers final: 47 residues processed: 245 average time/residue: 0.3497 time to fit residues: 137.9420 Evaluate side-chains 211 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 164 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 12 residues processed: 47 average time/residue: 0.2634 time to fit residues: 25.0455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 866 GLN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095758 restraints weight = 51763.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.093249 restraints weight = 63799.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.093789 restraints weight = 73772.824| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.9375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.089 0.499 23968 Z= 5.652 Angle : 4.944 45.360 32860 Z= 2.366 Chirality : 0.271 1.413 4015 Planarity : 0.031 0.282 4062 Dihedral : 20.819 146.845 5220 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 112.50 Ramachandran Plot: Outliers : 6.38 % Allowed : 44.44 % Favored : 49.18 % Rotamer: Outliers : 5.56 % Allowed : 47.16 % Favored : 47.28 % Cbeta Deviations : 3.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 8.77 % 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: -8.59 (0.07), residues: 2428 helix: -5.17 (0.05), residues: 1720 sheet: None (None), residues: 0 loop : -6.50 (0.11), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.017 TRP D 649 HIS 0.054 0.013 HIS D 453 PHE 0.125 0.019 PHE A 935 TYR 0.101 0.017 TYR D 971 ARG 0.048 0.005 ARG C1138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10071.17 seconds wall clock time: 179 minutes 0.64 seconds (10740.64 seconds total)