Starting phenix.real_space_refine on Sat Dec 16 10:16:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/12_2023/7dk4_30702.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/12_2023/7dk4_30702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/12_2023/7dk4_30702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/12_2023/7dk4_30702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/12_2023/7dk4_30702.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/12_2023/7dk4_30702.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 159 5.16 5 C 22017 2.51 5 N 5805 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34707 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Chain: "A" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "B" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "c" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "d" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Chain: "e" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "f" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Time building chain proxies: 17.86, per 1000 atoms: 0.51 Number of scatterers: 34707 At special positions: 0 Unit cell: (148.92, 161.16, 234.6, 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 159 16.00 O 6726 8.00 N 5805 7.00 C 22017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 95 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 95 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 199 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS d 138 " - pdb=" SG CYS d 198 " distance=2.03 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 95 " distance=2.03 Simple disulfide: pdb=" SG CYS e 144 " - pdb=" SG CYS e 199 " distance=2.03 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 92 " distance=2.03 Simple disulfide: pdb=" SG CYS f 138 " - pdb=" SG CYS f 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 6.7 seconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 77 sheets defined 17.9% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'a' and resid 86 through 90 removed outlier: 3.685A pdb=" N THR a 90 " --> pdb=" O THR a 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 131 Processing helix chain 'b' and resid 187 through 191 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.506A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.628A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.104A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.570A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.560A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.055A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.675A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.607A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.801A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.648A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.745A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.550A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.677A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.503A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.598A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 782 removed outlier: 4.122A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.746A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.341A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.521A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.567A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.697A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.600A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.539A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.696A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.543A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.530A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.723A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.861A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 192 No H-bonds generated for 'chain 'c' and resid 190 through 192' Processing helix chain 'd' and resid 125 through 132 Processing helix chain 'd' and resid 187 through 191 Processing helix chain 'e' and resid 86 through 90 Processing helix chain 'f' and resid 125 through 132 Processing helix chain 'f' and resid 187 through 191 Processing sheet with id=AA1, first strand: chain 'a' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'a' and resid 57 through 59 removed outlier: 3.621A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE a 106 " --> pdb=" O LYS a 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 57 through 59 removed outlier: 3.621A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 125 through 128 removed outlier: 6.087A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 125 through 128 removed outlier: 6.087A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU a 178 " --> pdb=" O GLN a 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 155 through 158 removed outlier: 4.730A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.680A pdb=" N ILE b 79 " --> pdb=" O ALA b 19 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE b 21 " --> pdb=" O LEU b 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.456A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA b 88 " --> pdb=" O LEU b 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 49 through 52 removed outlier: 6.106A pdb=" N LEU b 50 " --> pdb=" O GLN b 41 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN b 41 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE b 52 " --> pdb=" O TRP b 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 121 through 122 removed outlier: 3.553A pdb=" N LEU b 140 " --> pdb=" O MET b 179 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER b 178 " --> pdb=" O THR b 168 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 182 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.774A pdb=" N TRP b 152 " --> pdb=" O ARG b 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.531A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.029A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 537 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.518A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.793A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.981A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.381A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.926A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.663A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.067A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.156A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.156A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.554A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AD1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.921A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.269A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AD4, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.693A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.644A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.812A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.712A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.422A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.255A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.466A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.136A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.242A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.005A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.725A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.210A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 153 through 157 removed outlier: 6.370A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR C 259 " --> pdb=" O HIS C 245 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.670A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.831A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.991A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.534A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.622A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'c' and resid 6 through 7 removed outlier: 5.946A pdb=" N GLN c 16 " --> pdb=" O SER c 84 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 57 through 58 removed outlier: 6.784A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL c 50 " --> pdb=" O VAL c 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL c 34 " --> pdb=" O VAL c 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL c 37 " --> pdb=" O TYR c 94 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS c 95 " --> pdb=" O TRP c 107 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP c 107 " --> pdb=" O CYS c 95 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS c 97 " --> pdb=" O ASP c 105 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 57 through 58 removed outlier: 6.784A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL c 50 " --> pdb=" O VAL c 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL c 34 " --> pdb=" O VAL c 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL c 37 " --> pdb=" O TYR c 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.707A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS c 144 " --> pdb=" O SER c 183 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER c 183 " --> pdb=" O CYS c 144 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER c 184 " --> pdb=" O HIS c 168 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.707A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR c 179 " --> pdb=" O GLY c 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU c 178 " --> pdb=" O GLN c 175 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c' and resid 155 through 158 Processing sheet with id=AH1, first strand: chain 'd' and resid 6 through 7 Processing sheet with id=AH2, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.373A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS d 38 " --> pdb=" O GLN d 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE d 52 " --> pdb=" O TRP d 39 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN d 41 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU d 50 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS d 43 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN d 57 " --> pdb=" O TYR d 53 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 120 through 122 removed outlier: 4.384A pdb=" N SER d 120 " --> pdb=" O PHE d 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL d 136 " --> pdb=" O LEU d 183 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR d 177 " --> pdb=" O ASN d 142 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU d 164 " --> pdb=" O THR d 182 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 148 through 153 removed outlier: 3.859A pdb=" N GLU d 199 " --> pdb=" O LYS d 151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS d 153 " --> pdb=" O THR d 197 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR d 197 " --> pdb=" O LYS d 153 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 6 through 7 removed outlier: 3.693A pdb=" N MET e 82 " --> pdb=" O LEU e 18 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 57 through 59 removed outlier: 7.034A pdb=" N TRP e 36 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA e 96 " --> pdb=" O HIS e 35 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS e 95 " --> pdb=" O TRP e 107 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP e 107 " --> pdb=" O CYS e 95 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS e 97 " --> pdb=" O ASP e 105 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 57 through 59 removed outlier: 7.034A pdb=" N TRP e 36 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA e 96 " --> pdb=" O HIS e 35 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.842A pdb=" N LYS e 147 " --> pdb=" O SER e 124 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS e 144 " --> pdb=" O SER e 183 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.842A pdb=" N LYS e 147 " --> pdb=" O SER e 124 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS e 144 " --> pdb=" O SER e 183 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 155 through 158 Processing sheet with id=AI2, first strand: chain 'f' and resid 6 through 7 removed outlier: 3.511A pdb=" N SER f 7 " --> pdb=" O SER f 22 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 10 through 13 removed outlier: 5.908A pdb=" N LEU f 11 " --> pdb=" O GLU f 109 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN f 41 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU f 50 " --> pdb=" O GLN f 41 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR f 53 " --> pdb=" O ASN f 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN f 57 " --> pdb=" O TYR f 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'f' and resid 120 through 122 removed outlier: 3.524A pdb=" N SER f 120 " --> pdb=" O PHE f 139 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL f 137 " --> pdb=" O PHE f 122 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER f 181 " --> pdb=" O CYS f 138 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR f 177 " --> pdb=" O ASN f 142 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER f 178 " --> pdb=" O THR f 168 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'f' and resid 148 through 154 removed outlier: 3.772A pdb=" N ASN f 149 " --> pdb=" O THR f 201 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3564 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: 20.13 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11199 1.34 - 1.46: 8444 1.46 - 1.58: 15667 1.58 - 1.70: 0 1.70 - 1.82: 207 Bond restraints: 35517 Sorted by residual: bond pdb=" C THR A 599 " pdb=" N PRO A 600 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.44e-02 4.82e+03 3.49e+00 bond pdb=" C THR B 599 " pdb=" N PRO B 600 " ideal model delta sigma weight residual 1.326 1.352 -0.026 1.44e-02 4.82e+03 3.19e+00 bond pdb=" N GLN A 14 " pdb=" CA GLN A 14 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" C THR C 599 " pdb=" N PRO C 600 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.44e-02 4.82e+03 2.99e+00 bond pdb=" N GLN e 1 " pdb=" CA GLN e 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 35512 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.12: 1140 107.12 - 113.85: 19551 113.85 - 120.59: 13245 120.59 - 127.32: 14018 127.32 - 134.06: 400 Bond angle restraints: 48354 Sorted by residual: angle pdb=" CA VAL e 187 " pdb=" C VAL e 187 " pdb=" N PRO e 188 " ideal model delta sigma weight residual 116.57 120.52 -3.95 9.80e-01 1.04e+00 1.62e+01 angle pdb=" C GLU f 27 " pdb=" N SER f 28 " pdb=" CA SER f 28 " ideal model delta sigma weight residual 121.70 128.45 -6.75 1.80e+00 3.09e-01 1.40e+01 angle pdb=" C GLU d 27 " pdb=" N SER d 28 " pdb=" CA SER d 28 " ideal model delta sigma weight residual 121.70 128.29 -6.59 1.80e+00 3.09e-01 1.34e+01 angle pdb=" C ASP C 215 " pdb=" N LEU C 216 " pdb=" CA LEU C 216 " ideal model delta sigma weight residual 120.83 125.79 -4.96 1.43e+00 4.89e-01 1.20e+01 angle pdb=" C GLU b 27 " pdb=" N SER b 28 " pdb=" CA SER b 28 " ideal model delta sigma weight residual 121.70 127.62 -5.92 1.80e+00 3.09e-01 1.08e+01 ... (remaining 48349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 20668 17.82 - 35.64: 422 35.64 - 53.46: 74 53.46 - 71.29: 14 71.29 - 89.11: 11 Dihedral angle restraints: 21189 sinusoidal: 8196 harmonic: 12993 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 149.62 -56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 143.43 -50.43 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 21186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3540 0.032 - 0.065: 1317 0.065 - 0.097: 245 0.097 - 0.130: 340 0.130 - 0.162: 30 Chirality restraints: 5472 Sorted by residual: chirality pdb=" CA ILE A 714 " pdb=" N ILE A 714 " pdb=" C ILE A 714 " pdb=" CB ILE A 714 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 5469 not shown) Planarity restraints: 6267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 580 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C GLN B 580 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN B 580 " 0.009 2.00e-02 2.50e+03 pdb=" N THR B 581 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE b 122 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO b 123 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO b 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO b 123 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY e 8 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO e 9 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO e 9 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO e 9 " 0.018 5.00e-02 4.00e+02 ... (remaining 6264 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 546 2.67 - 3.22: 32207 3.22 - 3.78: 52117 3.78 - 4.34: 76162 4.34 - 4.90: 124668 Nonbonded interactions: 285700 Sorted by model distance: nonbonded pdb=" OG SER A 968 " pdb=" O GLN C 755 " model vdw 2.106 2.440 nonbonded pdb=" O GLN A 755 " pdb=" OG SER B 968 " model vdw 2.111 2.440 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.111 2.440 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.125 2.440 nonbonded pdb=" OG1 THR A 29 " pdb=" OD2 ASP A 215 " model vdw 2.144 2.440 ... (remaining 285695 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 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.610 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 98.710 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 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 : 0.003 0.048 35517 Z= 0.193 Angle : 0.551 6.745 48354 Z= 0.302 Chirality : 0.043 0.162 5472 Planarity : 0.003 0.035 6267 Dihedral : 7.923 89.108 12672 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.15 % Allowed : 0.64 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.10), residues: 4416 helix: -1.67 (0.14), residues: 699 sheet: -2.04 (0.13), residues: 1216 loop : -2.41 (0.10), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 107 HIS 0.003 0.001 HIS A1048 PHE 0.010 0.001 PHE A 497 TYR 0.013 0.001 TYR B 873 ARG 0.002 0.000 ARG d 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1245 time to evaluate : 4.276 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 outliers start: 6 outliers final: 2 residues processed: 1250 average time/residue: 0.5007 time to fit residues: 1008.3218 Evaluate side-chains 574 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 572 time to evaluate : 3.655 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3318 time to fit residues: 6.2554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 3.9990 chunk 334 optimal weight: 0.0980 chunk 185 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 400 optimal weight: 4.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 175 GLN b 160 GLN A 99 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 804 GLN A 949 GLN A 955 ASN B 188 ASN B 360 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 919 ASN B 920 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 99 ASN C 188 ASN C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS c 86 GLN c 200 ASN d 94 GLN e 102 HIS ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 38 HIS ** f 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 216 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 35517 Z= 0.429 Angle : 0.785 17.144 48354 Z= 0.411 Chirality : 0.050 0.299 5472 Planarity : 0.006 0.062 6267 Dihedral : 4.840 27.931 4776 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.79 % Allowed : 10.38 % Favored : 85.83 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.11), residues: 4416 helix: -0.12 (0.18), residues: 711 sheet: -1.55 (0.13), residues: 1235 loop : -2.04 (0.11), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP e 47 HIS 0.010 0.002 HIS f 193 PHE 0.028 0.003 PHE B 400 TYR 0.032 0.003 TYR B 204 ARG 0.008 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 632 time to evaluate : 3.842 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 outliers start: 148 outliers final: 103 residues processed: 740 average time/residue: 0.4546 time to fit residues: 553.8214 Evaluate side-chains 555 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 452 time to evaluate : 3.871 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.3401 time to fit residues: 71.5507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 3.9990 chunk 124 optimal weight: 0.0070 chunk 333 optimal weight: 0.5980 chunk 272 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 401 optimal weight: 0.9980 chunk 433 optimal weight: 0.9990 chunk 357 optimal weight: 6.9990 chunk 397 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 321 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 39 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 925 ASN B 314 GLN B 448 ASN B 450 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 907 ASN B 955 ASN B1054 GLN C 913 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** c 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 149 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 35517 Z= 0.220 Angle : 0.600 13.205 48354 Z= 0.313 Chirality : 0.044 0.228 5472 Planarity : 0.005 0.049 6267 Dihedral : 4.435 33.790 4776 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.61 % Allowed : 13.04 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 4416 helix: 0.45 (0.19), residues: 705 sheet: -1.26 (0.14), residues: 1183 loop : -1.83 (0.11), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 886 HIS 0.007 0.001 HIS B1088 PHE 0.026 0.002 PHE C 464 TYR 0.028 0.002 TYR d 53 ARG 0.008 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 554 time to evaluate : 4.093 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 outliers start: 63 outliers final: 22 residues processed: 599 average time/residue: 0.4679 time to fit residues: 464.9166 Evaluate side-chains 478 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 456 time to evaluate : 3.638 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3411 time to fit residues: 19.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 5.9990 chunk 301 optimal weight: 0.9980 chunk 208 optimal weight: 0.0980 chunk 44 optimal weight: 0.2980 chunk 191 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 402 optimal weight: 7.9990 chunk 426 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 381 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 146 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 856 ASN B 907 ASN B 920 GLN C 474 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1010 GLN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** c 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 86 GLN c 98 ASN ** d 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 35517 Z= 0.294 Angle : 0.643 12.905 48354 Z= 0.336 Chirality : 0.046 0.222 5472 Planarity : 0.005 0.060 6267 Dihedral : 4.801 29.799 4776 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.02 % Allowed : 15.12 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.12), residues: 4416 helix: 0.51 (0.19), residues: 709 sheet: -1.10 (0.14), residues: 1186 loop : -1.84 (0.11), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 886 HIS 0.011 0.001 HIS B 146 PHE 0.018 0.002 PHE B 400 TYR 0.027 0.002 TYR f 177 ARG 0.011 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 487 time to evaluate : 3.891 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 outliers start: 79 outliers final: 46 residues processed: 533 average time/residue: 0.4674 time to fit residues: 410.1676 Evaluate side-chains 468 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 422 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3221 time to fit residues: 33.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 175 optimal weight: 0.0980 chunk 363 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 382 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 96 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 146 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 755 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** c 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN d 57 ASN ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 41 GLN ** f 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 35517 Z= 0.250 Angle : 0.600 11.980 48354 Z= 0.315 Chirality : 0.045 0.194 5472 Planarity : 0.005 0.059 6267 Dihedral : 4.777 36.779 4776 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.54 % Allowed : 16.22 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4416 helix: 0.63 (0.19), residues: 710 sheet: -1.01 (0.14), residues: 1197 loop : -1.77 (0.11), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 PHE 0.021 0.002 PHE B 338 TYR 0.026 0.002 TYR A 904 ARG 0.009 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 452 time to evaluate : 3.903 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 outliers start: 60 outliers final: 27 residues processed: 490 average time/residue: 0.4593 time to fit residues: 371.4083 Evaluate side-chains 418 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 391 time to evaluate : 3.852 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3701 time to fit residues: 23.2229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 426 optimal weight: 0.9990 chunk 354 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 224 optimal weight: 0.0030 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 920 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN d 57 ASN ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35517 Z= 0.301 Angle : 0.639 11.686 48354 Z= 0.336 Chirality : 0.046 0.167 5472 Planarity : 0.005 0.064 6267 Dihedral : 5.040 30.803 4776 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.10 % Allowed : 16.86 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4416 helix: 0.64 (0.19), residues: 694 sheet: -1.09 (0.14), residues: 1237 loop : -1.79 (0.11), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 886 HIS 0.008 0.001 HIS f 38 PHE 0.030 0.002 PHE A 906 TYR 0.031 0.002 TYR f 177 ARG 0.012 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 451 time to evaluate : 4.275 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 outliers start: 82 outliers final: 45 residues processed: 506 average time/residue: 0.4712 time to fit residues: 397.2462 Evaluate side-chains 433 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 388 time to evaluate : 4.253 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3730 time to fit residues: 35.9602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 359 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 425 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 907 ASN B 920 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 35517 Z= 0.238 Angle : 0.595 10.774 48354 Z= 0.313 Chirality : 0.044 0.191 5472 Planarity : 0.005 0.059 6267 Dihedral : 4.907 28.671 4776 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.41 % Allowed : 17.58 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4416 helix: 0.70 (0.19), residues: 699 sheet: -0.99 (0.14), residues: 1222 loop : -1.76 (0.11), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 886 HIS 0.006 0.001 HIS B 146 PHE 0.024 0.002 PHE A 906 TYR 0.025 0.002 TYR A 904 ARG 0.008 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 434 time to evaluate : 3.987 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 outliers start: 55 outliers final: 32 residues processed: 472 average time/residue: 0.4720 time to fit residues: 371.8420 Evaluate side-chains 420 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 388 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3404 time to fit residues: 26.3627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 0.5980 chunk 169 optimal weight: 9.9990 chunk 253 optimal weight: 0.0070 chunk 128 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 334 optimal weight: 0.9980 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 920 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1106 GLN ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 35517 Z= 0.260 Angle : 0.612 10.890 48354 Z= 0.322 Chirality : 0.045 0.240 5472 Planarity : 0.005 0.064 6267 Dihedral : 5.000 37.514 4776 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.90 % Allowed : 18.09 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.21 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4416 helix: 0.62 (0.19), residues: 704 sheet: -1.02 (0.15), residues: 1242 loop : -1.80 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 886 HIS 0.007 0.001 HIS B1088 PHE 0.039 0.002 PHE C1109 TYR 0.026 0.002 TYR A 904 ARG 0.008 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 420 time to evaluate : 4.472 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 outliers start: 35 outliers final: 20 residues processed: 438 average time/residue: 0.4724 time to fit residues: 343.8227 Evaluate side-chains 409 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 389 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3161 time to fit residues: 17.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2245 > 50: distance: 51 - 60: 6.965 distance: 60 - 61: 3.281 distance: 61 - 62: 6.252 distance: 61 - 64: 9.712 distance: 62 - 63: 8.150 distance: 62 - 69: 11.944 distance: 64 - 65: 13.565 distance: 65 - 66: 18.719 distance: 66 - 67: 28.287 distance: 66 - 68: 4.639 distance: 69 - 70: 20.310 distance: 70 - 71: 24.525 distance: 70 - 73: 24.074 distance: 71 - 72: 12.840 distance: 71 - 77: 17.773 distance: 73 - 74: 5.332 distance: 74 - 75: 11.632 distance: 74 - 76: 11.947 distance: 77 - 78: 12.684 distance: 78 - 79: 21.086 distance: 79 - 80: 9.781 distance: 79 - 81: 12.846 distance: 81 - 82: 15.217 distance: 82 - 83: 10.015 distance: 82 - 85: 8.131 distance: 83 - 84: 9.992 distance: 83 - 88: 15.450 distance: 85 - 87: 13.936 distance: 88 - 89: 8.275 distance: 89 - 90: 8.133 distance: 89 - 92: 20.710 distance: 90 - 91: 13.707 distance: 90 - 96: 5.726 distance: 91 - 185: 17.114 distance: 92 - 93: 11.082 distance: 93 - 94: 9.101 distance: 93 - 95: 13.710 distance: 96 - 97: 4.814 distance: 97 - 98: 11.675 distance: 97 - 100: 17.988 distance: 98 - 99: 6.347 distance: 98 - 104: 16.854 distance: 100 - 101: 17.448 distance: 101 - 102: 13.178 distance: 101 - 103: 10.442 distance: 104 - 105: 32.364 distance: 104 - 176: 23.052 distance: 105 - 106: 10.873 distance: 105 - 108: 28.677 distance: 106 - 107: 10.001 distance: 107 - 173: 15.819 distance: 108 - 109: 9.050 distance: 110 - 111: 10.187 distance: 111 - 112: 7.982 distance: 111 - 114: 10.859 distance: 112 - 113: 6.208 distance: 112 - 124: 24.892 distance: 114 - 115: 18.348 distance: 115 - 116: 11.442 distance: 115 - 117: 17.658 distance: 116 - 118: 13.029 distance: 117 - 119: 16.316 distance: 117 - 120: 8.258 distance: 118 - 119: 10.332 distance: 119 - 121: 6.456 distance: 120 - 122: 11.888 distance: 121 - 123: 3.651 distance: 122 - 123: 9.157 distance: 124 - 125: 7.207 distance: 124 - 162: 12.291 distance: 125 - 126: 18.875 distance: 125 - 128: 7.562 distance: 126 - 127: 24.116 distance: 126 - 131: 7.644 distance: 127 - 159: 27.504 distance: 128 - 129: 8.592 distance: 128 - 130: 8.854 distance: 131 - 132: 7.471 distance: 132 - 133: 7.700 distance: 132 - 135: 31.775 distance: 133 - 134: 8.295 distance: 133 - 139: 13.128 distance: 135 - 136: 16.477 distance: 136 - 137: 28.168 distance: 136 - 138: 13.107