Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 09:28:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/07_2023/6bwi_7299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/07_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_7299/07_2023/6bwi_7299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/07_2023/6bwi_7299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/07_2023/6bwi_7299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/07_2023/6bwi_7299.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 10.45, per 1000 atoms: 0.44 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: 8.48 Conformation dependent library (CDL) restraints added in 2.8 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: 1.34 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: 7.59 Time building geometry restraints manager: 9.28 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 - 15.58: 12800 15.58 - 31.16: 762 31.16 - 46.74: 194 46.74 - 62.32: 49 62.32 - 77.90: 15 Dihedral angle restraints: 13820 sinusoidal: 4276 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 13817 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: 2.350 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: 5.650 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 54.490 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.130 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.670 ------------------------------------------------------------------------------- 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 : 12.093 77.900 7528 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 % 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 *********************** 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 : 2.399 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 677 average time/residue: 0.4022 time to fit residues: 400.2883 Evaluate side-chains 367 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 357 time to evaluate : 2.213 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3750 time to fit residues: 8.5113 ------------------------------------------------------------------------------- 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: 0.8330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.505 23968 Z= 5.669 Angle : 5.028 48.371 32860 Z= 2.390 Chirality : 0.269 1.787 4015 Planarity : 0.031 0.263 4062 Dihedral : 17.717 101.282 3732 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 102.44 Ramachandran Plot: Outliers : 10.58 % Allowed : 25.37 % Favored : 64.04 % Rotamer Outliers : 21.45 % Cbeta Deviations : 4.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 6.27 % 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 *********************** 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 580 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 202 time to evaluate : 2.372 Fit side-chains outliers start: 378 outliers final: 254 residues processed: 547 average time/residue: 0.3454 time to fit residues: 301.8372 Evaluate side-chains 452 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 198 time to evaluate : 2.286 Switching outliers to nearest non-outliers outliers start: 254 outliers final: 6 residues processed: 254 average time/residue: 0.2369 time to fit residues: 112.0016 ------------------------------------------------------------------------------- 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** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- 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 0.503 23968 Z= 5.628 Angle : 4.952 45.976 32860 Z= 2.361 Chirality : 0.266 1.682 4015 Planarity : 0.030 0.269 4062 Dihedral : 18.599 111.442 3732 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 108.32 Ramachandran Plot: Outliers : 7.83 % Allowed : 36.86 % Favored : 55.31 % Rotamer Outliers : 27.75 % Cbeta Deviations : 3.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 7.50 % 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: -8.48 (0.07), residues: 2428 helix: -5.07 (0.05), residues: 1660 sheet: None (None), residues: 0 loop : -6.49 (0.11), residues: 768 *********************** 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 671 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 489 poor density : 182 time to evaluate : 2.364 Fit side-chains outliers start: 489 outliers final: 307 residues processed: 620 average time/residue: 0.3347 time to fit residues: 322.5946 Evaluate side-chains 485 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 178 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 307 outliers final: 12 residues processed: 307 average time/residue: 0.2155 time to fit residues: 124.7649 ------------------------------------------------------------------------------- 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** ** 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: 0.8192 moved from start: 0.9058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.500 23968 Z= 5.638 Angle : 4.955 45.581 32860 Z= 2.359 Chirality : 0.267 1.632 4015 Planarity : 0.031 0.286 4062 Dihedral : 18.785 109.818 3732 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 110.58 Ramachandran Plot: Outliers : 7.74 % Allowed : 39.37 % Favored : 52.88 % Rotamer Outliers : 26.79 % Cbeta Deviations : 3.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 8.05 % 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: -5.11 (0.05), residues: 1680 sheet: None (None), residues: 0 loop : -6.54 (0.11), residues: 748 *********************** 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 648 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 472 poor density : 176 time to evaluate : 2.671 Fit side-chains outliers start: 472 outliers final: 328 residues processed: 614 average time/residue: 0.3623 time to fit residues: 341.2484 Evaluate side-chains 514 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 186 time to evaluate : 2.437 Switching outliers to nearest non-outliers outliers start: 328 outliers final: 16 residues processed: 328 average time/residue: 0.2677 time to fit residues: 161.2435 ------------------------------------------------------------------------------- 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: 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 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 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: 0.8193 moved from start: 0.9211 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 : 4.950 45.931 32860 Z= 2.356 Chirality : 0.267 1.653 4015 Planarity : 0.030 0.265 4062 Dihedral : 19.053 105.380 3732 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 111.65 Ramachandran Plot: Outliers : 7.04 % Allowed : 41.10 % Favored : 51.85 % Rotamer Outliers : 24.91 % Cbeta Deviations : 3.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 8.22 % 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: -5.11 (0.05), residues: 1728 sheet: None (None), residues: 0 loop : -6.42 (0.12), residues: 700 *********************** 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 601 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 439 poor density : 162 time to evaluate : 2.496 Fit side-chains outliers start: 439 outliers final: 290 residues processed: 576 average time/residue: 0.3388 time to fit residues: 304.5167 Evaluate side-chains 466 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 176 time to evaluate : 2.233 Switching outliers to nearest non-outliers outliers start: 290 outliers final: 16 residues processed: 290 average time/residue: 0.2599 time to fit residues: 135.5670 ------------------------------------------------------------------------------- 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 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8195 moved from start: 0.9280 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 : 4.944 45.947 32860 Z= 2.353 Chirality : 0.268 1.626 4015 Planarity : 0.030 0.279 4062 Dihedral : 19.130 105.371 3732 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 109.81 Ramachandran Plot: Outliers : 6.84 % Allowed : 42.34 % Favored : 50.82 % Rotamer Outliers : 21.34 % Cbeta Deviations : 3.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 13.54 % Twisted General : 8.56 % 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: -8.48 (0.07), residues: 2428 helix: -5.11 (0.05), residues: 1708 sheet: None (None), residues: 0 loop : -6.40 (0.12), residues: 720 *********************** 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 545 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 169 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 376 outliers final: 237 residues processed: 513 average time/residue: 0.3753 time to fit residues: 291.5503 Evaluate side-chains 413 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 176 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 237 outliers final: 14 residues processed: 237 average time/residue: 0.2342 time to fit residues: 102.1177 ------------------------------------------------------------------------------- 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 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: 0.8199 moved from start: 0.9328 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= 5.635 Angle : 4.956 45.844 32860 Z= 2.359 Chirality : 0.271 1.510 4015 Planarity : 0.031 0.300 4062 Dihedral : 19.206 105.764 3732 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 110.48 Ramachandran Plot: Outliers : 6.55 % Allowed : 43.37 % Favored : 50.08 % Rotamer Outliers : 17.14 % Cbeta Deviations : 3.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 13.54 % Twisted General : 8.60 % 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 : -6.45 (0.12), residues: 700 *********************** 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 479 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 177 time to evaluate : 2.229 Fit side-chains outliers start: 302 outliers final: 203 residues processed: 452 average time/residue: 0.3501 time to fit residues: 247.5989 Evaluate side-chains 370 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 167 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 203 outliers final: 12 residues processed: 203 average time/residue: 0.2353 time to fit residues: 88.3772 ------------------------------------------------------------------------------- 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: 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 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 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: 0.8197 moved from start: 0.9356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.500 23968 Z= 5.648 Angle : 4.959 45.878 32860 Z= 2.364 Chirality : 0.269 1.457 4015 Planarity : 0.030 0.281 4062 Dihedral : 19.261 107.969 3732 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 111.21 Ramachandran Plot: Outliers : 6.63 % Allowed : 43.86 % Favored : 49.51 % Rotamer Outliers : 12.26 % Cbeta Deviations : 3.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 13.54 % 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: -8.53 (0.07), residues: 2428 helix: -5.13 (0.05), residues: 1712 sheet: None (None), residues: 0 loop : -6.45 (0.12), residues: 716 *********************** 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 381 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 165 time to evaluate : 2.573 Fit side-chains outliers start: 216 outliers final: 120 residues processed: 368 average time/residue: 0.3546 time to fit residues: 204.2401 Evaluate side-chains 288 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 168 time to evaluate : 2.296 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 12 residues processed: 120 average time/residue: 0.2384 time to fit residues: 53.9048 ------------------------------------------------------------------------------- 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: 0.8197 moved from start: 0.9371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.498 23968 Z= 5.650 Angle : 4.962 45.878 32860 Z= 2.366 Chirality : 0.272 1.404 4015 Planarity : 0.031 0.285 4062 Dihedral : 19.312 107.308 3732 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 111.92 Ramachandran Plot: Outliers : 6.63 % Allowed : 43.66 % Favored : 49.71 % Rotamer Outliers : 9.93 % Cbeta Deviations : 3.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.58 % Twisted General : 8.90 % 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: -8.58 (0.07), residues: 2428 helix: -5.15 (0.05), residues: 1708 sheet: None (None), residues: 0 loop : -6.53 (0.11), residues: 720 *********************** 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 346 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 171 time to evaluate : 2.443 Fit side-chains outliers start: 175 outliers final: 102 residues processed: 332 average time/residue: 0.3477 time to fit residues: 179.5911 Evaluate side-chains 275 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 173 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 12 residues processed: 102 average time/residue: 0.2292 time to fit residues: 44.7961 ------------------------------------------------------------------------------- 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: 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 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** ** D1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.9374 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= 5.651 Angle : 4.963 45.844 32860 Z= 2.370 Chirality : 0.271 1.377 4015 Planarity : 0.032 0.285 4062 Dihedral : 19.367 105.725 3732 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 112.40 Ramachandran Plot: Outliers : 6.63 % Allowed : 44.15 % Favored : 49.22 % Rotamer Outliers : 4.88 % Cbeta Deviations : 3.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.58 % Twisted General : 8.90 % 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: -8.58 (0.07), residues: 2428 helix: -5.17 (0.05), residues: 1720 sheet: None (None), residues: 0 loop : -6.49 (0.12), residues: 708 ********************** 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: 86 poor density : 168 time to evaluate : 2.482 Fit side-chains outliers start: 86 outliers final: 48 residues processed: 245 average time/residue: 0.3196 time to fit residues: 127.9041 Evaluate side-chains 214 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 2.280 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 12 residues processed: 48 average time/residue: 0.2152 time to fit residues: 22.1125 ------------------------------------------------------------------------------- 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: 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 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** ** 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** ** D1164 HIS ** 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 = 0.3220 r_free = 0.3220 target = 0.111061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.094422 restraints weight = 51749.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.092316 restraints weight = 66331.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.092906 restraints weight = 69015.134| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.9377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.498 23968 Z= 5.650 Angle : 4.948 45.860 32860 Z= 2.366 Chirality : 0.270 1.372 4015 Planarity : 0.031 0.295 4062 Dihedral : 19.377 102.936 3732 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 112.56 Ramachandran Plot: Outliers : 6.47 % Allowed : 44.11 % Favored : 49.42 % Rotamer Outliers : 5.68 % Cbeta Deviations : 3.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.58 % 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: -8.57 (0.07), residues: 2428 helix: -5.16 (0.05), residues: 1720 sheet: None (None), residues: 0 loop : -6.49 (0.12), residues: 708 =============================================================================== Job complete usr+sys time: 9952.53 seconds wall clock time: 176 minutes 24.62 seconds (10584.62 seconds total)