Starting phenix.real_space_refine (version: dev) on Tue Dec 20 16:51:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgc_10498/12_2022/6tgc_10498.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgc_10498/12_2022/6tgc_10498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgc_10498/12_2022/6tgc_10498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgc_10498/12_2022/6tgc_10498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgc_10498/12_2022/6tgc_10498.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgc_10498/12_2022/6tgc_10498.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6546 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 8": "OD1" <-> "OD2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1002": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1137": "OD1" <-> "OD2" Residue "A TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "A ASP 1198": "OD1" <-> "OD2" Residue "A TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1303": "OE1" <-> "OE2" Residue "A TYR 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "A PHE 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1396": "OD1" <-> "OD2" Residue "A GLU 1507": "OE1" <-> "OE2" Residue "A TYR 1516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1564": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": not complete - not flipped Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": not complete - not flipped Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 206": not complete - not flipped Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": not complete - not flipped Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 355": not complete - not flipped Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 419": not complete - not flipped Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B ASP 602": "OD1" <-> "OD2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B ASP 612": "OD1" <-> "OD2" Residue "B ASP 621": "OD1" <-> "OD2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 658": "OD1" <-> "OD2" Residue "B ASP 667": "OD1" <-> "OD2" Residue "B ASP 680": "OD1" <-> "OD2" Residue "B ASP 685": "OD1" <-> "OD2" Residue "B ASP 687": "OD1" <-> "OD2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "B ASP 725": "OD1" <-> "OD2" Residue "D ASP 8": "OD1" <-> "OD2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 123": "OD1" <-> "OD2" Residue "D PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 421": "OD1" <-> "OD2" Residue "D ASP 434": "OD1" <-> "OD2" Residue "D GLU 447": "OE1" <-> "OE2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 538": "OD1" <-> "OD2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1002": "NH1" <-> "NH2" Residue "D PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1137": "OD1" <-> "OD2" Residue "D TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1183": "OE1" <-> "OE2" Residue "D ASP 1198": "OD1" <-> "OD2" Residue "D TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1303": "OE1" <-> "OE2" Residue "D TYR 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1311": "OE1" <-> "OE2" Residue "D PHE 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1396": "OD1" <-> "OD2" Residue "D GLU 1507": "OE1" <-> "OE2" Residue "D TYR 1516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1564": "OD1" <-> "OD2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 90": not complete - not flipped Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": not complete - not flipped Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 206": not complete - not flipped Residue "E GLU 289": not complete - not flipped Residue "E ASP 355": not complete - not flipped Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 419": not complete - not flipped Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 538": "OE1" <-> "OE2" Residue "E GLU 543": "OE1" <-> "OE2" Residue "E GLU 639": "OE1" <-> "OE2" Residue "E ASP 721": "OD1" <-> "OD2" Residue "E TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33282 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1450, 10203 Classifications: {'peptide': 1450} Incomplete info: {'truncation_to_alanine': 522} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1408} Chain breaks: 15 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1245 Unresolved non-hydrogen angles: 1750 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'UNK:plan-1': 404, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 23, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 664 Chain: "B" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5054 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 650} Chain breaks: 3 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 614 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 35, 'ASP:plan': 30} Unresolved non-hydrogen planarities: 295 Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "D" Number of atoms: 10203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1450, 10203 Classifications: {'peptide': 1450} Incomplete info: {'truncation_to_alanine': 522} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1408} Chain breaks: 15 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1245 Unresolved non-hydrogen angles: 1750 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'UNK:plan-1': 404, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 23, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 664 Chain: "E" Number of atoms: 5056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5056 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 651} Chain breaks: 3 Unresolved non-hydrogen bonds: 459 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 35, 'ASP:plan': 30} Unresolved non-hydrogen planarities: 295 Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 11, 'TRANS': 165} Time building chain proxies: 17.88, per 1000 atoms: 0.54 Number of scatterers: 33282 At special positions: 0 Unit cell: (298.87, 261.69, 141.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6138 8.00 N 5721 7.00 C 21243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.10 Conformation dependent library (CDL) restraints added in 4.5 seconds 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8908 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 21 sheets defined 68.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 83 through 108 Processing helix chain 'A' and resid 110 through 132 removed outlier: 3.900A pdb=" N PHE A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 removed outlier: 3.567A pdb=" N THR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 572 through 576 removed outlier: 3.501A pdb=" N GLU A 576 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.755A pdb=" N UNK A 634 " --> pdb=" O UNK A 630 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK A 635 " --> pdb=" O UNK A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 removed outlier: 4.222A pdb=" N HIS A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 690 through 701 removed outlier: 4.596A pdb=" N UNK A 697 " --> pdb=" O UNK A 693 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N UNK A 698 " --> pdb=" O UNK A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 708 through 719 removed outlier: 3.826A pdb=" N UNK A 712 " --> pdb=" O UNK A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 736 removed outlier: 3.975A pdb=" N UNK A 733 " --> pdb=" O UNK A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 761 Processing helix chain 'A' and resid 765 through 783 removed outlier: 4.100A pdb=" N UNK A 769 " --> pdb=" O UNK A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 5.438A pdb=" N UNK A 795 " --> pdb=" O UNK A 791 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK A 796 " --> pdb=" O UNK A 792 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK A 797 " --> pdb=" O UNK A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.868A pdb=" N UNK A 807 " --> pdb=" O UNK A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 824 Processing helix chain 'A' and resid 830 through 846 removed outlier: 3.868A pdb=" N UNK A 834 " --> pdb=" O UNK A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 870 Processing helix chain 'A' and resid 873 through 891 removed outlier: 4.767A pdb=" N UNK A 877 " --> pdb=" O UNK A 873 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK A 884 " --> pdb=" O UNK A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 911 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 935 through 949 Processing helix chain 'A' and resid 950 through 959 Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.522A pdb=" N LEU A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1014 Processing helix chain 'A' and resid 1023 through 1039 removed outlier: 3.800A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1059 Processing helix chain 'A' and resid 1061 through 1076 removed outlier: 3.795A pdb=" N LEU A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 4.074A pdb=" N VAL A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A1090 " --> pdb=" O PRO A1086 " (cutoff:3.500A) Proline residue: A1091 - end of helix Processing helix chain 'A' and resid 1098 through 1104 removed outlier: 3.592A pdb=" N GLU A1102 " --> pdb=" O ILE A1098 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1104 " --> pdb=" O GLU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1117 removed outlier: 3.961A pdb=" N ILE A1110 " --> pdb=" O ALA A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1140 removed outlier: 4.095A pdb=" N LEU A1134 " --> pdb=" O ASN A1130 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A1135 " --> pdb=" O GLU A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1162 removed outlier: 4.529A pdb=" N GLN A1151 " --> pdb=" O GLU A1147 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A1155 " --> pdb=" O GLN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1192 removed outlier: 3.825A pdb=" N ASP A1187 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1214 Processing helix chain 'A' and resid 1216 through 1235 removed outlier: 3.951A pdb=" N TYR A1220 " --> pdb=" O ARG A1216 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG A1222 " --> pdb=" O GLU A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1250 removed outlier: 3.599A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1291 Processing helix chain 'A' and resid 1293 through 1311 removed outlier: 4.207A pdb=" N ALA A1297 " --> pdb=" O MET A1293 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A1298 " --> pdb=" O TRP A1294 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1330 removed outlier: 3.719A pdb=" N GLN A1320 " --> pdb=" O GLU A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1382 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1418 through 1423 Processing helix chain 'A' and resid 1430 through 1434 Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1493 through 1519 Processing helix chain 'A' and resid 1524 through 1536 removed outlier: 3.739A pdb=" N SER A1528 " --> pdb=" O ILE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1550 Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 4.129A pdb=" N VAL A1556 " --> pdb=" O THR A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1589 Proline residue: A1578 - end of helix removed outlier: 3.747A pdb=" N LYS A1589 " --> pdb=" O LYS A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1618 removed outlier: 4.190A pdb=" N PHE A1598 " --> pdb=" O ASN A1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.514A pdb=" N ILE B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.829A pdb=" N GLU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.677A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.535A pdb=" N GLY B 234 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 253 removed outlier: 3.517A pdb=" N GLN B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 4.157A pdb=" N GLN B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 287 through 304 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 317 through 333 removed outlier: 3.844A pdb=" N ALA B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.748A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.836A pdb=" N HIS B 448 " --> pdb=" O PHE B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 471 Processing helix chain 'B' and resid 476 through 489 Processing helix chain 'B' and resid 490 through 495 removed outlier: 4.581A pdb=" N THR B 493 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 509 Processing helix chain 'B' and resid 512 through 529 removed outlier: 3.705A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 Processing helix chain 'B' and resid 535 through 540 removed outlier: 3.829A pdb=" N LYS B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 535 through 540' Processing helix chain 'B' and resid 540 through 559 removed outlier: 3.760A pdb=" N GLN B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.576A pdb=" N GLU B 639 " --> pdb=" O LYS B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.597A pdb=" N THR B 666 " --> pdb=" O TYR B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.702A pdb=" N MET B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.653A pdb=" N LEU C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.899A pdb=" N TYR C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 65' Processing helix chain 'C' and resid 87 through 96 removed outlier: 5.356A pdb=" N ARG C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.350A pdb=" N GLU C 171 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 108 Processing helix chain 'D' and resid 110 through 132 removed outlier: 3.899A pdb=" N PHE D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 159 removed outlier: 3.567A pdb=" N THR D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 498 through 504 Processing helix chain 'D' and resid 572 through 576 removed outlier: 3.501A pdb=" N GLU D 576 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.755A pdb=" N UNK D 634 " --> pdb=" O UNK D 630 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNK D 635 " --> pdb=" O UNK D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 661 removed outlier: 4.222A pdb=" N HIS D 652 " --> pdb=" O ILE D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 690 through 701 removed outlier: 4.596A pdb=" N UNK D 697 " --> pdb=" O UNK D 693 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK D 698 " --> pdb=" O UNK D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 708 through 719 removed outlier: 3.826A pdb=" N UNK D 712 " --> pdb=" O UNK D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 736 removed outlier: 3.975A pdb=" N UNK D 733 " --> pdb=" O UNK D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 761 Processing helix chain 'D' and resid 765 through 783 removed outlier: 4.099A pdb=" N UNK D 769 " --> pdb=" O UNK D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 797 removed outlier: 5.436A pdb=" N UNK D 795 " --> pdb=" O UNK D 791 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK D 796 " --> pdb=" O UNK D 792 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK D 797 " --> pdb=" O UNK D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 807 removed outlier: 3.868A pdb=" N UNK D 807 " --> pdb=" O UNK D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 824 Processing helix chain 'D' and resid 830 through 846 removed outlier: 3.868A pdb=" N UNK D 834 " --> pdb=" O UNK D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 870 Processing helix chain 'D' and resid 873 through 891 removed outlier: 4.767A pdb=" N UNK D 877 " --> pdb=" O UNK D 873 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK D 884 " --> pdb=" O UNK D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 911 Processing helix chain 'D' and resid 912 through 921 Processing helix chain 'D' and resid 935 through 949 Processing helix chain 'D' and resid 950 through 959 Processing helix chain 'D' and resid 965 through 982 removed outlier: 3.522A pdb=" N LEU D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1014 Processing helix chain 'D' and resid 1023 through 1039 removed outlier: 3.800A pdb=" N GLN D1039 " --> pdb=" O ALA D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1059 Processing helix chain 'D' and resid 1061 through 1076 removed outlier: 3.796A pdb=" N LEU D1065 " --> pdb=" O ASP D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 4.074A pdb=" N VAL D1089 " --> pdb=" O ILE D1085 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY D1090 " --> pdb=" O PRO D1086 " (cutoff:3.500A) Proline residue: D1091 - end of helix Processing helix chain 'D' and resid 1098 through 1104 removed outlier: 3.592A pdb=" N GLU D1102 " --> pdb=" O ILE D1098 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D1104 " --> pdb=" O GLU D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1117 removed outlier: 3.961A pdb=" N ILE D1110 " --> pdb=" O ALA D1106 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1140 removed outlier: 4.095A pdb=" N LEU D1134 " --> pdb=" O ASN D1130 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS D1135 " --> pdb=" O GLU D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1162 removed outlier: 4.528A pdb=" N GLN D1151 " --> pdb=" O GLU D1147 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D1155 " --> pdb=" O GLN D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1192 removed outlier: 3.825A pdb=" N ASP D1187 " --> pdb=" O GLU D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1196 through 1214 Processing helix chain 'D' and resid 1216 through 1235 removed outlier: 3.951A pdb=" N TYR D1220 " --> pdb=" O ARG D1216 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG D1222 " --> pdb=" O GLU D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1250 removed outlier: 3.598A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1272 through 1291 Processing helix chain 'D' and resid 1293 through 1311 removed outlier: 4.207A pdb=" N ALA D1297 " --> pdb=" O MET D1293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D1298 " --> pdb=" O TRP D1294 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS D1301 " --> pdb=" O ALA D1297 " (cutoff:3.500A) Processing helix chain 'D' and resid 1316 through 1330 removed outlier: 3.719A pdb=" N GLN D1320 " --> pdb=" O GLU D1316 " (cutoff:3.500A) Processing helix chain 'D' and resid 1371 through 1382 Processing helix chain 'D' and resid 1395 through 1401 Processing helix chain 'D' and resid 1418 through 1423 Processing helix chain 'D' and resid 1430 through 1434 Processing helix chain 'D' and resid 1457 through 1462 Processing helix chain 'D' and resid 1493 through 1519 Processing helix chain 'D' and resid 1524 through 1536 removed outlier: 3.738A pdb=" N SER D1528 " --> pdb=" O ILE D1524 " (cutoff:3.500A) Processing helix chain 'D' and resid 1542 through 1550 Processing helix chain 'D' and resid 1552 through 1559 removed outlier: 4.129A pdb=" N VAL D1556 " --> pdb=" O THR D1552 " (cutoff:3.500A) Processing helix chain 'D' and resid 1562 through 1589 Proline residue: D1578 - end of helix removed outlier: 3.746A pdb=" N LYS D1589 " --> pdb=" O LYS D1585 " (cutoff:3.500A) Processing helix chain 'D' and resid 1594 through 1618 removed outlier: 4.190A pdb=" N PHE D1598 " --> pdb=" O ASN D1594 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 41 removed outlier: 3.502A pdb=" N ILE E 33 " --> pdb=" O PRO E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 80 through 92 Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.631A pdb=" N GLU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 136 Processing helix chain 'E' and resid 154 through 167 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 194 through 212 Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.651A pdb=" N GLN E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 230 through 234 removed outlier: 3.534A pdb=" N GLY E 234 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 254 Processing helix chain 'E' and resid 255 through 269 removed outlier: 4.028A pdb=" N GLN E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 279 Processing helix chain 'E' and resid 287 through 304 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 317 through 333 removed outlier: 3.664A pdb=" N ILE E 324 " --> pdb=" O GLN E 320 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.634A pdb=" N LEU E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 404 removed outlier: 3.540A pdb=" N ASN E 402 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 442 through 447 Processing helix chain 'E' and resid 450 through 471 Processing helix chain 'E' and resid 476 through 492 removed outlier: 4.003A pdb=" N ARG E 490 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 495 No H-bonds generated for 'chain 'E' and resid 493 through 495' Processing helix chain 'E' and resid 498 through 508 Processing helix chain 'E' and resid 513 through 522 removed outlier: 5.008A pdb=" N GLN E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER E 520 " --> pdb=" O LYS E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 529 removed outlier: 4.147A pdb=" N PHE E 528 " --> pdb=" O ASN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 540 removed outlier: 3.566A pdb=" N ILE E 540 " --> pdb=" O LEU E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 559 removed outlier: 3.841A pdb=" N GLY E 559 " --> pdb=" O ARG E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 658 through 672 Processing helix chain 'E' and resid 680 through 701 removed outlier: 4.120A pdb=" N MET E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 699 " --> pdb=" O LYS E 695 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP E 700 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 701 " --> pdb=" O ARG E 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.653A pdb=" N LEU F 19 " --> pdb=" O GLY F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.899A pdb=" N TYR F 64 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 65 " --> pdb=" O GLU F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 65' Processing helix chain 'F' and resid 87 through 96 removed outlier: 5.357A pdb=" N ARG F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 122 through 131 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.349A pdb=" N GLU F 171 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 172 " --> pdb=" O VAL F 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.016A pdb=" N TYR A 48 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 37 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 12 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 67 " --> pdb=" O HIS A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 460 removed outlier: 3.622A pdb=" N VAL A 452 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1361 through 1363 Processing sheet with id=AA5, first strand: chain 'A' and resid 1386 through 1387 removed outlier: 4.772A pdb=" N GLU A1386 " --> pdb=" O ILE A1406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1412 through 1414 removed outlier: 4.560A pdb=" N ARG A1441 " --> pdb=" O VAL A1414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1447 through 1448 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 25 removed outlier: 10.395A pdb=" N THR B 73 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LYS B 9 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 75 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA B 11 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 77 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU B 13 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N THR B 79 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 589 through 590 removed outlier: 4.343A pdb=" N HIS B 601 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 615 through 618 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.567A pdb=" N VAL C 46 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL C 77 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 7 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE C 82 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 56 through 57 removed outlier: 6.017A pdb=" N TYR D 48 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 37 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS D 12 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D 67 " --> pdb=" O HIS D 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 427 through 430 Processing sheet with id=AB5, first strand: chain 'D' and resid 458 through 460 removed outlier: 3.623A pdb=" N VAL D 452 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1361 through 1363 Processing sheet with id=AB7, first strand: chain 'D' and resid 1386 through 1387 removed outlier: 4.772A pdb=" N GLU D1386 " --> pdb=" O ILE D1406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 1412 through 1414 removed outlier: 4.560A pdb=" N ARG D1441 " --> pdb=" O VAL D1414 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1447 through 1448 Processing sheet with id=AC1, first strand: chain 'E' and resid 20 through 25 removed outlier: 10.361A pdb=" N THR E 73 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS E 9 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU E 75 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA E 11 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU E 77 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU E 13 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR E 79 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU E 51 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 615 through 618 Processing sheet with id=AC3, first strand: chain 'F' and resid 41 through 46 removed outlier: 3.566A pdb=" N VAL F 46 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL F 77 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 7 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL F 113 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 80 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE F 82 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5268 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: 14.77 Time building geometry restraints manager: 17.09 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: 6766 1.32 - 1.45: 8946 1.45 - 1.58: 17843 1.58 - 1.71: 17 1.71 - 1.84: 304 Bond restraints: 33876 Sorted by residual: bond pdb=" N LEU E 608 " pdb=" CA LEU E 608 " ideal model delta sigma weight residual 1.457 1.328 0.129 1.41e-02 5.03e+03 8.35e+01 bond pdb=" C LYS D1474 " pdb=" N LEU D1475 " ideal model delta sigma weight residual 1.331 1.256 0.075 9.80e-03 1.04e+04 5.79e+01 bond pdb=" C LYS A1474 " pdb=" N LEU A1475 " ideal model delta sigma weight residual 1.331 1.256 0.074 9.80e-03 1.04e+04 5.75e+01 bond pdb=" CB TRP A1294 " pdb=" CG TRP A1294 " ideal model delta sigma weight residual 1.498 1.314 0.184 3.10e-02 1.04e+03 3.53e+01 bond pdb=" N LYS A1327 " pdb=" CA LYS A1327 " ideal model delta sigma weight residual 1.458 1.391 0.066 1.12e-02 7.97e+03 3.51e+01 ... (remaining 33871 not shown) Histogram of bond angle deviations from ideal: 78.78 - 93.52: 8 93.52 - 108.27: 2869 108.27 - 123.02: 40522 123.02 - 137.76: 2611 137.76 - 152.51: 4 Bond angle restraints: 46014 Sorted by residual: angle pdb=" C THR D1521 " pdb=" N LEU D1522 " pdb=" CA LEU D1522 " ideal model delta sigma weight residual 121.83 152.51 -30.68 1.56e+00 4.11e-01 3.87e+02 angle pdb=" C THR A1521 " pdb=" N LEU A1522 " pdb=" CA LEU A1522 " ideal model delta sigma weight residual 121.83 152.49 -30.66 1.56e+00 4.11e-01 3.86e+02 angle pdb=" CA LEU A1300 " pdb=" CB LEU A1300 " pdb=" CG LEU A1300 " ideal model delta sigma weight residual 116.30 78.78 37.52 3.50e+00 8.16e-02 1.15e+02 angle pdb=" CA LEU D1300 " pdb=" CB LEU D1300 " pdb=" CG LEU D1300 " ideal model delta sigma weight residual 116.30 78.78 37.52 3.50e+00 8.16e-02 1.15e+02 angle pdb=" C ARG E 578 " pdb=" N LEU E 579 " pdb=" CA LEU E 579 " ideal model delta sigma weight residual 122.21 106.08 16.13 1.62e+00 3.81e-01 9.91e+01 ... (remaining 46009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 19458 35.88 - 71.76: 976 71.76 - 107.65: 32 107.65 - 143.53: 2 143.53 - 179.41: 8 Dihedral angle restraints: 20476 sinusoidal: 6856 harmonic: 13620 Sorted by residual: dihedral pdb=" CA GLU A1195 " pdb=" C GLU A1195 " pdb=" N SER A1196 " pdb=" CA SER A1196 " ideal model delta harmonic sigma weight residual 180.00 126.48 53.52 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA GLU D1195 " pdb=" C GLU D1195 " pdb=" N SER D1196 " pdb=" CA SER D1196 " ideal model delta harmonic sigma weight residual 180.00 126.53 53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASN D 445 " pdb=" C ASN D 445 " pdb=" N VAL D 446 " pdb=" CA VAL D 446 " ideal model delta harmonic sigma weight residual -180.00 -126.91 -53.09 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4694 0.105 - 0.210: 607 0.210 - 0.315: 92 0.315 - 0.419: 12 0.419 - 0.524: 7 Chirality restraints: 5412 Sorted by residual: chirality pdb=" CB ILE E 548 " pdb=" CA ILE E 548 " pdb=" CG1 ILE E 548 " pdb=" CG2 ILE E 548 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CG LEU D1300 " pdb=" CB LEU D1300 " pdb=" CD1 LEU D1300 " pdb=" CD2 LEU D1300 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CG LEU A1300 " pdb=" CB LEU A1300 " pdb=" CD1 LEU A1300 " pdb=" CD2 LEU A1300 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 5409 not shown) Planarity restraints: 5928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A1587 " 0.027 2.00e-02 2.50e+03 5.61e-02 3.14e+01 pdb=" C HIS A1587 " -0.097 2.00e-02 2.50e+03 pdb=" O HIS A1587 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1588 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D1587 " -0.027 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" C HIS D1587 " 0.097 2.00e-02 2.50e+03 pdb=" O HIS D1587 " -0.037 2.00e-02 2.50e+03 pdb=" N GLU D1588 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D1607 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C LYS D1607 " 0.079 2.00e-02 2.50e+03 pdb=" O LYS D1607 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN D1608 " -0.027 2.00e-02 2.50e+03 ... (remaining 5925 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 758 2.45 - 3.06: 31889 3.06 - 3.67: 61931 3.67 - 4.29: 89315 4.29 - 4.90: 124749 Nonbonded interactions: 308642 Sorted by model distance: nonbonded pdb=" OG SER A 109 " pdb=" NZ LYS A 110 " model vdw 1.835 2.520 nonbonded pdb=" OG SER D 109 " pdb=" NZ LYS D 110 " model vdw 1.835 2.520 nonbonded pdb=" O LEU A1152 " pdb=" OG SER A1155 " model vdw 1.881 2.440 nonbonded pdb=" O LEU D1152 " pdb=" OG SER D1155 " model vdw 1.881 2.440 nonbonded pdb=" O ILE E 548 " pdb=" NH1 ARG E 552 " model vdw 1.924 2.520 ... (remaining 308637 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 'D' } ncs_group { reference = (chain 'B' and (resid 5 through 583 or (resid 584 and (name N or name CA or name \ C or name O or name CB )) or resid 585 through 726)) selection = (chain 'E' and (resid 5 through 676 or (resid 677 through 678 and (name N or nam \ e CA or name C or name O or name CB )) or resid 679 through 726)) } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 21243 2.51 5 N 5721 2.21 5 O 6138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.040 Extract box with map and model: 7.830 Check model and map are aligned: 0.500 Convert atoms to be neutral: 0.310 Process input model: 89.520 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 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 : 0.016 0.184 33876 Z= 0.996 Angle : 1.861 37.523 46014 Z= 0.999 Chirality : 0.076 0.524 5412 Planarity : 0.011 0.096 5928 Dihedral : 20.202 179.409 11568 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 102.01 Ramachandran Plot: Outliers : 1.92 % Allowed : 22.03 % Favored : 76.05 % Rotamer Outliers : 15.44 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 2.53 % Twisted General : 1.91 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.63 (0.11), residues: 3750 helix: -3.53 (0.08), residues: 1780 sheet: -4.46 (0.23), residues: 268 loop : -3.79 (0.13), residues: 1702 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 457 poor density : 363 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 457 outliers final: 188 residues processed: 759 average time/residue: 0.4932 time to fit residues: 584.9287 Evaluate side-chains 474 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 286 time to evaluate : 3.550 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 188 outliers final: 5 residues processed: 188 average time/residue: 0.3892 time to fit residues: 127.1149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 68 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 chunk 51 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 146 GLN A 156 ASN A 424 ASN A 577 ASN A1173 ASN ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1418 HIS ** A1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 366 ASN B 383 ASN B 442 HIS B 448 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 ASN B 660 HIS C 92 ASN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 118 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 ASN D1005 ASN D1012 ASN ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1173 ASN D1206 ASN ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1412 GLN D1418 HIS ** D1599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN E 211 ASN ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN E 248 ASN ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 GLN E 439 ASN E 487 GLN ** E 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 GLN E 660 HIS ** E 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 103 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.128 33876 Z= 0.430 Angle : 1.146 26.464 46014 Z= 0.573 Chirality : 0.053 0.370 5412 Planarity : 0.008 0.130 5928 Dihedral : 8.659 56.784 4826 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 45.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.68 % Favored : 85.87 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.90 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.12), residues: 3750 helix: -2.30 (0.10), residues: 1916 sheet: -3.91 (0.23), residues: 340 loop : -2.87 (0.15), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 347 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 19 residues processed: 389 average time/residue: 0.4929 time to fit residues: 309.4527 Evaluate side-chains 293 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 274 time to evaluate : 3.662 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.3159 time to fit residues: 16.1471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 50.0000 chunk 154 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 124 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 HIS ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1489 GLN A1514 ASN ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 ASN B 211 ASN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 601 HIS ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 HIS D 573 HIS ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1275 GLN ** D1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS E 293 GLN ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.126 33876 Z= 0.581 Angle : 1.200 18.888 46014 Z= 0.610 Chirality : 0.056 0.361 5412 Planarity : 0.009 0.183 5928 Dihedral : 8.422 52.818 4826 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 57.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 15.23 % Favored : 84.29 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.90 % Twisted General : 0.80 % 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: -3.54 (0.13), residues: 3750 helix: -1.74 (0.11), residues: 1958 sheet: -3.82 (0.23), residues: 348 loop : -2.64 (0.16), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 327 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 365 average time/residue: 0.4783 time to fit residues: 281.9759 Evaluate side-chains 296 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 270 time to evaluate : 3.774 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 5 residues processed: 26 average time/residue: 0.3207 time to fit residues: 20.6168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 8.9990 chunk 116 optimal weight: 50.0000 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 50.0000 chunk 155 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 GLN ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1231 HIS ** D1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1608 ASN E 122 ASN ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN E 554 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 33876 Z= 0.365 Angle : 0.953 12.192 46014 Z= 0.484 Chirality : 0.048 0.260 5412 Planarity : 0.007 0.114 5928 Dihedral : 7.610 53.322 4826 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 37.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.97 % Favored : 87.76 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.90 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3750 helix: -1.23 (0.11), residues: 1976 sheet: -3.77 (0.23), residues: 350 loop : -2.38 (0.17), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 333 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 344 average time/residue: 0.4851 time to fit residues: 267.2151 Evaluate side-chains 287 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 277 time to evaluate : 3.469 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 10 average time/residue: 0.3355 time to fit residues: 10.5291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 50.0000 chunk 122 optimal weight: 50.0000 chunk 67 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 113 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 83 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1307 GLN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1486 HIS ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1209 ASN ** D1321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.132 33876 Z= 0.678 Angle : 1.277 24.823 46014 Z= 0.648 Chirality : 0.059 0.431 5412 Planarity : 0.009 0.236 5928 Dihedral : 8.265 56.438 4826 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 60.56 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.55 % Favored : 83.92 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.90 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.13), residues: 3750 helix: -1.27 (0.11), residues: 1963 sheet: -3.75 (0.26), residues: 291 loop : -2.74 (0.16), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 304 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 330 average time/residue: 0.4682 time to fit residues: 249.8551 Evaluate side-chains 272 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 6 residues processed: 16 average time/residue: 0.3209 time to fit residues: 14.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 20.0000 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 50.0000 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 50.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1563 GLN ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 146 GLN ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1049 HIS D1381 GLN ** D1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 33876 Z= 0.258 Angle : 0.891 11.972 46014 Z= 0.447 Chirality : 0.047 0.282 5412 Planarity : 0.006 0.104 5928 Dihedral : 7.238 53.880 4826 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 31.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.05 % Favored : 89.71 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.13), residues: 3750 helix: -0.72 (0.11), residues: 1994 sheet: -3.88 (0.25), residues: 314 loop : -2.34 (0.16), residues: 1442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 334 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 344 average time/residue: 0.4858 time to fit residues: 269.3605 Evaluate side-chains 273 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 266 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 7 average time/residue: 0.3125 time to fit residues: 9.2566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 50.0000 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 163 optimal weight: 0.0030 chunk 102 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.7608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 33876 Z= 0.334 Angle : 0.902 13.940 46014 Z= 0.456 Chirality : 0.046 0.230 5412 Planarity : 0.007 0.150 5928 Dihedral : 7.009 51.679 4826 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 34.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.60 % Favored : 88.16 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.14), residues: 3750 helix: -0.52 (0.11), residues: 1990 sheet: -3.63 (0.28), residues: 244 loop : -2.36 (0.16), residues: 1516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 318 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 325 average time/residue: 0.4702 time to fit residues: 248.3230 Evaluate side-chains 264 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 6 average time/residue: 0.3111 time to fit residues: 8.4212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 50.0000 chunk 49 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN D 20 GLN ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1525 ASN ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.8104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.108 33876 Z= 0.427 Angle : 0.986 16.004 46014 Z= 0.500 Chirality : 0.049 0.273 5412 Planarity : 0.007 0.182 5928 Dihedral : 7.114 52.677 4826 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.03 % Favored : 87.71 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.14), residues: 3750 helix: -0.49 (0.12), residues: 1962 sheet: -3.69 (0.27), residues: 258 loop : -2.25 (0.16), residues: 1530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 312 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 318 average time/residue: 0.4769 time to fit residues: 246.9281 Evaluate side-chains 261 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 255 time to evaluate : 3.820 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 6 average time/residue: 0.3122 time to fit residues: 8.8014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1489 GLN ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 33876 Z= 0.243 Angle : 0.839 14.293 46014 Z= 0.423 Chirality : 0.045 0.223 5412 Planarity : 0.006 0.097 5928 Dihedral : 6.578 51.004 4826 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.28 % Favored : 90.48 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.30 % 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: -1.77 (0.14), residues: 3750 helix: -0.12 (0.12), residues: 1982 sheet: -3.67 (0.25), residues: 295 loop : -2.03 (0.17), residues: 1473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 330 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 336 average time/residue: 0.4742 time to fit residues: 260.0801 Evaluate side-chains 274 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 268 time to evaluate : 3.671 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 6 average time/residue: 0.3158 time to fit residues: 8.6181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 169 optimal weight: 0.0020 chunk 155 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 104 optimal weight: 50.0000 chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 overall best weight: 3.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS B 448 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 HIS ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.8803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 33876 Z= 0.334 Angle : 0.891 13.417 46014 Z= 0.451 Chirality : 0.046 0.245 5412 Planarity : 0.007 0.156 5928 Dihedral : 6.615 50.365 4826 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 33.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.59 % Favored : 89.17 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.39 % 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: -1.76 (0.14), residues: 3750 helix: -0.12 (0.12), residues: 1970 sheet: -3.47 (0.27), residues: 294 loop : -2.04 (0.17), residues: 1486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 318 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 324 average time/residue: 0.4781 time to fit residues: 252.7618 Evaluate side-chains 282 residues out of total 3442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 276 time to evaluate : 3.332 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 6 average time/residue: 0.2894 time to fit residues: 7.9249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 0.0040 chunk 17 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 7 optimal weight: 50.0000 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS B 448 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1209 ASN D1215 ASN ** D1375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.162050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.125191 restraints weight = 120826.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.119981 restraints weight = 134058.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.119706 restraints weight = 126526.293| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.9239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 33876 Z= 0.344 Angle : 0.891 13.643 46014 Z= 0.452 Chirality : 0.046 0.281 5412 Planarity : 0.007 0.114 5928 Dihedral : 6.620 51.050 4826 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 33.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.75 % Favored : 89.01 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3750 helix: -0.12 (0.12), residues: 1973 sheet: -3.41 (0.27), residues: 293 loop : -2.09 (0.17), residues: 1484 =============================================================================== Job complete usr+sys time: 6785.50 seconds wall clock time: 124 minutes 2.49 seconds (7442.49 seconds total)