Starting phenix.real_space_refine on Tue Feb 20 22:29:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz4_24750/02_2024/7rz4_24750_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz4_24750/02_2024/7rz4_24750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz4_24750/02_2024/7rz4_24750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz4_24750/02_2024/7rz4_24750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz4_24750/02_2024/7rz4_24750_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz4_24750/02_2024/7rz4_24750_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 142 5.16 5 C 18762 2.51 5 N 4678 2.21 5 O 5388 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28998 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7823 Classifications: {'peptide': 993} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 965} Chain breaks: 3 Chain: "B" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6254 Classifications: {'peptide': 794} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 770} Chain breaks: 1 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7823 Classifications: {'peptide': 993} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 965} Chain breaks: 3 Chain: "D" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6254 Classifications: {'peptide': 794} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 770} Chain breaks: 1 Chain: "A" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 2, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 2, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 2, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 2, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 14.73, per 1000 atoms: 0.51 Number of scatterers: 28998 At special positions: 0 Unit cell: (124.3, 168.3, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 142 16.00 P 16 15.00 F 12 9.00 O 5388 8.00 N 4678 7.00 C 18762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1102 " - " ASN A 355 " " NAG B1102 " - " ASN B 355 " " NAG C1102 " - " ASN C 355 " " NAG D1103 " - " ASN D 355 " Time building additional restraints: 10.17 Conformation dependent library (CDL) restraints added in 4.8 seconds 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 30 sheets defined 44.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.32 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.555A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.601A pdb=" N PHE A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.549A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.552A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.726A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.512A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.716A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 629 removed outlier: 3.735A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 654 through 660 removed outlier: 3.750A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 695 removed outlier: 3.530A pdb=" N LYS A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.503A pdb=" N VAL A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 793 through 821 Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.721A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 917 through 927 removed outlier: 3.505A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 951 Processing helix chain 'A' and resid 956 through 985 removed outlier: 3.847A pdb=" N ALA A 959 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 961 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 962 " --> pdb=" O ALA A 959 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 965 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 968 " --> pdb=" O PHE A 965 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 971 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 975 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 978 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 979 " --> pdb=" O GLY A 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 981 " --> pdb=" O VAL A 978 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 982 " --> pdb=" O LEU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 removed outlier: 3.558A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1026 " --> pdb=" O VAL A1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.784A pdb=" N VAL B 82 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN B 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 86 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 89 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 92 " --> pdb=" O CYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.630A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.803A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.584A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.509A pdb=" N ARG B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.645A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 488' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.611A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 3.603A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.613A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.503A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.599A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 793 through 819 removed outlier: 3.510A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 144 through 156 removed outlier: 3.556A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.601A pdb=" N PHE C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.549A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.551A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.726A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.511A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.716A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 629 removed outlier: 3.735A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 660 removed outlier: 3.749A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 695 removed outlier: 3.531A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 755 removed outlier: 3.503A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 776 through 778 No H-bonds generated for 'chain 'C' and resid 776 through 778' Processing helix chain 'C' and resid 793 through 821 Processing helix chain 'C' and resid 832 through 857 removed outlier: 3.722A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 917 through 927 removed outlier: 3.505A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 951 Processing helix chain 'C' and resid 956 through 985 removed outlier: 3.848A pdb=" N ALA C 959 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL C 961 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 962 " --> pdb=" O ALA C 959 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C 968 " --> pdb=" O PHE C 965 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 971 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 975 " --> pdb=" O SER C 972 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 978 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 979 " --> pdb=" O GLY C 976 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 981 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER C 982 " --> pdb=" O LEU C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1034 removed outlier: 3.559A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C1026 " --> pdb=" O VAL C1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.784A pdb=" N VAL D 82 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASN D 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR D 86 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS D 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 92 " --> pdb=" O CYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.630A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.803A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.585A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.509A pdb=" N ARG D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.645A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 483 through 488' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.611A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.603A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.614A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.503A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 removed outlier: 3.599A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 793 through 819 removed outlier: 3.511A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.789A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER A 95 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY A 75 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE A 97 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.554A pdb=" N TYR A 137 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.532A pdb=" N VAL A 381 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= E, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= F, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.080A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.126A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 997 through 1003 removed outlier: 5.679A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 870 " --> pdb=" O THR A 876 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N THR A 876 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 888 through 890 Processing sheet with id= J, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.201A pdb=" N ARG B 42 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.438A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER B 95 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY B 75 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 97 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.398A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.777A pdb=" N LYS B 439 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL B 397 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.119A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.197A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.788A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER C 95 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY C 75 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE C 97 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.554A pdb=" N TYR C 137 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.533A pdb=" N VAL C 381 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= T, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= U, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.080A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.126A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 997 through 1003 removed outlier: 5.679A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 870 " --> pdb=" O THR C 876 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N THR C 876 " --> pdb=" O LEU C 870 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 888 through 890 Processing sheet with id= Y, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.201A pdb=" N ARG D 42 " --> pdb=" O ILE D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.438A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER D 95 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY D 75 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 97 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.399A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.777A pdb=" N LYS D 439 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL D 397 " --> pdb=" O LYS D 439 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS D 441 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR D 399 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR D 443 " --> pdb=" O THR D 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.119A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.198A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 1167 hydrogen bonds defined for protein. 3336 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: 11.08 Time building geometry restraints manager: 11.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4646 1.32 - 1.46: 8707 1.46 - 1.59: 15969 1.59 - 1.73: 24 1.73 - 1.86: 236 Bond restraints: 29582 Sorted by residual: bond pdb=" CAT ZK1 B1101 " pdb=" OAA ZK1 B1101 " ideal model delta sigma weight residual 1.214 1.401 -0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" CAT ZK1 D1102 " pdb=" OAA ZK1 D1102 " ideal model delta sigma weight residual 1.214 1.399 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" CAT ZK1 C1101 " pdb=" OAA ZK1 C1101 " ideal model delta sigma weight residual 1.214 1.399 -0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" CAT ZK1 A1101 " pdb=" OAA ZK1 A1101 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" CAU ZK1 B1101 " pdb=" OAB ZK1 B1101 " ideal model delta sigma weight residual 1.215 1.398 -0.183 2.00e-02 2.50e+03 8.39e+01 ... (remaining 29577 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.31: 593 106.31 - 113.28: 16011 113.28 - 120.25: 10310 120.25 - 127.22: 12684 127.22 - 134.19: 248 Bond angle restraints: 39846 Sorted by residual: angle pdb=" C ASP D 378 " pdb=" N LYS D 379 " pdb=" CA LYS D 379 " ideal model delta sigma weight residual 121.19 128.95 -7.76 1.59e+00 3.96e-01 2.38e+01 angle pdb=" C ASP B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta sigma weight residual 121.19 128.89 -7.70 1.59e+00 3.96e-01 2.35e+01 angle pdb=" C ALA C 928 " pdb=" N THR C 929 " pdb=" CA THR C 929 " ideal model delta sigma weight residual 120.26 126.34 -6.08 1.34e+00 5.57e-01 2.06e+01 angle pdb=" C ALA A 928 " pdb=" N THR A 929 " pdb=" CA THR A 929 " ideal model delta sigma weight residual 120.26 126.30 -6.04 1.34e+00 5.57e-01 2.03e+01 angle pdb=" N ASP C 519 " pdb=" CA ASP C 519 " pdb=" C ASP C 519 " ideal model delta sigma weight residual 109.81 119.47 -9.66 2.21e+00 2.05e-01 1.91e+01 ... (remaining 39841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 17380 35.95 - 71.90: 336 71.90 - 107.86: 36 107.86 - 143.81: 3 143.81 - 179.76: 9 Dihedral angle restraints: 17764 sinusoidal: 7476 harmonic: 10288 Sorted by residual: dihedral pdb=" CA ASP C 378 " pdb=" C ASP C 378 " pdb=" N LYS C 379 " pdb=" CA LYS C 379 " ideal model delta harmonic sigma weight residual -180.00 -140.62 -39.38 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CA ASP A 378 " pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta harmonic sigma weight residual -180.00 -140.67 -39.33 0 5.00e+00 4.00e-02 6.19e+01 dihedral pdb=" CA ASP B 378 " pdb=" C ASP B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta harmonic sigma weight residual -180.00 -142.16 -37.84 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4278 0.133 - 0.265: 74 0.265 - 0.398: 0 0.398 - 0.530: 0 0.530 - 0.663: 2 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG B1102 " pdb=" ND2 ASN B 355 " pdb=" C2 NAG B1102 " pdb=" O5 NAG B1102 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C1 NAG D1103 " pdb=" ND2 ASN D 355 " pdb=" C2 NAG D1103 " pdb=" O5 NAG D1103 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4351 not shown) Planarity restraints: 4964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO D 99 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " 0.056 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO B 99 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO A 99 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.046 5.00e-02 4.00e+02 ... (remaining 4961 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9076 2.84 - 3.35: 24658 3.35 - 3.87: 43776 3.87 - 4.38: 49967 4.38 - 4.90: 89036 Nonbonded interactions: 216513 Sorted by model distance: nonbonded pdb=" O MET C 33 " pdb=" OG SER C 37 " model vdw 2.325 2.440 nonbonded pdb=" O MET A 33 " pdb=" OG SER A 37 " model vdw 2.325 2.440 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.346 2.440 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.346 2.440 nonbonded pdb=" OG SER C 544 " pdb=" ND2 ASN C 569 " model vdw 2.357 2.520 ... (remaining 216508 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 10 through 820 or resid 1104 through 1105 or (resid 1106 a \ nd (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1107 through 1108 and (name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or \ name C23)))) selection = (chain 'D' and (resid 10 through 820 or (resid 1104 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or n \ ame C45 or name C5 or name C6 or name C7 or name C8 or name O11 or name O1P or n \ ame O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) o \ r (resid 1105 and (name N or name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or n \ ame C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 o \ r name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44 or name C5 or name C6 or name C7 or name C8 or name O1 \ 1 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name \ O4P or name P )) or (resid 1106 and (name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19)) or (resid 1107 through 1108 and (name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C20 or name C21 or name C22 or name C23)))) } 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: 5.800 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: 0.000 Extract box with map and model: 10.200 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 73.070 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.007 0.187 29582 Z= 0.471 Angle : 0.974 14.087 39846 Z= 0.470 Chirality : 0.050 0.663 4354 Planarity : 0.006 0.086 4960 Dihedral : 14.069 179.761 11166 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.26 % Allowed : 4.33 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.10), residues: 3550 helix: -3.58 (0.06), residues: 1700 sheet: 0.10 (0.24), residues: 456 loop : -2.01 (0.12), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 323 HIS 0.011 0.002 HIS D 93 PHE 0.021 0.002 PHE A 245 TYR 0.024 0.002 TYR B 177 ARG 0.005 0.001 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 709 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8758 (m) cc_final: 0.8405 (p) REVERT: A 591 ILE cc_start: 0.5789 (OUTLIER) cc_final: 0.5539 (pp) REVERT: A 638 ASP cc_start: 0.8505 (m-30) cc_final: 0.8089 (m-30) REVERT: A 663 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8039 (mptt) REVERT: A 705 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 989 LEU cc_start: 0.8017 (tm) cc_final: 0.7734 (tp) REVERT: B 26 TYR cc_start: 0.8172 (t80) cc_final: 0.7806 (t80) REVERT: B 41 PHE cc_start: 0.5709 (p90) cc_final: 0.5413 (p90) REVERT: B 42 ARG cc_start: 0.6417 (mtp-110) cc_final: 0.5800 (mpt180) REVERT: B 293 THR cc_start: 0.7348 (m) cc_final: 0.7148 (p) REVERT: B 629 MET cc_start: 0.6394 (mtm) cc_final: 0.5982 (mmt) REVERT: B 712 ILE cc_start: 0.8716 (mm) cc_final: 0.8469 (mt) REVERT: C 297 ARG cc_start: 0.6322 (ttm170) cc_final: 0.6109 (ttm170) REVERT: C 373 TYR cc_start: 0.7949 (p90) cc_final: 0.7603 (p90) REVERT: C 511 LYS cc_start: 0.8277 (tttm) cc_final: 0.8022 (ttpt) REVERT: C 597 SER cc_start: 0.8472 (p) cc_final: 0.8100 (t) REVERT: C 642 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 663 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8262 (mptt) REVERT: C 859 ASP cc_start: 0.6787 (p0) cc_final: 0.6252 (m-30) REVERT: C 866 GLU cc_start: 0.6576 (tt0) cc_final: 0.6273 (pt0) REVERT: C 924 MET cc_start: 0.7243 (mmt) cc_final: 0.6656 (mmt) REVERT: C 983 SER cc_start: 0.8032 (m) cc_final: 0.7248 (p) REVERT: C 1023 MET cc_start: 0.6490 (mtt) cc_final: 0.6261 (mtp) REVERT: D 34 VAL cc_start: 0.7926 (t) cc_final: 0.7702 (m) REVERT: D 172 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7744 (mtpp) REVERT: D 266 GLU cc_start: 0.7095 (mp0) cc_final: 0.6344 (mm-30) REVERT: D 438 PHE cc_start: 0.6871 (p90) cc_final: 0.6618 (p90) REVERT: D 515 PHE cc_start: 0.8569 (m-10) cc_final: 0.8274 (m-80) outliers start: 8 outliers final: 1 residues processed: 715 average time/residue: 0.4751 time to fit residues: 507.2613 Evaluate side-chains 351 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 279 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 323 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 311 ASN A 337 GLN A 344 ASN A 411 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 874 GLN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN A 947 ASN B 13 GLN B 60 ASN B 207 GLN B 318 ASN B 344 ASN B 587 GLN B 764 ASN C 10 ASN C 46 HIS C 170 ASN C 219 HIS C 311 ASN C 337 GLN C 344 ASN C 873 ASN C 874 GLN C 920 ASN C 947 ASN D 60 ASN D 318 ASN D 344 ASN D 508 GLN D 586 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29582 Z= 0.207 Angle : 0.535 8.515 39846 Z= 0.285 Chirality : 0.042 0.331 4354 Planarity : 0.005 0.075 4960 Dihedral : 14.071 179.525 4582 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.80 % Allowed : 8.99 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 3550 helix: -0.20 (0.11), residues: 1708 sheet: 0.31 (0.24), residues: 490 loop : -1.66 (0.13), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 262 HIS 0.005 0.001 HIS D 219 PHE 0.022 0.002 PHE D 546 TYR 0.020 0.002 TYR C 523 ARG 0.005 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 363 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8846 (m) cc_final: 0.8483 (p) REVERT: A 251 ASP cc_start: 0.8031 (m-30) cc_final: 0.7757 (p0) REVERT: A 591 ILE cc_start: 0.5974 (OUTLIER) cc_final: 0.5656 (pp) REVERT: A 663 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8050 (mptt) REVERT: A 664 ILE cc_start: 0.7950 (mm) cc_final: 0.7537 (mm) REVERT: B 26 TYR cc_start: 0.7897 (t80) cc_final: 0.7323 (t80) REVERT: B 42 ARG cc_start: 0.6408 (mtp-110) cc_final: 0.5688 (mpt180) REVERT: B 414 MET cc_start: 0.5588 (mmt) cc_final: 0.5339 (mmt) REVERT: B 649 THR cc_start: 0.9053 (p) cc_final: 0.8785 (p) REVERT: B 788 SER cc_start: 0.8688 (p) cc_final: 0.8486 (m) REVERT: C 151 ASP cc_start: 0.7587 (m-30) cc_final: 0.7373 (m-30) REVERT: C 203 ASP cc_start: 0.7971 (t0) cc_final: 0.7731 (t0) REVERT: C 339 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6894 (mm-30) REVERT: C 373 TYR cc_start: 0.8006 (p90) cc_final: 0.7682 (p90) REVERT: C 408 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7223 (mmt) REVERT: C 490 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: C 511 LYS cc_start: 0.8266 (tttm) cc_final: 0.8029 (ttpt) REVERT: C 642 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7549 (tm-30) REVERT: C 663 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8253 (mptt) REVERT: C 819 ARG cc_start: 0.5904 (tmm160) cc_final: 0.5247 (ttp80) REVERT: C 888 ARG cc_start: 0.6036 (mpt180) cc_final: 0.5781 (mpt180) REVERT: C 924 MET cc_start: 0.6856 (mmt) cc_final: 0.6590 (mmt) REVERT: C 988 MET cc_start: 0.7094 (mpp) cc_final: 0.6788 (mpp) REVERT: C 1029 MET cc_start: 0.5098 (mtp) cc_final: 0.4798 (mtm) REVERT: D 172 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7824 (mtpp) REVERT: D 527 MET cc_start: 0.6656 (mtm) cc_final: 0.6433 (mmt) REVERT: D 761 LYS cc_start: 0.7818 (tmmt) cc_final: 0.7613 (ttmm) outliers start: 55 outliers final: 28 residues processed: 399 average time/residue: 0.4217 time to fit residues: 265.3166 Evaluate side-chains 320 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 289 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 760 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 269 optimal weight: 0.1980 chunk 220 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 321 optimal weight: 0.0670 chunk 110 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 344 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS B 219 HIS C 46 HIS C 337 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29582 Z= 0.142 Angle : 0.456 8.805 39846 Z= 0.239 Chirality : 0.040 0.273 4354 Planarity : 0.004 0.068 4960 Dihedral : 12.728 178.072 4582 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.77 % Allowed : 10.43 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 3550 helix: 1.20 (0.13), residues: 1706 sheet: 0.39 (0.24), residues: 490 loop : -1.45 (0.14), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 262 HIS 0.004 0.001 HIS D 219 PHE 0.019 0.001 PHE A 999 TYR 0.014 0.001 TYR C 523 ARG 0.006 0.000 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 312 time to evaluate : 3.391 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.8730 (m) cc_final: 0.8376 (p) REVERT: A 591 ILE cc_start: 0.6145 (OUTLIER) cc_final: 0.5739 (pp) REVERT: A 663 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8048 (mptt) REVERT: A 664 ILE cc_start: 0.7918 (mm) cc_final: 0.7491 (mm) REVERT: B 42 ARG cc_start: 0.6431 (mtp-110) cc_final: 0.5718 (mpt180) REVERT: B 266 GLU cc_start: 0.7035 (mp0) cc_final: 0.6789 (tt0) REVERT: B 378 ASP cc_start: 0.7246 (p0) cc_final: 0.6793 (p0) REVERT: B 473 ASP cc_start: 0.6131 (t0) cc_final: 0.5839 (t0) REVERT: B 629 MET cc_start: 0.6370 (mtm) cc_final: 0.6075 (mmt) REVERT: B 649 THR cc_start: 0.9121 (p) cc_final: 0.8851 (p) REVERT: B 719 ASP cc_start: 0.7973 (t70) cc_final: 0.7401 (t0) REVERT: B 788 SER cc_start: 0.8787 (p) cc_final: 0.8560 (m) REVERT: C 203 ASP cc_start: 0.7795 (t0) cc_final: 0.7572 (t0) REVERT: C 373 TYR cc_start: 0.8008 (p90) cc_final: 0.7634 (p90) REVERT: C 408 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7123 (mmt) REVERT: C 511 LYS cc_start: 0.8285 (tttm) cc_final: 0.8039 (ttpt) REVERT: C 663 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8211 (mptt) REVERT: C 888 ARG cc_start: 0.5791 (mpt180) cc_final: 0.5590 (mpt180) REVERT: C 924 MET cc_start: 0.6780 (mmt) cc_final: 0.6500 (mmt) REVERT: C 988 MET cc_start: 0.6999 (mpp) cc_final: 0.6711 (mpt) REVERT: D 172 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7681 (mtpp) REVERT: D 438 PHE cc_start: 0.7690 (p90) cc_final: 0.7299 (p90) REVERT: D 527 MET cc_start: 0.6661 (mtm) cc_final: 0.6428 (mmt) REVERT: D 808 LEU cc_start: 0.7086 (mt) cc_final: 0.6868 (mt) outliers start: 54 outliers final: 30 residues processed: 348 average time/residue: 0.4241 time to fit residues: 233.6090 Evaluate side-chains 312 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 280 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 4.9990 chunk 243 optimal weight: 0.0010 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 325 optimal weight: 0.4980 chunk 344 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 412 HIS ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN C 412 HIS ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29582 Z= 0.172 Angle : 0.470 8.007 39846 Z= 0.245 Chirality : 0.040 0.278 4354 Planarity : 0.004 0.067 4960 Dihedral : 12.233 177.935 4582 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.33 % Allowed : 11.45 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3550 helix: 1.68 (0.13), residues: 1708 sheet: 0.27 (0.24), residues: 468 loop : -1.33 (0.14), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.020 0.001 HIS A 883 PHE 0.017 0.001 PHE A 999 TYR 0.012 0.001 TYR A 218 ARG 0.004 0.000 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 301 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8648 (m) cc_final: 0.8221 (p) REVERT: A 399 THR cc_start: 0.8898 (m) cc_final: 0.8467 (p) REVERT: A 591 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5664 (pp) REVERT: A 663 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8245 (mptt) REVERT: A 1029 MET cc_start: 0.6043 (tmm) cc_final: 0.5387 (ttm) REVERT: B 42 ARG cc_start: 0.6546 (mtp-110) cc_final: 0.5907 (mpt180) REVERT: B 266 GLU cc_start: 0.7307 (mp0) cc_final: 0.7007 (tt0) REVERT: B 378 ASP cc_start: 0.7210 (p0) cc_final: 0.6638 (p0) REVERT: B 473 ASP cc_start: 0.6151 (t0) cc_final: 0.5813 (t0) REVERT: B 629 MET cc_start: 0.6503 (mtm) cc_final: 0.6174 (mmt) REVERT: B 719 ASP cc_start: 0.7988 (t70) cc_final: 0.7505 (t0) REVERT: B 788 SER cc_start: 0.8802 (p) cc_final: 0.8524 (m) REVERT: C 203 ASP cc_start: 0.7828 (t0) cc_final: 0.7571 (t0) REVERT: C 251 ASP cc_start: 0.8266 (m-30) cc_final: 0.8010 (p0) REVERT: C 373 TYR cc_start: 0.7893 (p90) cc_final: 0.7642 (p90) REVERT: C 399 THR cc_start: 0.8852 (m) cc_final: 0.8490 (p) REVERT: C 408 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7140 (mmt) REVERT: C 490 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: C 511 LYS cc_start: 0.8325 (tttm) cc_final: 0.8083 (ttpt) REVERT: C 663 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8240 (mptt) REVERT: C 888 ARG cc_start: 0.5759 (mpt180) cc_final: 0.5417 (mpt180) REVERT: D 438 PHE cc_start: 0.7678 (p90) cc_final: 0.7327 (p90) REVERT: D 719 ASP cc_start: 0.7909 (t70) cc_final: 0.7481 (t0) outliers start: 71 outliers final: 49 residues processed: 347 average time/residue: 0.4237 time to fit residues: 231.8801 Evaluate side-chains 320 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 268 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 0.5980 chunk 195 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 237 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 883 HIS B 10 ASN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29582 Z= 0.176 Angle : 0.465 8.699 39846 Z= 0.242 Chirality : 0.040 0.273 4354 Planarity : 0.004 0.065 4960 Dihedral : 12.012 178.079 4582 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.49 % Allowed : 11.68 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3550 helix: 1.91 (0.13), residues: 1704 sheet: 0.27 (0.25), residues: 458 loop : -1.27 (0.14), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 262 HIS 0.005 0.001 HIS D 219 PHE 0.019 0.001 PHE A 999 TYR 0.013 0.001 TYR A 77 ARG 0.004 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 295 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8554 (m) cc_final: 0.8172 (p) REVERT: A 182 GLN cc_start: 0.7309 (pp30) cc_final: 0.6671 (mt0) REVERT: A 399 THR cc_start: 0.8905 (m) cc_final: 0.8528 (p) REVERT: A 591 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.5869 (pp) REVERT: A 663 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8283 (mptt) REVERT: A 849 LEU cc_start: 0.7309 (mm) cc_final: 0.6969 (mt) REVERT: A 892 LEU cc_start: 0.6637 (tt) cc_final: 0.6290 (mp) REVERT: B 10 ASN cc_start: 0.3730 (OUTLIER) cc_final: 0.3486 (t160) REVERT: B 42 ARG cc_start: 0.6531 (mtp-110) cc_final: 0.5910 (mpt180) REVERT: B 266 GLU cc_start: 0.7360 (mp0) cc_final: 0.6975 (tt0) REVERT: B 378 ASP cc_start: 0.7206 (p0) cc_final: 0.6621 (p0) REVERT: B 629 MET cc_start: 0.6717 (mtm) cc_final: 0.6183 (mmt) REVERT: B 719 ASP cc_start: 0.8015 (t70) cc_final: 0.7571 (t0) REVERT: B 788 SER cc_start: 0.8901 (p) cc_final: 0.8615 (m) REVERT: C 203 ASP cc_start: 0.7854 (t0) cc_final: 0.7605 (t0) REVERT: C 251 ASP cc_start: 0.8305 (m-30) cc_final: 0.8035 (p0) REVERT: C 373 TYR cc_start: 0.7934 (p90) cc_final: 0.7713 (p90) REVERT: C 399 THR cc_start: 0.8794 (m) cc_final: 0.8499 (p) REVERT: C 408 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7123 (mmt) REVERT: C 490 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: C 511 LYS cc_start: 0.8368 (tttm) cc_final: 0.8114 (ttpt) REVERT: C 663 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8296 (mptt) REVERT: C 805 LEU cc_start: 0.7799 (tp) cc_final: 0.7389 (tt) REVERT: C 866 GLU cc_start: 0.6294 (tt0) cc_final: 0.5325 (mp0) REVERT: C 888 ARG cc_start: 0.5960 (mpt180) cc_final: 0.5634 (mpt180) REVERT: D 438 PHE cc_start: 0.7684 (p90) cc_final: 0.7371 (p90) REVERT: D 542 LEU cc_start: 0.7582 (mm) cc_final: 0.7172 (tt) REVERT: D 543 VAL cc_start: 0.7911 (t) cc_final: 0.7660 (t) REVERT: D 719 ASP cc_start: 0.7950 (t70) cc_final: 0.7535 (t0) outliers start: 76 outliers final: 54 residues processed: 347 average time/residue: 0.4160 time to fit residues: 229.9440 Evaluate side-chains 332 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 274 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 68 optimal weight: 0.0470 chunk 202 optimal weight: 0.0050 chunk 84 optimal weight: 7.9990 chunk 344 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 159 optimal weight: 0.0050 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 0.0770 chunk 180 optimal weight: 8.9990 overall best weight: 0.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29582 Z= 0.107 Angle : 0.422 9.023 39846 Z= 0.219 Chirality : 0.039 0.268 4354 Planarity : 0.003 0.060 4960 Dihedral : 11.637 175.602 4582 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.10 % Allowed : 12.60 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3550 helix: 2.20 (0.13), residues: 1700 sheet: 0.35 (0.25), residues: 468 loop : -1.21 (0.14), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 262 HIS 0.007 0.001 HIS A 883 PHE 0.021 0.001 PHE A 999 TYR 0.013 0.001 TYR A 356 ARG 0.003 0.000 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 299 time to evaluate : 3.235 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.8467 (m) cc_final: 0.8123 (p) REVERT: A 182 GLN cc_start: 0.7228 (pp30) cc_final: 0.6613 (mt0) REVERT: A 399 THR cc_start: 0.8879 (m) cc_final: 0.8540 (p) REVERT: A 543 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7925 (p) REVERT: A 591 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5918 (pp) REVERT: A 663 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8163 (mptt) REVERT: A 849 LEU cc_start: 0.7352 (mm) cc_final: 0.6924 (mt) REVERT: A 1029 MET cc_start: 0.5649 (tmm) cc_final: 0.5096 (ttm) REVERT: B 42 ARG cc_start: 0.6643 (mtp-110) cc_final: 0.5976 (mpt180) REVERT: B 266 GLU cc_start: 0.7318 (mp0) cc_final: 0.6908 (tt0) REVERT: B 378 ASP cc_start: 0.7151 (p0) cc_final: 0.6572 (p0) REVERT: B 629 MET cc_start: 0.6666 (mtm) cc_final: 0.6131 (mmt) REVERT: B 719 ASP cc_start: 0.7973 (t70) cc_final: 0.7577 (t0) REVERT: C 187 LYS cc_start: 0.7285 (mmtt) cc_final: 0.7082 (tptm) REVERT: C 251 ASP cc_start: 0.8300 (m-30) cc_final: 0.7943 (p0) REVERT: C 373 TYR cc_start: 0.7878 (p90) cc_final: 0.7656 (p90) REVERT: C 399 THR cc_start: 0.8718 (m) cc_final: 0.8467 (p) REVERT: C 511 LYS cc_start: 0.8339 (tttm) cc_final: 0.8064 (ttpt) REVERT: C 591 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5979 (pp) REVERT: C 663 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8247 (mptt) REVERT: C 866 GLU cc_start: 0.5834 (tt0) cc_final: 0.5107 (mp0) REVERT: D 438 PHE cc_start: 0.7640 (p90) cc_final: 0.7301 (p90) REVERT: D 543 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7636 (t) REVERT: D 719 ASP cc_start: 0.7925 (t70) cc_final: 0.7533 (t0) REVERT: D 788 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8454 (m) REVERT: D 800 VAL cc_start: 0.7730 (t) cc_final: 0.7482 (p) outliers start: 64 outliers final: 41 residues processed: 343 average time/residue: 0.4181 time to fit residues: 227.7880 Evaluate side-chains 325 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 279 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 196 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 289 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 343 optimal weight: 0.0670 chunk 214 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS B 337 GLN C 411 ASN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29582 Z= 0.128 Angle : 0.430 8.804 39846 Z= 0.223 Chirality : 0.039 0.222 4354 Planarity : 0.003 0.061 4960 Dihedral : 11.435 175.372 4582 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.20 % Allowed : 12.60 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3550 helix: 2.31 (0.13), residues: 1700 sheet: 0.31 (0.25), residues: 448 loop : -1.19 (0.14), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 323 HIS 0.005 0.001 HIS A 883 PHE 0.021 0.001 PHE A 999 TYR 0.010 0.001 TYR C 77 ARG 0.004 0.000 ARG D 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 284 time to evaluate : 3.042 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.8476 (m) cc_final: 0.8115 (p) REVERT: A 182 GLN cc_start: 0.7293 (pp30) cc_final: 0.6700 (mt0) REVERT: A 399 THR cc_start: 0.8876 (m) cc_final: 0.8540 (p) REVERT: A 577 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 591 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.5991 (pp) REVERT: A 663 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8090 (mptt) REVERT: A 849 LEU cc_start: 0.7366 (mm) cc_final: 0.6945 (mt) REVERT: A 866 GLU cc_start: 0.5672 (tt0) cc_final: 0.5041 (mp0) REVERT: A 892 LEU cc_start: 0.6831 (mm) cc_final: 0.6508 (pp) REVERT: B 42 ARG cc_start: 0.6585 (mtp-110) cc_final: 0.5940 (mpt180) REVERT: B 266 GLU cc_start: 0.7352 (mp0) cc_final: 0.6932 (tt0) REVERT: B 378 ASP cc_start: 0.7163 (p0) cc_final: 0.6567 (p0) REVERT: B 629 MET cc_start: 0.6687 (mtm) cc_final: 0.6156 (mmt) REVERT: B 719 ASP cc_start: 0.7973 (t70) cc_final: 0.7498 (t0) REVERT: C 187 LYS cc_start: 0.7385 (mmtt) cc_final: 0.7161 (tptm) REVERT: C 251 ASP cc_start: 0.8298 (m-30) cc_final: 0.7939 (p0) REVERT: C 373 TYR cc_start: 0.7865 (p90) cc_final: 0.7649 (p90) REVERT: C 399 THR cc_start: 0.8734 (m) cc_final: 0.8491 (p) REVERT: C 408 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: C 511 LYS cc_start: 0.8342 (tttm) cc_final: 0.8055 (ttpt) REVERT: C 591 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5894 (pp) REVERT: C 627 GLU cc_start: 0.7881 (tp30) cc_final: 0.7370 (tt0) REVERT: C 663 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8196 (mptt) REVERT: D 438 PHE cc_start: 0.7673 (p90) cc_final: 0.7348 (p90) REVERT: D 719 ASP cc_start: 0.7924 (t70) cc_final: 0.7537 (t0) REVERT: D 800 VAL cc_start: 0.7728 (t) cc_final: 0.7465 (p) outliers start: 67 outliers final: 47 residues processed: 329 average time/residue: 0.4143 time to fit residues: 214.6432 Evaluate side-chains 332 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 281 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 760 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 204 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 31 optimal weight: 0.0470 chunk 269 optimal weight: 10.0000 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29582 Z= 0.115 Angle : 0.423 9.437 39846 Z= 0.218 Chirality : 0.039 0.209 4354 Planarity : 0.003 0.059 4960 Dihedral : 11.175 175.008 4582 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.07 % Allowed : 12.73 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3550 helix: 2.42 (0.13), residues: 1688 sheet: 0.30 (0.25), residues: 448 loop : -1.16 (0.14), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 323 HIS 0.005 0.001 HIS A 883 PHE 0.020 0.001 PHE A 999 TYR 0.010 0.001 TYR B 77 ARG 0.004 0.000 ARG D 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 290 time to evaluate : 3.502 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.8454 (m) cc_final: 0.8112 (p) REVERT: A 182 GLN cc_start: 0.7317 (pp30) cc_final: 0.6707 (mt0) REVERT: A 399 THR cc_start: 0.8841 (m) cc_final: 0.8519 (p) REVERT: A 577 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8140 (mt) REVERT: A 591 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.5966 (pp) REVERT: A 663 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8135 (mptt) REVERT: A 849 LEU cc_start: 0.7351 (mm) cc_final: 0.6941 (mt) REVERT: A 866 GLU cc_start: 0.5706 (tt0) cc_final: 0.5108 (mp0) REVERT: A 892 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6478 (pp) REVERT: A 1029 MET cc_start: 0.5635 (tmm) cc_final: 0.5005 (ttm) REVERT: B 42 ARG cc_start: 0.6588 (mtp-110) cc_final: 0.5941 (mpt180) REVERT: B 266 GLU cc_start: 0.7361 (mp0) cc_final: 0.6943 (tt0) REVERT: B 378 ASP cc_start: 0.7160 (p0) cc_final: 0.6551 (p0) REVERT: B 629 MET cc_start: 0.6706 (mtm) cc_final: 0.6139 (mmt) REVERT: B 719 ASP cc_start: 0.7956 (t70) cc_final: 0.7498 (t0) REVERT: C 251 ASP cc_start: 0.8152 (m-30) cc_final: 0.7862 (p0) REVERT: C 318 ASN cc_start: 0.6440 (t0) cc_final: 0.6203 (t0) REVERT: C 399 THR cc_start: 0.8707 (m) cc_final: 0.8494 (p) REVERT: C 408 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7045 (mmt) REVERT: C 511 LYS cc_start: 0.8344 (tttm) cc_final: 0.8057 (ttpt) REVERT: C 627 GLU cc_start: 0.7782 (tp30) cc_final: 0.7313 (tt0) REVERT: C 663 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8195 (mptt) REVERT: C 849 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6145 (mt) REVERT: D 438 PHE cc_start: 0.7672 (p90) cc_final: 0.7348 (p90) REVERT: D 719 ASP cc_start: 0.7863 (t70) cc_final: 0.7556 (t0) REVERT: D 800 VAL cc_start: 0.7672 (t) cc_final: 0.7403 (p) outliers start: 63 outliers final: 47 residues processed: 332 average time/residue: 0.4231 time to fit residues: 221.6390 Evaluate side-chains 334 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 282 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 760 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.1980 chunk 328 optimal weight: 0.9990 chunk 299 optimal weight: 0.1980 chunk 319 optimal weight: 5.9990 chunk 192 optimal weight: 0.0020 chunk 139 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 288 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 318 optimal weight: 0.8980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29582 Z= 0.119 Angle : 0.426 9.620 39846 Z= 0.219 Chirality : 0.039 0.196 4354 Planarity : 0.003 0.059 4960 Dihedral : 10.948 173.912 4582 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.13 % Allowed : 12.80 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3550 helix: 2.47 (0.13), residues: 1688 sheet: 0.30 (0.26), residues: 448 loop : -1.15 (0.14), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 262 HIS 0.003 0.001 HIS A 883 PHE 0.019 0.001 PHE A 999 TYR 0.010 0.001 TYR B 77 ARG 0.004 0.000 ARG D 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 286 time to evaluate : 3.082 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.8453 (m) cc_final: 0.8139 (p) REVERT: A 182 GLN cc_start: 0.7308 (pp30) cc_final: 0.6708 (mt0) REVERT: A 399 THR cc_start: 0.8822 (m) cc_final: 0.8521 (p) REVERT: A 577 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 591 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6019 (pp) REVERT: A 627 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7757 (tp30) REVERT: A 663 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8148 (mptt) REVERT: A 697 LYS cc_start: 0.8338 (mttm) cc_final: 0.8135 (mttp) REVERT: A 849 LEU cc_start: 0.7176 (mm) cc_final: 0.6775 (mt) REVERT: A 866 GLU cc_start: 0.5678 (tt0) cc_final: 0.5117 (mp0) REVERT: A 892 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6476 (pp) REVERT: A 1029 MET cc_start: 0.5570 (tmm) cc_final: 0.4921 (ttm) REVERT: B 42 ARG cc_start: 0.6492 (mtp-110) cc_final: 0.5851 (mpt180) REVERT: B 266 GLU cc_start: 0.7380 (mp0) cc_final: 0.6970 (tt0) REVERT: B 378 ASP cc_start: 0.7134 (p0) cc_final: 0.6460 (p0) REVERT: B 629 MET cc_start: 0.6699 (mtm) cc_final: 0.6084 (mmt) REVERT: B 719 ASP cc_start: 0.7934 (t70) cc_final: 0.7462 (t0) REVERT: C 157 LYS cc_start: 0.8058 (mttm) cc_final: 0.7581 (mtmt) REVERT: C 318 ASN cc_start: 0.6509 (t0) cc_final: 0.6183 (t0) REVERT: C 408 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7025 (mmt) REVERT: C 627 GLU cc_start: 0.7815 (tp30) cc_final: 0.7310 (tt0) REVERT: C 663 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8227 (mptt) REVERT: C 805 LEU cc_start: 0.7793 (tp) cc_final: 0.7388 (tt) REVERT: C 849 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6160 (mt) REVERT: D 71 TYR cc_start: 0.8037 (m-80) cc_final: 0.7784 (m-80) REVERT: D 438 PHE cc_start: 0.7676 (p90) cc_final: 0.7417 (p90) REVERT: D 543 VAL cc_start: 0.7633 (t) cc_final: 0.7424 (t) REVERT: D 719 ASP cc_start: 0.7861 (t70) cc_final: 0.7553 (t0) REVERT: D 788 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8497 (m) REVERT: D 800 VAL cc_start: 0.7690 (t) cc_final: 0.7417 (p) outliers start: 65 outliers final: 49 residues processed: 330 average time/residue: 0.4168 time to fit residues: 217.2345 Evaluate side-chains 327 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 272 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 3.9990 chunk 338 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 354 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29582 Z= 0.317 Angle : 0.565 9.064 39846 Z= 0.295 Chirality : 0.044 0.267 4354 Planarity : 0.004 0.067 4960 Dihedral : 11.738 178.665 4582 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.10 % Allowed : 12.83 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3550 helix: 1.87 (0.13), residues: 1684 sheet: 0.07 (0.27), residues: 404 loop : -1.28 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 323 HIS 0.019 0.002 HIS A 883 PHE 0.019 0.002 PHE A 667 TYR 0.018 0.002 TYR A 280 ARG 0.004 0.001 ARG C 897 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 278 time to evaluate : 3.213 Fit side-chains REVERT: A 95 SER cc_start: 0.8526 (m) cc_final: 0.8236 (p) REVERT: A 399 THR cc_start: 0.8868 (m) cc_final: 0.8590 (p) REVERT: A 591 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5953 (pp) REVERT: A 663 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8437 (mptt) REVERT: A 866 GLU cc_start: 0.5730 (tt0) cc_final: 0.5147 (mp0) REVERT: A 1029 MET cc_start: 0.5503 (tmm) cc_final: 0.4785 (ttm) REVERT: B 42 ARG cc_start: 0.6379 (mtp-110) cc_final: 0.5735 (mpt180) REVERT: B 266 GLU cc_start: 0.7490 (mp0) cc_final: 0.7051 (tt0) REVERT: B 378 ASP cc_start: 0.7237 (p0) cc_final: 0.6700 (p0) REVERT: B 719 ASP cc_start: 0.8013 (t70) cc_final: 0.7572 (t0) REVERT: C 369 ARG cc_start: 0.7486 (mtp-110) cc_final: 0.7141 (mtp85) REVERT: C 408 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7236 (mmt) REVERT: C 490 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: C 591 ILE cc_start: 0.6258 (OUTLIER) cc_final: 0.5983 (pp) REVERT: C 663 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8381 (mptt) REVERT: C 805 LEU cc_start: 0.7864 (tp) cc_final: 0.7568 (tt) REVERT: C 849 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6211 (mt) REVERT: D 438 PHE cc_start: 0.7773 (p90) cc_final: 0.7564 (p90) REVERT: D 542 LEU cc_start: 0.7542 (mm) cc_final: 0.7131 (tt) REVERT: D 719 ASP cc_start: 0.8001 (t70) cc_final: 0.7571 (t0) outliers start: 64 outliers final: 53 residues processed: 324 average time/residue: 0.4268 time to fit residues: 217.5228 Evaluate side-chains 324 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 883 HIS Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 984 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 290 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109217 restraints weight = 41359.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107636 restraints weight = 42760.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108678 restraints weight = 47032.421| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29582 Z= 0.172 Angle : 0.468 9.451 39846 Z= 0.243 Chirality : 0.040 0.243 4354 Planarity : 0.003 0.059 4960 Dihedral : 11.430 179.244 4582 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 13.22 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3550 helix: 2.11 (0.13), residues: 1682 sheet: 0.13 (0.25), residues: 458 loop : -1.22 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 323 HIS 0.005 0.001 HIS B 93 PHE 0.018 0.001 PHE A 999 TYR 0.016 0.001 TYR B 373 ARG 0.005 0.000 ARG B 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5789.73 seconds wall clock time: 106 minutes 57.19 seconds (6417.19 seconds total)