Starting phenix.real_space_refine on Fri Mar 22 22:18:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/03_2024/7dk4_30702.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/03_2024/7dk4_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_30702/03_2024/7dk4_30702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/03_2024/7dk4_30702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/03_2024/7dk4_30702.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk4_30702/03_2024/7dk4_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-dev-5265/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: 17.53, 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: 13.14 Conformation dependent library (CDL) restraints added in 6.2 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: 4.51 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: 18.62 Time building geometry restraints manager: 14.37 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: 4.600 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: 0.560 Set scattering table: 0.340 Process input model: 94.860 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.210 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.910 ------------------------------------------------------------------------------- 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 : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7280 (p0) cc_final: 0.6097 (t0) REVERT: A 869 MET cc_start: 0.7390 (mtp) cc_final: 0.6741 (mtp) REVERT: A 1004 LEU cc_start: 0.8120 (mt) cc_final: 0.7906 (mt) REVERT: B 900 MET cc_start: 0.6436 (mtp) cc_final: 0.6205 (mtp) REVERT: B 928 ASN cc_start: 0.7190 (m-40) cc_final: 0.6959 (m110) REVERT: C 510 VAL cc_start: 0.5779 (t) cc_final: 0.5554 (t) REVERT: C 573 THR cc_start: 0.6569 (m) cc_final: 0.6244 (m) REVERT: C 644 GLN cc_start: 0.7688 (tp40) cc_final: 0.7480 (tp40) REVERT: C 699 LEU cc_start: 0.8062 (mt) cc_final: 0.7781 (mt) REVERT: C 730 SER cc_start: 0.8460 (p) cc_final: 0.8121 (m) REVERT: C 740 MET cc_start: 0.5429 (mtp) cc_final: 0.4935 (mtm) REVERT: C 753 LEU cc_start: 0.7914 (tp) cc_final: 0.7698 (tt) REVERT: C 777 ASN cc_start: 0.7811 (m-40) cc_final: 0.7609 (m-40) REVERT: e 95 CYS cc_start: 0.2303 (OUTLIER) cc_final: 0.1506 (m) outliers start: 6 outliers final: 2 residues processed: 1250 average time/residue: 0.4670 time to fit residues: 932.2721 Evaluate side-chains 580 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 577 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 95 CYS 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 39 GLN 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 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** ** B1054 GLN ** 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: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 35517 Z= 0.430 Angle : 0.792 18.276 48354 Z= 0.414 Chirality : 0.050 0.246 5472 Planarity : 0.006 0.064 6267 Dihedral : 5.028 48.893 4779 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.87 % Allowed : 10.30 % Favored : 85.83 % 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: -2.40 (0.11), residues: 4416 helix: -0.09 (0.18), residues: 706 sheet: -1.59 (0.13), residues: 1223 loop : -2.08 (0.11), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP e 47 HIS 0.011 0.002 HIS f 38 PHE 0.028 0.003 PHE C 157 TYR 0.034 0.003 TYR B 204 ARG 0.013 0.001 ARG A 273 *********************** 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 785 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 634 time to evaluate : 3.990 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: b 143 PHE cc_start: 0.1351 (p90) cc_final: 0.1118 (p90) REVERT: A 750 SER cc_start: 0.6869 (p) cc_final: 0.6665 (t) REVERT: A 902 MET cc_start: 0.7611 (mmm) cc_final: 0.7349 (tpt) REVERT: B 59 PHE cc_start: 0.6315 (m-80) cc_final: 0.6063 (m-80) REVERT: B 724 THR cc_start: 0.8779 (t) cc_final: 0.8510 (t) REVERT: B 732 THR cc_start: 0.8565 (m) cc_final: 0.7922 (p) REVERT: B 952 VAL cc_start: 0.8560 (m) cc_final: 0.8280 (t) REVERT: C 987 PRO cc_start: 0.5683 (Cg_endo) cc_final: 0.5422 (Cg_exo) REVERT: d 153 LYS cc_start: 0.3845 (ptpt) cc_final: 0.3364 (pttp) REVERT: e 142 LEU cc_start: 0.3742 (OUTLIER) cc_final: 0.2642 (tp) outliers start: 151 outliers final: 103 residues processed: 745 average time/residue: 0.4672 time to fit residues: 578.8788 Evaluate side-chains 555 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 451 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 23 THR Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 118 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 63 PHE Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 139 MET Chi-restraints excluded: chain e residue 142 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 149 ASN Chi-restraints excluded: chain f residue 216 ASN 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: 0.8980 chunk 333 optimal weight: 0.5980 chunk 272 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 433 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 chunk 397 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 321 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A 949 GLN B 360 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 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 ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1101 HIS ** c 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 41 GLN ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 216 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 35517 Z= 0.256 Angle : 0.626 13.405 48354 Z= 0.326 Chirality : 0.045 0.227 5472 Planarity : 0.005 0.050 6267 Dihedral : 4.686 48.838 4778 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.87 % Allowed : 13.25 % Favored : 82.88 % 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: -2.00 (0.11), residues: 4416 helix: 0.31 (0.18), residues: 706 sheet: -1.31 (0.14), residues: 1194 loop : -1.86 (0.11), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 886 HIS 0.008 0.001 HIS B1088 PHE 0.032 0.002 PHE C 464 TYR 0.027 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 668 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 517 time to evaluate : 3.963 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: a 109 GLN cc_start: 0.5016 (OUTLIER) cc_final: 0.4709 (tm-30) REVERT: b 98 ASP cc_start: 0.3739 (OUTLIER) cc_final: 0.2218 (p0) REVERT: A 902 MET cc_start: 0.7474 (mmm) cc_final: 0.7272 (tpt) REVERT: B 132 GLU cc_start: 0.1748 (OUTLIER) cc_final: 0.1478 (mm-30) REVERT: B 549 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6279 (p) REVERT: B 952 VAL cc_start: 0.8584 (m) cc_final: 0.8176 (t) REVERT: B 1005 GLN cc_start: 0.6593 (mt0) cc_final: 0.6243 (mt0) REVERT: d 174 ASP cc_start: 0.2536 (t0) cc_final: 0.1553 (m-30) REVERT: e 142 LEU cc_start: 0.3909 (OUTLIER) cc_final: 0.2632 (tp) outliers start: 151 outliers final: 103 residues processed: 624 average time/residue: 0.4530 time to fit residues: 470.5336 Evaluate side-chains 550 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 442 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 98 ASP Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain e residue 20 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 63 PHE Chi-restraints excluded: chain e residue 71 LYS Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 142 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 74 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 208 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 402 optimal weight: 7.9990 chunk 426 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 381 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 46 GLN b 96 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 146 HIS B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 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 856 ASN B 907 ASN B 920 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 474 GLN C 755 GLN C 777 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** c 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 35517 Z= 0.407 Angle : 0.739 13.262 48354 Z= 0.389 Chirality : 0.049 0.221 5472 Planarity : 0.006 0.066 6267 Dihedral : 5.441 59.021 4777 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.94 % Allowed : 14.48 % Favored : 80.58 % 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: -2.13 (0.12), residues: 4416 helix: 0.23 (0.19), residues: 704 sheet: -1.34 (0.14), residues: 1222 loop : -1.98 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 886 HIS 0.008 0.002 HIS A 49 PHE 0.025 0.003 PHE B 400 TYR 0.028 0.003 TYR f 53 ARG 0.013 0.001 ARG B 102 *********************** 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 671 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 478 time to evaluate : 3.775 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: a 109 GLN cc_start: 0.4900 (OUTLIER) cc_final: 0.4634 (tm-30) REVERT: b 129 LEU cc_start: -0.0195 (OUTLIER) cc_final: -0.0792 (mm) REVERT: B 132 GLU cc_start: 0.2043 (OUTLIER) cc_final: 0.1593 (mm-30) REVERT: B 549 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6436 (p) REVERT: B 732 THR cc_start: 0.8612 (m) cc_final: 0.8128 (p) REVERT: B 952 VAL cc_start: 0.8716 (m) cc_final: 0.8345 (t) REVERT: C 739 THR cc_start: 0.6478 (OUTLIER) cc_final: 0.6185 (m) REVERT: C 1130 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7814 (tp) REVERT: f 60 SER cc_start: 0.5053 (OUTLIER) cc_final: 0.4799 (t) REVERT: f 65 ARG cc_start: 0.3439 (OUTLIER) cc_final: 0.2047 (ptm-80) outliers start: 193 outliers final: 131 residues processed: 617 average time/residue: 0.4366 time to fit residues: 448.0179 Evaluate side-chains 540 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 401 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 211 ASP Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 65 ARG Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 317 optimal weight: 0.3980 chunk 175 optimal weight: 2.9990 chunk 363 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 382 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 46 GLN b 96 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 450 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 ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 804 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN d 42 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 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35517 Z= 0.241 Angle : 0.610 12.276 48354 Z= 0.319 Chirality : 0.045 0.208 5472 Planarity : 0.005 0.058 6267 Dihedral : 5.045 47.475 4777 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.00 % Allowed : 16.32 % Favored : 79.68 % 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: -1.91 (0.12), residues: 4416 helix: 0.52 (0.19), residues: 701 sheet: -1.23 (0.14), residues: 1196 loop : -1.86 (0.11), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 886 HIS 0.008 0.001 HIS A 49 PHE 0.030 0.002 PHE B 374 TYR 0.028 0.002 TYR A 904 ARG 0.005 0.000 ARG c 38 *********************** 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 625 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 469 time to evaluate : 4.217 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: a 107 TRP cc_start: 0.1326 (m100) cc_final: 0.0784 (m100) REVERT: a 109 GLN cc_start: 0.4855 (OUTLIER) cc_final: 0.4647 (tm-30) REVERT: b 129 LEU cc_start: -0.0217 (OUTLIER) cc_final: -0.0811 (mm) REVERT: B 132 GLU cc_start: 0.1881 (OUTLIER) cc_final: 0.1358 (mm-30) REVERT: B 549 THR cc_start: 0.7041 (OUTLIER) cc_final: 0.6503 (p) REVERT: B 732 THR cc_start: 0.8552 (m) cc_final: 0.8134 (p) REVERT: B 952 VAL cc_start: 0.8697 (m) cc_final: 0.8304 (t) REVERT: B 1005 GLN cc_start: 0.6554 (mt0) cc_final: 0.6285 (mt0) REVERT: C 119 ILE cc_start: 0.7925 (mp) cc_final: 0.7496 (mt) REVERT: C 571 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6973 (t0) REVERT: C 581 THR cc_start: 0.6757 (OUTLIER) cc_final: 0.6532 (t) REVERT: C 1130 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7779 (tp) REVERT: c 209 LYS cc_start: 0.4270 (mmtm) cc_final: 0.3308 (ttmm) REVERT: f 65 ARG cc_start: 0.3295 (OUTLIER) cc_final: 0.2000 (ptm-80) REVERT: f 169 ASP cc_start: 0.4401 (p0) cc_final: 0.4146 (p0) outliers start: 156 outliers final: 119 residues processed: 582 average time/residue: 0.4333 time to fit residues: 419.4262 Evaluate side-chains 537 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 410 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 23 THR Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 ASP Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 35 HIS Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 58 ASP Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 65 ARG Chi-restraints excluded: chain f residue 74 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 2.9990 chunk 383 optimal weight: 5.9990 chunk 84 optimal weight: 0.0970 chunk 250 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 426 optimal weight: 0.9990 chunk 354 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 96 ASN A 777 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 450 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 955 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN d 42 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 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 35517 Z= 0.247 Angle : 0.602 11.948 48354 Z= 0.314 Chirality : 0.045 0.243 5472 Planarity : 0.005 0.063 6267 Dihedral : 4.959 34.796 4777 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.25 % Allowed : 16.71 % Favored : 79.04 % 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: -1.85 (0.12), residues: 4416 helix: 0.67 (0.19), residues: 689 sheet: -1.23 (0.14), residues: 1213 loop : -1.82 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 PHE 0.027 0.002 PHE b 143 TYR 0.031 0.002 TYR A 904 ARG 0.005 0.000 ARG C 355 *********************** 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 619 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 453 time to evaluate : 3.569 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: a 109 GLN cc_start: 0.5037 (OUTLIER) cc_final: 0.4725 (tm-30) REVERT: b 129 LEU cc_start: -0.0309 (OUTLIER) cc_final: -0.0898 (mm) REVERT: A 472 ILE cc_start: -0.0031 (pt) cc_final: -0.0344 (pt) REVERT: A 740 MET cc_start: 0.6163 (tpt) cc_final: 0.5678 (tpt) REVERT: B 132 GLU cc_start: 0.1835 (OUTLIER) cc_final: 0.1335 (mm-30) REVERT: B 200 TYR cc_start: 0.4060 (OUTLIER) cc_final: 0.3675 (m-80) REVERT: B 549 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6499 (p) REVERT: B 732 THR cc_start: 0.8523 (m) cc_final: 0.8142 (p) REVERT: B 952 VAL cc_start: 0.8731 (m) cc_final: 0.8319 (t) REVERT: C 119 ILE cc_start: 0.7831 (mp) cc_final: 0.7367 (mt) REVERT: C 410 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7144 (tp) REVERT: C 581 THR cc_start: 0.6931 (OUTLIER) cc_final: 0.6718 (t) REVERT: C 1130 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7898 (tp) REVERT: c 209 LYS cc_start: 0.4236 (mmtm) cc_final: 0.3321 (ttmm) REVERT: f 65 ARG cc_start: 0.3541 (OUTLIER) cc_final: 0.2174 (ptm-80) REVERT: f 85 ASP cc_start: 0.4720 (t0) cc_final: 0.4447 (t0) REVERT: f 169 ASP cc_start: 0.4391 (p0) cc_final: 0.4115 (p0) outliers start: 166 outliers final: 129 residues processed: 575 average time/residue: 0.4196 time to fit residues: 405.3467 Evaluate side-chains 544 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 406 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 ASP Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 35 HIS Chi-restraints excluded: chain c residue 58 ASP Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 65 ARG Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 168 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 311 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 359 optimal weight: 9.9990 chunk 238 optimal weight: 0.7980 chunk 425 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 96 ASN A 777 ASN A 784 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 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 955 ASN B1005 GLN ** B1054 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 35517 Z= 0.211 Angle : 0.580 11.510 48354 Z= 0.303 Chirality : 0.044 0.210 5472 Planarity : 0.004 0.060 6267 Dihedral : 4.837 32.906 4777 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.10 % Allowed : 17.19 % Favored : 78.71 % 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: 0.76 (0.19), residues: 697 sheet: -1.09 (0.15), residues: 1219 loop : -1.75 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 886 HIS 0.006 0.001 HIS A 49 PHE 0.036 0.002 PHE C1109 TYR 0.024 0.002 TYR A 904 ARG 0.007 0.000 ARG B 765 *********************** 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 594 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 434 time to evaluate : 3.870 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: a 107 TRP cc_start: 0.1650 (m100) cc_final: 0.1315 (m100) REVERT: a 109 GLN cc_start: 0.5141 (OUTLIER) cc_final: 0.4803 (tm-30) REVERT: b 129 LEU cc_start: -0.0303 (OUTLIER) cc_final: -0.0888 (mm) REVERT: A 100 ILE cc_start: 0.6466 (mm) cc_final: 0.5993 (mm) REVERT: A 320 VAL cc_start: 0.6546 (OUTLIER) cc_final: 0.6306 (t) REVERT: A 472 ILE cc_start: -0.0512 (pt) cc_final: -0.0775 (pt) REVERT: A 923 ILE cc_start: 0.8673 (pt) cc_final: 0.8371 (mt) REVERT: A 1037 SER cc_start: 0.8984 (t) cc_final: 0.8423 (m) REVERT: B 132 GLU cc_start: 0.1816 (OUTLIER) cc_final: 0.1238 (mm-30) REVERT: B 200 TYR cc_start: 0.4071 (OUTLIER) cc_final: 0.3712 (m-80) REVERT: B 492 LEU cc_start: 0.0169 (mp) cc_final: -0.0456 (mp) REVERT: B 549 THR cc_start: 0.6982 (OUTLIER) cc_final: 0.6438 (p) REVERT: B 732 THR cc_start: 0.8439 (m) cc_final: 0.8179 (p) REVERT: C 119 ILE cc_start: 0.7790 (mp) cc_final: 0.7328 (mt) REVERT: C 1130 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7919 (tp) REVERT: c 209 LYS cc_start: 0.4184 (mmtm) cc_final: 0.3308 (ttmm) REVERT: e 47 TRP cc_start: 0.4141 (t60) cc_final: 0.3913 (t60) REVERT: f 169 ASP cc_start: 0.4424 (p0) cc_final: 0.4123 (p0) outliers start: 160 outliers final: 131 residues processed: 553 average time/residue: 0.4369 time to fit residues: 403.5335 Evaluate side-chains 535 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 397 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 35 HIS Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 58 ASP Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 150 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 168 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 334 optimal weight: 0.0980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 96 ASN A 777 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 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 955 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** 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 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35517 Z= 0.237 Angle : 0.593 10.986 48354 Z= 0.311 Chirality : 0.044 0.232 5472 Planarity : 0.005 0.067 6267 Dihedral : 4.884 29.797 4777 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.07 % Allowed : 17.37 % Favored : 78.55 % 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: -1.67 (0.12), residues: 4416 helix: 0.73 (0.19), residues: 691 sheet: -1.05 (0.15), residues: 1236 loop : -1.71 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 PHE 0.033 0.002 PHE C1109 TYR 0.023 0.002 TYR B 505 ARG 0.005 0.000 ARG B 765 *********************** 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 597 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 438 time to evaluate : 3.770 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: a 109 GLN cc_start: 0.5444 (OUTLIER) cc_final: 0.5113 (tm-30) REVERT: a 139 MET cc_start: 0.2912 (tpp) cc_final: 0.2069 (ttt) REVERT: b 129 LEU cc_start: -0.0261 (OUTLIER) cc_final: -0.0844 (mm) REVERT: A 472 ILE cc_start: -0.0874 (pt) cc_final: -0.1080 (pt) REVERT: A 1029 MET cc_start: 0.8079 (tpp) cc_final: 0.7793 (ttm) REVERT: A 1037 SER cc_start: 0.8984 (t) cc_final: 0.8474 (m) REVERT: B 132 GLU cc_start: 0.1972 (OUTLIER) cc_final: 0.1477 (mm-30) REVERT: B 200 TYR cc_start: 0.4128 (OUTLIER) cc_final: 0.3828 (m-80) REVERT: B 458 LYS cc_start: 0.5195 (tppt) cc_final: 0.4980 (tptt) REVERT: B 492 LEU cc_start: 0.0372 (mp) cc_final: -0.0281 (mp) REVERT: B 549 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6488 (p) REVERT: B 732 THR cc_start: 0.8384 (m) cc_final: 0.8073 (p) REVERT: C 119 ILE cc_start: 0.7795 (mp) cc_final: 0.7316 (mt) REVERT: C 410 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7113 (tp) REVERT: C 1130 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7907 (tp) REVERT: c 209 LYS cc_start: 0.4211 (mmtm) cc_final: 0.3319 (ttmm) REVERT: f 144 TYR cc_start: 0.0910 (t80) cc_final: 0.0695 (t80) REVERT: f 169 ASP cc_start: 0.4369 (p0) cc_final: 0.4010 (p0) outliers start: 159 outliers final: 139 residues processed: 561 average time/residue: 0.4156 time to fit residues: 390.1024 Evaluate side-chains 542 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 396 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 106 PHE Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 ASP Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 95 CYS Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 132 SER Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 10.0000 chunk 407 optimal weight: 0.9990 chunk 371 optimal weight: 0.9980 chunk 396 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 357 optimal weight: 8.9990 chunk 374 optimal weight: 7.9990 chunk 394 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35517 Z= 0.271 Angle : 0.620 9.815 48354 Z= 0.326 Chirality : 0.045 0.272 5472 Planarity : 0.005 0.066 6267 Dihedral : 5.081 30.763 4777 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.07 % Allowed : 17.65 % Favored : 78.27 % 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: -1.72 (0.12), residues: 4416 helix: 0.67 (0.20), residues: 680 sheet: -1.08 (0.14), residues: 1245 loop : -1.72 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A 886 HIS 0.007 0.001 HIS A 49 PHE 0.031 0.002 PHE C1109 TYR 0.030 0.002 TYR A 904 ARG 0.008 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 9 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 572 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 413 time to evaluate : 3.780 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: a 109 GLN cc_start: 0.5542 (OUTLIER) cc_final: 0.5213 (tm-30) REVERT: a 139 MET cc_start: 0.2778 (tpp) cc_final: 0.1967 (ttt) REVERT: b 129 LEU cc_start: -0.0113 (OUTLIER) cc_final: -0.0705 (mm) REVERT: A 320 VAL cc_start: 0.6662 (OUTLIER) cc_final: 0.6414 (t) REVERT: A 472 ILE cc_start: -0.0629 (pt) cc_final: -0.0938 (pt) REVERT: A 574 ASP cc_start: 0.7643 (p0) cc_final: 0.6690 (t0) REVERT: A 950 ASP cc_start: 0.6663 (p0) cc_final: 0.6441 (p0) REVERT: B 132 GLU cc_start: 0.2183 (OUTLIER) cc_final: 0.1664 (mm-30) REVERT: B 200 TYR cc_start: 0.4287 (OUTLIER) cc_final: 0.3845 (m-80) REVERT: B 492 LEU cc_start: 0.0587 (mp) cc_final: 0.0249 (mt) REVERT: B 549 THR cc_start: 0.7091 (OUTLIER) cc_final: 0.6641 (p) REVERT: B 732 THR cc_start: 0.8423 (m) cc_final: 0.8100 (p) REVERT: C 119 ILE cc_start: 0.7865 (mp) cc_final: 0.7459 (mt) REVERT: C 410 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7205 (tp) REVERT: C 1130 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8067 (tp) REVERT: c 209 LYS cc_start: 0.3897 (mmtm) cc_final: 0.3103 (ttmm) REVERT: f 169 ASP cc_start: 0.4412 (p0) cc_final: 0.4026 (p0) outliers start: 159 outliers final: 140 residues processed: 537 average time/residue: 0.4344 time to fit residues: 390.7688 Evaluate side-chains 539 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 391 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 CYS Chi-restraints excluded: chain a residue 106 PHE Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 ASP Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 58 ASP Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 14 SER Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 0.9980 chunk 418 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 291 optimal weight: 4.9990 chunk 439 optimal weight: 6.9990 chunk 404 optimal weight: 2.9990 chunk 349 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 955 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35517 Z= 0.218 Angle : 0.599 12.677 48354 Z= 0.314 Chirality : 0.045 0.244 5472 Planarity : 0.005 0.065 6267 Dihedral : 4.971 29.062 4776 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.74 % Allowed : 18.14 % Favored : 78.12 % 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: -1.64 (0.12), residues: 4416 helix: 0.78 (0.20), residues: 680 sheet: -1.04 (0.15), residues: 1217 loop : -1.68 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP A 886 HIS 0.006 0.001 HIS A 49 PHE 0.037 0.002 PHE A 133 TYR 0.028 0.002 TYR A 904 ARG 0.007 0.000 ARG B 765 ********************** REFINEMENT MACRO_CYCLE 10 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 564 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 418 time to evaluate : 3.322 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: a 109 GLN cc_start: 0.5649 (OUTLIER) cc_final: 0.5269 (tm-30) REVERT: a 139 MET cc_start: 0.2701 (tpp) cc_final: 0.1978 (ttt) REVERT: b 129 LEU cc_start: -0.0013 (OUTLIER) cc_final: -0.0606 (mm) REVERT: A 320 VAL cc_start: 0.6636 (OUTLIER) cc_final: 0.6433 (t) REVERT: A 950 ASP cc_start: 0.6581 (p0) cc_final: 0.6366 (p0) REVERT: B 132 GLU cc_start: 0.2090 (OUTLIER) cc_final: 0.1477 (mm-30) REVERT: B 200 TYR cc_start: 0.4250 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: B 492 LEU cc_start: 0.0502 (mp) cc_final: -0.0356 (mp) REVERT: B 549 THR cc_start: 0.7067 (OUTLIER) cc_final: 0.6578 (p) REVERT: B 732 THR cc_start: 0.8426 (m) cc_final: 0.8133 (p) REVERT: C 119 ILE cc_start: 0.7751 (mp) cc_final: 0.7403 (mt) REVERT: C 171 VAL cc_start: 0.6408 (OUTLIER) cc_final: 0.6207 (p) REVERT: C 410 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7215 (tp) REVERT: c 209 LYS cc_start: 0.4104 (mmtm) cc_final: 0.3298 (ttmm) REVERT: f 169 ASP cc_start: 0.4305 (p0) cc_final: 0.3948 (p0) outliers start: 146 outliers final: 130 residues processed: 533 average time/residue: 0.4296 time to fit residues: 383.3244 Evaluate side-chains 533 residues out of total 3903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 395 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 ASP Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain c residue 1 GLN Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain c residue 58 ASP Chi-restraints excluded: chain c residue 82 MET Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 179 TYR Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 322 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 97 optimal weight: 0.0060 chunk 350 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 777 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN e 39 GLN ** e 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.142086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.120336 restraints weight = 105753.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122074 restraints weight = 56409.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.123210 restraints weight = 34957.320| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35517 Z= 0.177 Angle : 0.574 9.607 48354 Z= 0.299 Chirality : 0.044 0.221 5472 Planarity : 0.005 0.064 6267 Dihedral : 4.726 24.346 4776 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.07 % Allowed : 19.16 % Favored : 77.76 % 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: -1.54 (0.12), residues: 4416 helix: 0.87 (0.20), residues: 690 sheet: -0.96 (0.15), residues: 1218 loop : -1.64 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A 886 HIS 0.006 0.001 HIS a 35 PHE 0.030 0.001 PHE C1109 TYR 0.033 0.002 TYR A 904 ARG 0.012 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8577.18 seconds wall clock time: 155 minutes 23.15 seconds (9323.15 seconds total)