Starting phenix.real_space_refine on Wed May 28 23:19:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8keq_37164/05_2025/8keq_37164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8keq_37164/05_2025/8keq_37164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8keq_37164/05_2025/8keq_37164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8keq_37164/05_2025/8keq_37164.map" model { file = "/net/cci-nas-00/data/ceres_data/8keq_37164/05_2025/8keq_37164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8keq_37164/05_2025/8keq_37164.cif" } resolution = 3.14 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= 0.002 sd= 0.032 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 137 5.16 5 C 20107 2.51 5 N 5266 2.21 5 O 6065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.48s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31575 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "A" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "G" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "F" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "C" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Time building chain proxies: 16.12, per 1000 atoms: 0.51 Number of scatterers: 31575 At special positions: 0 Unit cell: (164.032, 173.352, 224.612, 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 137 16.00 O 6065 8.00 N 5266 7.00 C 20107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS B 132 " - 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 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 E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - 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 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 G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - 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 379 " - pdb=" SG CYS C 432 " 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 7.03 Conformation dependent library (CDL) restraints added in 3.8 seconds 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7590 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 66 sheets defined 17.8% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.168A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.220A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 756 removed outlier: 3.634A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.827A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.395A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.824A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.113A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.969A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 185 through 191 removed outlier: 3.534A pdb=" N HIS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 4.418A pdb=" N GLY A 261 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 262 " --> pdb=" O THR A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 262' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.013A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 4.089A pdb=" N GLY A 545 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.586A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.532A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.555A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 7.070A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (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 removed outlier: 3.742A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.542A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.686A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.960A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 removed outlier: 3.573A pdb=" N LYS F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 removed outlier: 3.720A pdb=" N GLU F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 185 through 190' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.510A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.641A pdb=" N PHE C 371 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.813A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.935A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.568A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.661A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.518A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 7.215A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) 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: 3.726A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.145A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.819A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.742A pdb=" N ASP B 54 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.502A pdb=" N LEU B 85 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.529A pdb=" N ILE B 129 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.593A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.714A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.191A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.979A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AB2, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.786A pdb=" N PHE B 565 " --> pdb=" O PHE C 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.959A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.172A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.172A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.336A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.892A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.538A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 83 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.530A pdb=" N THR E 119 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.709A pdb=" N LEU E 185 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP E 151 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.709A pdb=" N LEU E 185 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP E 151 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 160 through 161 Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.568A pdb=" N LEU D 13 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR D 87 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.890A pdb=" N ALA D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.645A pdb=" N ASN D 139 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR D 175 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 155 through 157 removed outlier: 4.451A pdb=" N TRP D 150 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS D 147 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR D 199 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR D 194 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.515A pdb=" N VAL A 267 " --> pdb=" O THR A 64 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 37 through 38 removed outlier: 7.347A pdb=" N VAL A 37 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AD3, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.643A pdb=" N PHE A 56 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.581A pdb=" N LEU A 85 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.892A pdb=" N SER A 95 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 97 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.041A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.018A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AD9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.928A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 712 through 728 removed outlier: 7.095A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 712 through 728 removed outlier: 7.095A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.347A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AE5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AE6, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.506A pdb=" N VAL G 18 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 83 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.905A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 9 through 12 removed outlier: 4.535A pdb=" N TYR G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.723A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER G 187 " --> pdb=" O CYS G 147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 149 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 185 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP G 151 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR G 183 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.723A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER G 187 " --> pdb=" O CYS G 147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 149 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 185 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP G 151 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR G 183 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 160 through 161 removed outlier: 3.524A pdb=" N SER G 160 " --> pdb=" O ASN G 204 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR G 201 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.512A pdb=" N TYR F 86 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR F 87 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 62 through 67 removed outlier: 3.631A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 116 through 120 removed outlier: 3.536A pdb=" N ASN F 139 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 156 through 157 removed outlier: 4.419A pdb=" N TRP F 150 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR F 194 " --> pdb=" O PHE F 211 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE F 211 " --> pdb=" O TYR F 194 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.824A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 49 through 56 removed outlier: 6.250A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.567A pdb=" N LEU C 85 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 94 through 95 removed outlier: 3.790A pdb=" N SER C 95 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 127 through 130 Processing sheet with id=AG3, first strand: chain 'C' and resid 194 through 196 removed outlier: 3.717A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.040A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.554A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG7, first strand: chain 'C' and resid 538 through 541 Processing sheet with id=AG8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.015A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 712 through 728 removed outlier: 7.130A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 712 through 728 removed outlier: 7.130A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.158A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 1120 through 1122 972 hydrogen bonds defined for protein. 2625 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: 12.16 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10037 1.34 - 1.46: 5876 1.46 - 1.58: 16246 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 32336 Sorted by residual: bond pdb=" N VAL C 48 " pdb=" CA VAL C 48 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.32e-02 5.74e+03 9.89e+00 bond pdb=" N LYS B 528 " pdb=" CA LYS B 528 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.70e+00 bond pdb=" N ASN A 532 " pdb=" CA ASN A 532 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.09e-02 8.42e+03 8.64e+00 bond pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.18e-02 7.18e+03 8.11e+00 bond pdb=" CA SER B 691 " pdb=" CB SER B 691 " ideal model delta sigma weight residual 1.535 1.481 0.054 1.90e-02 2.77e+03 8.02e+00 ... (remaining 32331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 42809 1.51 - 3.03: 1034 3.03 - 4.54: 138 4.54 - 6.05: 29 6.05 - 7.57: 4 Bond angle restraints: 44014 Sorted by residual: angle pdb=" N VAL B 524 " pdb=" CA VAL B 524 " pdb=" C VAL B 524 " ideal model delta sigma weight residual 111.67 106.76 4.91 9.50e-01 1.11e+00 2.67e+01 angle pdb=" CA PRO B 521 " pdb=" C PRO B 521 " pdb=" O PRO B 521 " ideal model delta sigma weight residual 121.97 117.20 4.77 1.22e+00 6.72e-01 1.53e+01 angle pdb=" O SER B 673 " pdb=" C SER B 673 " pdb=" N TYR B 674 " ideal model delta sigma weight residual 123.42 119.27 4.15 1.07e+00 8.73e-01 1.51e+01 angle pdb=" N ARG B 214 " pdb=" CA ARG B 214 " pdb=" C ARG B 214 " ideal model delta sigma weight residual 112.93 107.77 5.16 1.33e+00 5.65e-01 1.51e+01 angle pdb=" CA ALA B 522 " pdb=" C ALA B 522 " pdb=" O ALA B 522 " ideal model delta sigma weight residual 121.54 117.12 4.42 1.16e+00 7.43e-01 1.45e+01 ... (remaining 44009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 18452 17.83 - 35.67: 701 35.67 - 53.50: 122 53.50 - 71.34: 30 71.34 - 89.17: 7 Dihedral angle restraints: 19312 sinusoidal: 7497 harmonic: 11815 Sorted by residual: dihedral pdb=" CA THR A 523 " pdb=" C THR A 523 " pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C THR A 523 " pdb=" N THR A 523 " pdb=" CA THR A 523 " pdb=" CB THR A 523 " ideal model delta harmonic sigma weight residual -122.00 -130.30 8.30 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" CB GLU C 224 " pdb=" CG GLU C 224 " pdb=" CD GLU C 224 " pdb=" OE1 GLU C 224 " ideal model delta sinusoidal sigma weight residual 0.00 85.64 -85.64 1 3.00e+01 1.11e-03 9.86e+00 ... (remaining 19309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3935 0.045 - 0.091: 695 0.091 - 0.136: 306 0.136 - 0.181: 17 0.181 - 0.226: 7 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA LEU A 518 " pdb=" N LEU A 518 " pdb=" C LEU A 518 " pdb=" CB LEU A 518 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LEU C 49 " pdb=" N LEU C 49 " pdb=" C LEU C 49 " pdb=" CB LEU C 49 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE B 693 " pdb=" N ILE B 693 " pdb=" C ILE B 693 " pdb=" CB ILE B 693 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4957 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO A 330 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 142 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO D 143 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 143 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 143 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 321 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO C 322 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.026 5.00e-02 4.00e+02 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2987 2.75 - 3.29: 30435 3.29 - 3.83: 51754 3.83 - 4.36: 59162 4.36 - 4.90: 102765 Nonbonded interactions: 247103 Sorted by model distance: nonbonded pdb=" OG SER D 92 " pdb=" O PRO D 95 " model vdw 2.215 3.040 nonbonded pdb=" OG SER F 92 " pdb=" O PRO F 95 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP C 808 " pdb=" OG SER C 810 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR B 741 " pdb=" O LEU B 962 " model vdw 2.234 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.234 3.040 ... (remaining 247098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 63.630 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.140 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 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 0.054 32379 Z= 0.168 Angle : 0.551 7.566 44100 Z= 0.341 Chirality : 0.042 0.226 4960 Planarity : 0.003 0.062 5697 Dihedral : 9.492 89.173 11593 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Rotamer: Outliers : 5.28 % Allowed : 6.07 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.11), residues: 4025 helix: 0.19 (0.20), residues: 608 sheet: -2.27 (0.15), residues: 933 loop : -3.11 (0.10), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP A 65 HIS 0.003 0.000 HIS C 50 PHE 0.016 0.001 PHE B 515 TYR 0.016 0.001 TYR B 695 ARG 0.002 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.23686 ( 927) hydrogen bonds : angle 8.65821 ( 2625) SS BOND : bond 0.00089 ( 43) SS BOND : angle 0.43647 ( 86) covalent geometry : bond 0.00256 (32336) covalent geometry : angle 0.55149 (44014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 721 time to evaluate : 3.189 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: B 86 PRO cc_start: 0.6887 (Cg_endo) cc_final: 0.6521 (Cg_exo) REVERT: B 224 GLU cc_start: 0.6646 (pm20) cc_final: 0.6104 (mp0) REVERT: B 457 ARG cc_start: -0.2177 (OUTLIER) cc_final: -0.3628 (mtt-85) REVERT: B 610 VAL cc_start: 0.8007 (m) cc_final: 0.7705 (t) REVERT: B 616 ASN cc_start: 0.5731 (t0) cc_final: 0.5335 (t0) REVERT: B 673 SER cc_start: 0.7838 (p) cc_final: 0.7324 (p) REVERT: B 695 TYR cc_start: 0.7202 (p90) cc_final: 0.6917 (p90) REVERT: B 933 LYS cc_start: 0.7428 (mtmm) cc_final: 0.7191 (mtmm) REVERT: B 1002 GLN cc_start: 0.6488 (tp-100) cc_final: 0.6274 (tp-100) REVERT: B 1101 HIS cc_start: 0.7267 (m90) cc_final: 0.6934 (m-70) REVERT: B 1132 ILE cc_start: 0.7992 (tt) cc_final: 0.7767 (pt) REVERT: B 1136 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7314 (p) REVERT: B 1143 PRO cc_start: 0.7552 (Cg_endo) cc_final: 0.7192 (Cg_exo) REVERT: A 55 LEU cc_start: 0.7559 (mm) cc_final: 0.7350 (mm) REVERT: A 190 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.4728 (ttm-80) REVERT: A 326 ILE cc_start: 0.7143 (tp) cc_final: 0.6801 (tp) REVERT: A 603 ASN cc_start: 0.7289 (t0) cc_final: 0.7080 (t0) REVERT: A 673 SER cc_start: 0.7729 (p) cc_final: 0.6952 (t) REVERT: A 773 GLU cc_start: 0.6367 (tt0) cc_final: 0.5928 (tt0) REVERT: A 819 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6709 (mt-10) REVERT: A 904 TYR cc_start: 0.6834 (m-10) cc_final: 0.6440 (m-10) REVERT: A 976 VAL cc_start: 0.8348 (t) cc_final: 0.8080 (m) REVERT: A 983 ARG cc_start: 0.5936 (mpp80) cc_final: 0.5045 (mtp85) REVERT: G 20 VAL cc_start: -0.0568 (OUTLIER) cc_final: -0.1899 (t) REVERT: G 70 MET cc_start: -0.3593 (mtp) cc_final: -0.4545 (mmt) REVERT: C 289 VAL cc_start: 0.7072 (t) cc_final: 0.6765 (t) REVERT: C 663 ASP cc_start: 0.6119 (t0) cc_final: 0.5898 (t0) REVERT: C 737 ASP cc_start: 0.6351 (t0) cc_final: 0.5929 (t0) REVERT: C 747 THR cc_start: 0.7868 (t) cc_final: 0.7495 (p) REVERT: C 816 SER cc_start: 0.7739 (p) cc_final: 0.7522 (p) REVERT: C 902 MET cc_start: 0.6582 (mmm) cc_final: 0.6227 (mmt) REVERT: C 1019 ARG cc_start: 0.6882 (ttm110) cc_final: 0.6618 (ttp80) REVERT: C 1146 ASP cc_start: 0.6264 (p0) cc_final: 0.5637 (m-30) outliers start: 187 outliers final: 65 residues processed: 867 average time/residue: 0.4485 time to fit residues: 612.0676 Evaluate side-chains 624 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 555 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 10.0000 chunk 304 optimal weight: 0.0670 chunk 169 optimal weight: 7.9990 chunk 104 optimal weight: 0.0370 chunk 205 optimal weight: 0.0870 chunk 162 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 234 optimal weight: 0.9990 chunk 365 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 218 GLN B 271 GLN B 282 ASN B 317 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 414 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 519 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 644 GLN B 710 ASN B 784 GLN B 853 GLN B 901 GLN B 913 GLN B 914 ASN B 957 GLN B1010 GLN B1011 GLN B1048 HIS B1125 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN D 38 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 149 GLN D 168 GLN A 88 ASN A 164 ASN A 218 GLN A 239 GLN A 331 ASN A 360 ASN A 409 GLN A 414 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 540 ASN A 563 GLN A 613 GLN A 710 ASN A 901 GLN A 913 GLN A 914 ASN A 949 GLN A 957 GLN A1011 GLN A1048 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN F 38 GLN F 42 GLN F 53 ASN F 102 GLN F 149 GLN C 50 HIS C 88 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 218 GLN C 245 HIS C 334 ASN C 439 ASN C 474 GLN C 540 ASN C 564 GLN C 613 GLN C 690 GLN C 751 ASN C 762 GLN C 901 GLN C 913 GLN C 914 ASN C 949 GLN C 965 GLN C1011 GLN C1119 ASN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.235527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170820 restraints weight = 50009.762| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.27 r_work: 0.3812 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32379 Z= 0.114 Angle : 0.544 11.492 44100 Z= 0.276 Chirality : 0.043 0.198 4960 Planarity : 0.004 0.059 5697 Dihedral : 6.598 69.345 4532 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 4.15 % Allowed : 11.81 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.12), residues: 4025 helix: 1.19 (0.21), residues: 635 sheet: -1.65 (0.16), residues: 930 loop : -2.73 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 112 HIS 0.003 0.001 HIS B 519 PHE 0.037 0.001 PHE C 194 TYR 0.019 0.001 TYR A 495 ARG 0.006 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 927) hydrogen bonds : angle 6.02338 ( 2625) SS BOND : bond 0.00252 ( 43) SS BOND : angle 1.03170 ( 86) covalent geometry : bond 0.00257 (32336) covalent geometry : angle 0.54220 (44014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 590 time to evaluate : 3.311 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 59 PHE cc_start: 0.8201 (m-10) cc_final: 0.7925 (m-10) REVERT: B 86 PRO cc_start: 0.7181 (Cg_endo) cc_final: 0.6969 (Cg_exo) REVERT: B 177 MET cc_start: 0.7372 (mpp) cc_final: 0.6955 (mpp) REVERT: B 233 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6593 (tt) REVERT: B 278 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7731 (ttmt) REVERT: B 280 ASN cc_start: 0.7573 (t0) cc_final: 0.7153 (t0) REVERT: B 307 THR cc_start: 0.8508 (m) cc_final: 0.8193 (p) REVERT: B 317 ASN cc_start: 0.8399 (m-40) cc_final: 0.7921 (m110) REVERT: B 616 ASN cc_start: 0.5979 (t0) cc_final: 0.5483 (t0) REVERT: B 695 TYR cc_start: 0.8204 (p90) cc_final: 0.7613 (p90) REVERT: B 756 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7468 (t80) REVERT: B 765 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7789 (ttm-80) REVERT: B 814 LYS cc_start: 0.8319 (mmtp) cc_final: 0.7827 (mmtm) REVERT: B 921 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8009 (mmmm) REVERT: B 933 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7640 (mtmm) REVERT: B 947 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8272 (mtpp) REVERT: B 965 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8253 (mt0) REVERT: B 977 LEU cc_start: 0.8246 (mp) cc_final: 0.8021 (mp) REVERT: B 1001 LEU cc_start: 0.8525 (tm) cc_final: 0.8251 (tp) REVERT: B 1038 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8123 (mttm) REVERT: B 1136 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8474 (p) REVERT: E 48 MET cc_start: 0.2644 (tpt) cc_final: 0.1680 (mpp) REVERT: A 43 VAL cc_start: 0.8563 (t) cc_final: 0.8319 (m) REVERT: A 47 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8165 (t) REVERT: A 55 LEU cc_start: 0.8594 (mm) cc_final: 0.8354 (mm) REVERT: A 190 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.5751 (ttm-80) REVERT: A 224 GLU cc_start: 0.7330 (pm20) cc_final: 0.7058 (mp0) REVERT: A 280 ASN cc_start: 0.7431 (t0) cc_final: 0.7101 (t0) REVERT: A 326 ILE cc_start: 0.7794 (tp) cc_final: 0.7363 (tp) REVERT: A 410 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4726 (pt) REVERT: A 578 ASP cc_start: 0.8021 (t0) cc_final: 0.7599 (t0) REVERT: A 581 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7829 (p) REVERT: A 603 ASN cc_start: 0.8323 (t0) cc_final: 0.8071 (t0) REVERT: A 719 THR cc_start: 0.8340 (t) cc_final: 0.8021 (p) REVERT: A 773 GLU cc_start: 0.7709 (tt0) cc_final: 0.7490 (tt0) REVERT: A 970 PHE cc_start: 0.7697 (m-80) cc_final: 0.7383 (m-80) REVERT: A 976 VAL cc_start: 0.8624 (t) cc_final: 0.8397 (m) REVERT: A 1029 MET cc_start: 0.8008 (ttm) cc_final: 0.7699 (ttm) REVERT: A 1086 LYS cc_start: 0.7229 (ptpt) cc_final: 0.7028 (mtmm) REVERT: A 1141 LEU cc_start: 0.8957 (tp) cc_final: 0.8628 (tp) REVERT: A 1145 LEU cc_start: 0.8611 (mm) cc_final: 0.8326 (mm) REVERT: G 70 MET cc_start: -0.2117 (mtp) cc_final: -0.3127 (mmt) REVERT: C 136 PHE cc_start: 0.6197 (t80) cc_final: 0.5901 (t80) REVERT: C 675 GLN cc_start: 0.7350 (tp40) cc_final: 0.7102 (tp40) REVERT: C 737 ASP cc_start: 0.7270 (t0) cc_final: 0.7006 (t0) REVERT: C 751 ASN cc_start: 0.7979 (m110) cc_final: 0.7695 (m-40) REVERT: C 755 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7477 (mm-40) REVERT: C 921 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8298 (mmmm) REVERT: C 964 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8297 (mtmm) REVERT: C 1072 GLU cc_start: 0.8511 (pm20) cc_final: 0.8303 (pm20) REVERT: C 1146 ASP cc_start: 0.7995 (p0) cc_final: 0.6647 (m-30) outliers start: 147 outliers final: 90 residues processed: 691 average time/residue: 0.4590 time to fit residues: 505.3479 Evaluate side-chains 631 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 533 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 397 optimal weight: 2.9990 chunk 233 optimal weight: 0.0070 chunk 170 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 277 optimal weight: 50.0000 chunk 201 optimal weight: 3.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 282 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 703 ASN B 777 ASN B1010 GLN B1048 HIS B1101 HIS E 107 ASN D 42 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN A 450 ASN A 563 GLN A 580 GLN A 690 GLN A 777 ASN A 913 GLN A1054 GLN A1074 ASN G 107 ASN F 42 GLN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 710 ASN C1048 HIS C1074 ASN C1125 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.229536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162276 restraints weight = 49088.921| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.45 r_work: 0.3666 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32379 Z= 0.229 Angle : 0.605 13.027 44100 Z= 0.306 Chirality : 0.046 0.170 4960 Planarity : 0.005 0.057 5697 Dihedral : 6.438 67.678 4501 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.66 % Favored : 93.32 % Rotamer: Outliers : 5.00 % Allowed : 12.54 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.12), residues: 4025 helix: 1.25 (0.20), residues: 629 sheet: -1.20 (0.16), residues: 910 loop : -2.54 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 65 HIS 0.009 0.001 HIS C1064 PHE 0.035 0.002 PHE A 797 TYR 0.020 0.002 TYR B 92 ARG 0.006 0.001 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 927) hydrogen bonds : angle 5.57806 ( 2625) SS BOND : bond 0.00367 ( 43) SS BOND : angle 1.17962 ( 86) covalent geometry : bond 0.00526 (32336) covalent geometry : angle 0.60383 (44014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 584 time to evaluate : 3.192 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: B 46 SER cc_start: 0.8653 (t) cc_final: 0.8327 (p) REVERT: B 67 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6913 (t-90) REVERT: B 86 PRO cc_start: 0.7204 (Cg_endo) cc_final: 0.6899 (Cg_exo) REVERT: B 136 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: B 233 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6584 (tt) REVERT: B 238 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6781 (t80) REVERT: B 278 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7730 (ttpt) REVERT: B 304 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8167 (mtmm) REVERT: B 307 THR cc_start: 0.8374 (m) cc_final: 0.8088 (p) REVERT: B 440 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5844 (tmmt) REVERT: B 543 PHE cc_start: 0.7173 (m-10) cc_final: 0.6855 (m-10) REVERT: B 695 TYR cc_start: 0.8174 (p90) cc_final: 0.7667 (p90) REVERT: B 703 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7293 (t0) REVERT: B 707 TYR cc_start: 0.8115 (t80) cc_final: 0.7830 (t80) REVERT: B 814 LYS cc_start: 0.8362 (mmtp) cc_final: 0.7874 (mmtt) REVERT: B 815 ARG cc_start: 0.8354 (mtm110) cc_final: 0.8106 (mtm180) REVERT: B 933 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7709 (mtmm) REVERT: B 947 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8202 (mtpp) REVERT: B 1031 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7563 (mt-10) REVERT: B 1038 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8351 (mttm) REVERT: B 1092 GLU cc_start: 0.7420 (mp0) cc_final: 0.7123 (mp0) REVERT: B 1101 HIS cc_start: 0.8353 (m90) cc_final: 0.8131 (m-70) REVERT: B 1137 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8162 (m) REVERT: E 48 MET cc_start: 0.2478 (tpt) cc_final: 0.1393 (mpp) REVERT: A 190 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.4703 (ttm-80) REVERT: A 192 PHE cc_start: 0.7433 (m-10) cc_final: 0.7208 (m-80) REVERT: A 224 GLU cc_start: 0.6990 (pm20) cc_final: 0.6759 (mp0) REVERT: A 269 TYR cc_start: 0.7757 (m-10) cc_final: 0.7527 (m-10) REVERT: A 280 ASN cc_start: 0.7346 (t0) cc_final: 0.7122 (t0) REVERT: A 410 ILE cc_start: 0.4686 (OUTLIER) cc_final: 0.4439 (pt) REVERT: A 547 THR cc_start: 0.7919 (p) cc_final: 0.7603 (t) REVERT: A 603 ASN cc_start: 0.8526 (t0) cc_final: 0.8253 (t0) REVERT: A 642 VAL cc_start: 0.8714 (t) cc_final: 0.8381 (p) REVERT: A 719 THR cc_start: 0.8225 (t) cc_final: 0.7996 (p) REVERT: A 773 GLU cc_start: 0.7580 (tt0) cc_final: 0.7379 (tt0) REVERT: A 787 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: A 790 LYS cc_start: 0.8493 (mttp) cc_final: 0.8201 (mttp) REVERT: A 819 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 869 MET cc_start: 0.8423 (mtt) cc_final: 0.8150 (mtt) REVERT: A 904 TYR cc_start: 0.8118 (m-10) cc_final: 0.7877 (m-80) REVERT: A 934 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7688 (tp) REVERT: A 947 LYS cc_start: 0.8077 (mptt) cc_final: 0.7870 (mttp) REVERT: A 950 ASP cc_start: 0.7797 (t70) cc_final: 0.7322 (t0) REVERT: A 976 VAL cc_start: 0.8592 (t) cc_final: 0.8313 (m) REVERT: G 70 MET cc_start: -0.2478 (mtp) cc_final: -0.3458 (mmt) REVERT: C 89 ASP cc_start: 0.8192 (m-30) cc_final: 0.7724 (m-30) REVERT: C 287 ASP cc_start: 0.7965 (p0) cc_final: 0.7723 (p0) REVERT: C 568 ASP cc_start: 0.7591 (p0) cc_final: 0.7322 (p0) REVERT: C 569 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7782 (mp) REVERT: C 617 CYS cc_start: 0.6687 (m) cc_final: 0.6388 (m) REVERT: C 675 GLN cc_start: 0.7234 (tp40) cc_final: 0.6960 (tp40) REVERT: C 755 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7164 (mm-40) REVERT: C 765 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7669 (ttp-170) REVERT: C 900 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7901 (mtt) REVERT: C 904 TYR cc_start: 0.7803 (m-10) cc_final: 0.7315 (m-10) REVERT: C 921 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8260 (mmmm) REVERT: C 964 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8306 (mtmm) REVERT: C 970 PHE cc_start: 0.8423 (m-80) cc_final: 0.8215 (m-80) REVERT: C 973 ILE cc_start: 0.8556 (pt) cc_final: 0.8300 (mm) REVERT: C 1002 GLN cc_start: 0.7920 (tp40) cc_final: 0.7699 (tp40) outliers start: 177 outliers final: 120 residues processed: 703 average time/residue: 0.4349 time to fit residues: 482.2147 Evaluate side-chains 662 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 527 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 371 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 401 optimal weight: 0.7980 chunk 309 optimal weight: 0.0020 chunk 272 optimal weight: 50.0000 chunk 218 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN D 42 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN A 317 ASN A 448 ASN A 563 GLN A 580 GLN A 913 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1074 ASN F 42 GLN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.230322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165044 restraints weight = 50939.215| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.11 r_work: 0.3698 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32379 Z= 0.116 Angle : 0.535 11.721 44100 Z= 0.266 Chirality : 0.043 0.175 4960 Planarity : 0.004 0.058 5697 Dihedral : 6.224 64.780 4499 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 4.52 % Allowed : 13.73 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 4025 helix: 1.60 (0.21), residues: 631 sheet: -1.14 (0.16), residues: 930 loop : -2.33 (0.11), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 112 HIS 0.010 0.001 HIS B 207 PHE 0.029 0.001 PHE A 797 TYR 0.027 0.001 TYR B 265 ARG 0.004 0.000 ARG C 995 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 927) hydrogen bonds : angle 5.23545 ( 2625) SS BOND : bond 0.00255 ( 43) SS BOND : angle 1.17159 ( 86) covalent geometry : bond 0.00269 (32336) covalent geometry : angle 0.53303 (44014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 546 time to evaluate : 3.356 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 46 SER cc_start: 0.8783 (t) cc_final: 0.8503 (p) REVERT: B 64 THR cc_start: 0.8323 (m) cc_final: 0.7765 (t) REVERT: B 86 PRO cc_start: 0.7458 (Cg_endo) cc_final: 0.7166 (Cg_exo) REVERT: B 122 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6429 (m-40) REVERT: B 131 VAL cc_start: 0.7321 (OUTLIER) cc_final: 0.7098 (m) REVERT: B 191 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 233 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6502 (tt) REVERT: B 238 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6999 (t80) REVERT: B 304 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8307 (mtmm) REVERT: B 307 THR cc_start: 0.8537 (m) cc_final: 0.8272 (p) REVERT: B 440 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5860 (tmmt) REVERT: B 586 ASP cc_start: 0.8094 (t0) cc_final: 0.7809 (t0) REVERT: B 615 VAL cc_start: 0.8230 (t) cc_final: 0.7697 (m) REVERT: B 695 TYR cc_start: 0.8321 (p90) cc_final: 0.7932 (p90) REVERT: B 703 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7435 (t0) REVERT: B 707 TYR cc_start: 0.8314 (t80) cc_final: 0.8000 (t80) REVERT: B 756 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7772 (t80) REVERT: B 762 GLN cc_start: 0.8154 (mt0) cc_final: 0.7853 (mt0) REVERT: B 811 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7404 (mmtm) REVERT: B 814 LYS cc_start: 0.8373 (mmtp) cc_final: 0.7835 (mmtt) REVERT: B 815 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7938 (mtm110) REVERT: B 933 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7709 (mtmm) REVERT: B 947 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8305 (mtpp) REVERT: B 1001 LEU cc_start: 0.8633 (tm) cc_final: 0.8299 (tp) REVERT: B 1092 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: B 1101 HIS cc_start: 0.8469 (m90) cc_final: 0.8253 (m-70) REVERT: B 1136 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (p) REVERT: E 37 VAL cc_start: 0.4806 (OUTLIER) cc_final: 0.4395 (t) REVERT: E 48 MET cc_start: 0.2570 (tpt) cc_final: 0.1435 (mpp) REVERT: A 47 SER cc_start: 0.8523 (t) cc_final: 0.8289 (p) REVERT: A 54 ASP cc_start: 0.7921 (t0) cc_final: 0.7651 (t70) REVERT: A 190 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.4896 (ttm-80) REVERT: A 192 PHE cc_start: 0.7666 (m-10) cc_final: 0.7209 (m-80) REVERT: A 224 GLU cc_start: 0.7125 (pm20) cc_final: 0.6875 (mp0) REVERT: A 239 GLN cc_start: 0.7583 (tp-100) cc_final: 0.7224 (tp-100) REVERT: A 280 ASN cc_start: 0.7470 (t0) cc_final: 0.7224 (t0) REVERT: A 410 ILE cc_start: 0.4892 (OUTLIER) cc_final: 0.4654 (pt) REVERT: A 547 THR cc_start: 0.8026 (p) cc_final: 0.7742 (t) REVERT: A 603 ASN cc_start: 0.8591 (t0) cc_final: 0.8326 (t0) REVERT: A 642 VAL cc_start: 0.8790 (t) cc_final: 0.8471 (p) REVERT: A 719 THR cc_start: 0.8259 (t) cc_final: 0.8039 (p) REVERT: A 790 LYS cc_start: 0.8628 (mttp) cc_final: 0.8356 (mttp) REVERT: A 869 MET cc_start: 0.8624 (mtt) cc_final: 0.8377 (mtt) REVERT: A 904 TYR cc_start: 0.8221 (m-10) cc_final: 0.7943 (m-80) REVERT: A 947 LYS cc_start: 0.8153 (mptt) cc_final: 0.7931 (mttp) REVERT: A 976 VAL cc_start: 0.8573 (t) cc_final: 0.8261 (m) REVERT: A 1139 ASP cc_start: 0.8265 (t70) cc_final: 0.7689 (p0) REVERT: G 70 MET cc_start: -0.2216 (mtp) cc_final: -0.3517 (mmt) REVERT: C 35 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7702 (mtp180) REVERT: C 237 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7632 (mtp-110) REVERT: C 568 ASP cc_start: 0.7747 (p0) cc_final: 0.7459 (p0) REVERT: C 569 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7793 (mp) REVERT: C 675 GLN cc_start: 0.7406 (tp40) cc_final: 0.7119 (tp40) REVERT: C 711 SER cc_start: 0.8245 (p) cc_final: 0.8032 (t) REVERT: C 737 ASP cc_start: 0.7535 (t0) cc_final: 0.7261 (t70) REVERT: C 755 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7429 (mm-40) REVERT: C 765 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7886 (ttp-170) REVERT: C 900 MET cc_start: 0.8317 (mtp) cc_final: 0.8044 (mtt) REVERT: C 902 MET cc_start: 0.8006 (mmt) cc_final: 0.7643 (mmt) REVERT: C 904 TYR cc_start: 0.7869 (m-10) cc_final: 0.7333 (m-10) REVERT: C 921 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8347 (mmmm) REVERT: C 964 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8419 (mtmm) REVERT: C 1002 GLN cc_start: 0.8150 (tp40) cc_final: 0.7852 (mm-40) REVERT: C 1138 TYR cc_start: 0.7923 (t80) cc_final: 0.7398 (t80) outliers start: 160 outliers final: 114 residues processed: 652 average time/residue: 0.4422 time to fit residues: 457.2592 Evaluate side-chains 648 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 520 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 338 optimal weight: 50.0000 chunk 255 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 311 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN D 42 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1058 HIS A1074 ASN C 50 HIS ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.226487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157896 restraints weight = 48636.716| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.27 r_work: 0.3628 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 32379 Z= 0.242 Angle : 0.603 14.727 44100 Z= 0.301 Chirality : 0.046 0.213 4960 Planarity : 0.005 0.064 5697 Dihedral : 6.379 65.468 4497 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.01 % Favored : 92.97 % Rotamer: Outliers : 5.17 % Allowed : 13.76 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 4025 helix: 1.43 (0.20), residues: 633 sheet: -0.93 (0.17), residues: 902 loop : -2.30 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 105 HIS 0.020 0.001 HIS B 207 PHE 0.032 0.002 PHE A 797 TYR 0.026 0.001 TYR B 265 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 927) hydrogen bonds : angle 5.20327 ( 2625) SS BOND : bond 0.00421 ( 43) SS BOND : angle 1.32469 ( 86) covalent geometry : bond 0.00561 (32336) covalent geometry : angle 0.60084 (44014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 552 time to evaluate : 3.044 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 46 SER cc_start: 0.8791 (t) cc_final: 0.8549 (p) REVERT: B 52 THR cc_start: 0.8561 (t) cc_final: 0.8217 (p) REVERT: B 64 THR cc_start: 0.8384 (m) cc_final: 0.7932 (t) REVERT: B 233 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6689 (tt) REVERT: B 238 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7032 (t80) REVERT: B 304 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8344 (mtmm) REVERT: B 307 THR cc_start: 0.8586 (m) cc_final: 0.8343 (p) REVERT: B 543 PHE cc_start: 0.7488 (m-10) cc_final: 0.7238 (m-10) REVERT: B 586 ASP cc_start: 0.8066 (t0) cc_final: 0.7802 (t0) REVERT: B 695 TYR cc_start: 0.8338 (p90) cc_final: 0.7959 (p90) REVERT: B 703 ASN cc_start: 0.7882 (t0) cc_final: 0.7426 (t0) REVERT: B 707 TYR cc_start: 0.8327 (t80) cc_final: 0.8088 (t80) REVERT: B 762 GLN cc_start: 0.8207 (mt0) cc_final: 0.7935 (mt0) REVERT: B 811 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7603 (mmtt) REVERT: B 814 LYS cc_start: 0.8424 (mmtp) cc_final: 0.7920 (mmtt) REVERT: B 904 TYR cc_start: 0.8226 (m-10) cc_final: 0.7993 (m-10) REVERT: B 921 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8375 (mmmt) REVERT: B 933 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7880 (mtmm) REVERT: B 947 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8372 (mtpp) REVERT: B 1084 ASP cc_start: 0.8380 (m-30) cc_final: 0.8064 (m-30) REVERT: B 1092 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: B 1136 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8479 (p) REVERT: E 48 MET cc_start: 0.1648 (tpt) cc_final: 0.0931 (mpp) REVERT: A 224 GLU cc_start: 0.7305 (pm20) cc_final: 0.7094 (mp0) REVERT: A 239 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7320 (tp-100) REVERT: A 242 LEU cc_start: 0.8062 (mp) cc_final: 0.7814 (mp) REVERT: A 326 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7220 (tp) REVERT: A 410 ILE cc_start: 0.5251 (OUTLIER) cc_final: 0.5018 (pt) REVERT: A 543 PHE cc_start: 0.8396 (m-10) cc_final: 0.8163 (m-10) REVERT: A 547 THR cc_start: 0.8134 (p) cc_final: 0.7886 (t) REVERT: A 586 ASP cc_start: 0.7998 (t0) cc_final: 0.7675 (t0) REVERT: A 619 GLU cc_start: 0.8424 (mp0) cc_final: 0.8061 (mp0) REVERT: A 787 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: A 790 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8344 (mttp) REVERT: A 819 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 869 MET cc_start: 0.8643 (mtt) cc_final: 0.8426 (mtt) REVERT: A 904 TYR cc_start: 0.8445 (m-10) cc_final: 0.8164 (m-80) REVERT: A 947 LYS cc_start: 0.8288 (mptt) cc_final: 0.8042 (mttp) REVERT: A 950 ASP cc_start: 0.8063 (t70) cc_final: 0.7646 (t0) REVERT: A 976 VAL cc_start: 0.8647 (t) cc_final: 0.8314 (m) REVERT: A 981 LEU cc_start: 0.8785 (mt) cc_final: 0.8558 (mt) REVERT: A 1139 ASP cc_start: 0.8260 (t70) cc_final: 0.7753 (p0) REVERT: G 70 MET cc_start: -0.2422 (mtp) cc_final: -0.3358 (mmt) REVERT: C 89 ASP cc_start: 0.8372 (m-30) cc_final: 0.7840 (m-30) REVERT: C 127 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.6922 (m) REVERT: C 130 LYS cc_start: 0.7939 (tppt) cc_final: 0.7352 (tppt) REVERT: C 177 MET cc_start: 0.6852 (mpp) cc_final: 0.5817 (mmm) REVERT: C 231 ILE cc_start: 0.8214 (mm) cc_final: 0.7997 (mp) REVERT: C 239 GLN cc_start: 0.8175 (tp40) cc_final: 0.7797 (tm-30) REVERT: C 281 GLU cc_start: 0.7903 (pp20) cc_final: 0.7439 (pp20) REVERT: C 321 GLN cc_start: 0.7804 (mp10) cc_final: 0.7554 (mp10) REVERT: C 537 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8542 (ttpp) REVERT: C 569 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8001 (mp) REVERT: C 675 GLN cc_start: 0.7538 (tp40) cc_final: 0.7234 (tp40) REVERT: C 765 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7985 (ttp-170) REVERT: C 900 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: C 921 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8419 (mmmm) REVERT: C 945 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8310 (mp) REVERT: C 957 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 964 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8504 (mtmm) REVERT: C 973 ILE cc_start: 0.8659 (pt) cc_final: 0.8433 (mm) REVERT: C 1019 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.7924 (ttp-170) outliers start: 183 outliers final: 137 residues processed: 678 average time/residue: 0.4472 time to fit residues: 477.6964 Evaluate side-chains 678 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 528 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 360 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 chunk 287 optimal weight: 40.0000 chunk 79 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 chunk 279 optimal weight: 50.0000 chunk 350 optimal weight: 0.1980 chunk 333 optimal weight: 50.0000 chunk 262 optimal weight: 7.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN B 992 GLN B1101 HIS D 42 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 913 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN F 42 GLN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.224797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156056 restraints weight = 48687.551| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.40 r_work: 0.3569 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 32379 Z= 0.324 Angle : 0.665 20.564 44100 Z= 0.334 Chirality : 0.048 0.182 4960 Planarity : 0.005 0.061 5697 Dihedral : 6.589 64.038 4495 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.37 % Allowed : 14.10 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 4025 helix: 1.05 (0.20), residues: 644 sheet: -0.95 (0.17), residues: 937 loop : -2.23 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 105 HIS 0.010 0.001 HIS C1064 PHE 0.036 0.002 PHE A 797 TYR 0.028 0.002 TYR A 269 ARG 0.010 0.001 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 927) hydrogen bonds : angle 5.29158 ( 2625) SS BOND : bond 0.00440 ( 43) SS BOND : angle 1.42435 ( 86) covalent geometry : bond 0.00750 (32336) covalent geometry : angle 0.66310 (44014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 555 time to evaluate : 3.177 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: B 46 SER cc_start: 0.8600 (t) cc_final: 0.8343 (p) REVERT: B 52 THR cc_start: 0.8419 (t) cc_final: 0.8068 (p) REVERT: B 307 THR cc_start: 0.8453 (m) cc_final: 0.8196 (p) REVERT: B 335 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6549 (tm) REVERT: B 543 PHE cc_start: 0.7284 (m-10) cc_final: 0.7041 (m-10) REVERT: B 586 ASP cc_start: 0.7622 (t0) cc_final: 0.7413 (t0) REVERT: B 695 TYR cc_start: 0.8208 (p90) cc_final: 0.7784 (p90) REVERT: B 711 SER cc_start: 0.8254 (t) cc_final: 0.8032 (t) REVERT: B 737 ASP cc_start: 0.7729 (t0) cc_final: 0.7378 (m-30) REVERT: B 756 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7776 (t80) REVERT: B 762 GLN cc_start: 0.7974 (mt0) cc_final: 0.7693 (mt0) REVERT: B 792 PRO cc_start: 0.8234 (Cg_exo) cc_final: 0.7994 (Cg_endo) REVERT: B 811 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7575 (mmtt) REVERT: B 814 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7765 (mmtt) REVERT: B 815 ARG cc_start: 0.8375 (mtm110) cc_final: 0.8163 (mtm110) REVERT: B 921 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8280 (mmmt) REVERT: B 933 LYS cc_start: 0.8347 (mtmm) cc_final: 0.8075 (mtmm) REVERT: B 947 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8207 (mtpp) REVERT: B 957 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7304 (tm-30) REVERT: B 983 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7740 (mtp-110) REVERT: B 1084 ASP cc_start: 0.8129 (m-30) cc_final: 0.7869 (m-30) REVERT: B 1092 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 1136 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8356 (p) REVERT: E 37 VAL cc_start: 0.4725 (OUTLIER) cc_final: 0.4319 (t) REVERT: E 48 MET cc_start: 0.2458 (tpt) cc_final: 0.1342 (mpp) REVERT: A 47 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8439 (t) REVERT: A 54 ASP cc_start: 0.7567 (t0) cc_final: 0.7313 (t70) REVERT: A 224 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: A 242 LEU cc_start: 0.8109 (mp) cc_final: 0.7862 (mp) REVERT: A 269 TYR cc_start: 0.8071 (m-10) cc_final: 0.7794 (m-10) REVERT: A 280 ASN cc_start: 0.7240 (t0) cc_final: 0.6997 (t0) REVERT: A 281 GLU cc_start: 0.6306 (pp20) cc_final: 0.5885 (pp20) REVERT: A 410 ILE cc_start: 0.5019 (OUTLIER) cc_final: 0.4776 (pt) REVERT: A 547 THR cc_start: 0.8133 (p) cc_final: 0.7856 (t) REVERT: A 586 ASP cc_start: 0.7635 (t0) cc_final: 0.7334 (t0) REVERT: A 750 SER cc_start: 0.8486 (m) cc_final: 0.8261 (p) REVERT: A 787 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: A 790 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8132 (mttp) REVERT: A 819 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 869 MET cc_start: 0.8400 (mtt) cc_final: 0.8166 (mtt) REVERT: A 904 TYR cc_start: 0.8413 (m-10) cc_final: 0.8108 (m-80) REVERT: A 934 ILE cc_start: 0.7996 (tp) cc_final: 0.7770 (tp) REVERT: A 976 VAL cc_start: 0.8555 (t) cc_final: 0.8248 (m) REVERT: A 984 LEU cc_start: 0.7943 (mm) cc_final: 0.7732 (mp) REVERT: A 1073 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7657 (ttpp) REVERT: A 1139 ASP cc_start: 0.7992 (t70) cc_final: 0.7516 (p0) REVERT: G 70 MET cc_start: -0.1820 (mtp) cc_final: -0.3721 (mmt) REVERT: C 35 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7891 (mtp-110) REVERT: C 54 ASP cc_start: 0.7044 (t0) cc_final: 0.6830 (t70) REVERT: C 89 ASP cc_start: 0.8206 (m-30) cc_final: 0.7640 (m-30) REVERT: C 127 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7035 (m) REVERT: C 130 LYS cc_start: 0.7659 (tppt) cc_final: 0.7152 (tppt) REVERT: C 177 MET cc_start: 0.7059 (mpp) cc_final: 0.6247 (mmm) REVERT: C 190 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6688 (tpm-80) REVERT: C 224 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6461 (mm-30) REVERT: C 231 ILE cc_start: 0.8342 (mm) cc_final: 0.8136 (mp) REVERT: C 287 ASP cc_start: 0.7854 (p0) cc_final: 0.7589 (p0) REVERT: C 321 GLN cc_start: 0.7560 (mp10) cc_final: 0.7291 (mp10) REVERT: C 569 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8119 (mp) REVERT: C 591 SER cc_start: 0.8574 (t) cc_final: 0.8283 (p) REVERT: C 615 VAL cc_start: 0.8277 (t) cc_final: 0.8077 (m) REVERT: C 675 GLN cc_start: 0.7247 (tp40) cc_final: 0.6939 (tp40) REVERT: C 779 GLN cc_start: 0.8444 (tp40) cc_final: 0.7877 (tp40) REVERT: C 900 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (mtt) REVERT: C 921 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8313 (mmmm) REVERT: C 945 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8190 (mp) REVERT: C 957 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7817 (tm-30) REVERT: C 964 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8369 (mtmm) REVERT: C 966 LEU cc_start: 0.8730 (mt) cc_final: 0.8446 (mp) REVERT: C 1019 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7845 (ttp-170) outliers start: 190 outliers final: 139 residues processed: 683 average time/residue: 0.4953 time to fit residues: 542.8140 Evaluate side-chains 695 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 541 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 278 optimal weight: 50.0000 chunk 259 optimal weight: 0.0030 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 323 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 322 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 703 ASN B 901 GLN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 563 GLN A1074 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.227884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.161649 restraints weight = 50236.170| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.07 r_work: 0.3654 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32379 Z= 0.112 Angle : 0.565 14.290 44100 Z= 0.280 Chirality : 0.043 0.184 4960 Planarity : 0.004 0.062 5697 Dihedral : 6.169 62.184 4489 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.29 % Allowed : 15.62 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 4025 helix: 1.75 (0.21), residues: 624 sheet: -0.71 (0.17), residues: 910 loop : -2.10 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 112 HIS 0.012 0.001 HIS B 207 PHE 0.032 0.001 PHE A 797 TYR 0.017 0.001 TYR B 265 ARG 0.010 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 927) hydrogen bonds : angle 4.95685 ( 2625) SS BOND : bond 0.00251 ( 43) SS BOND : angle 1.33788 ( 86) covalent geometry : bond 0.00257 (32336) covalent geometry : angle 0.56289 (44014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 543 time to evaluate : 3.219 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: B 105 TRP cc_start: 0.8083 (m-90) cc_final: 0.7734 (m-90) REVERT: B 233 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6584 (tt) REVERT: B 238 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7210 (t80) REVERT: B 305 SER cc_start: 0.8851 (p) cc_final: 0.8636 (m) REVERT: B 307 THR cc_start: 0.8564 (m) cc_final: 0.8308 (p) REVERT: B 335 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6631 (tm) REVERT: B 543 PHE cc_start: 0.7401 (m-10) cc_final: 0.7179 (m-10) REVERT: B 586 ASP cc_start: 0.7961 (t0) cc_final: 0.7737 (t70) REVERT: B 675 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7482 (tp40) REVERT: B 695 TYR cc_start: 0.8320 (p90) cc_final: 0.8029 (p90) REVERT: B 703 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7452 (t0) REVERT: B 711 SER cc_start: 0.8201 (t) cc_final: 0.7998 (t) REVERT: B 737 ASP cc_start: 0.7748 (t0) cc_final: 0.7417 (m-30) REVERT: B 756 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 792 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.7968 (Cg_endo) REVERT: B 811 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7648 (mmtt) REVERT: B 814 LYS cc_start: 0.8381 (mmtp) cc_final: 0.7865 (mmtt) REVERT: B 815 ARG cc_start: 0.8414 (mtm110) cc_final: 0.7963 (mtm110) REVERT: B 904 TYR cc_start: 0.8382 (m-10) cc_final: 0.8103 (m-10) REVERT: B 921 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8345 (mmmt) REVERT: B 933 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7791 (mtmm) REVERT: B 935 GLN cc_start: 0.7933 (tt0) cc_final: 0.7690 (tt0) REVERT: B 947 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8300 (mtpp) REVERT: B 957 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 983 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7987 (mtp-110) REVERT: B 1084 ASP cc_start: 0.8432 (m-30) cc_final: 0.8102 (m-30) REVERT: B 1092 GLU cc_start: 0.7925 (mp0) cc_final: 0.7646 (mp0) REVERT: B 1127 ASP cc_start: 0.8239 (t0) cc_final: 0.7693 (t0) REVERT: E 37 VAL cc_start: 0.4842 (OUTLIER) cc_final: 0.4416 (t) REVERT: E 48 MET cc_start: 0.1686 (tpt) cc_final: 0.0874 (mpp) REVERT: A 31 ASN cc_start: 0.7437 (p0) cc_final: 0.6804 (p0) REVERT: A 35 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7859 (mmm-85) REVERT: A 54 ASP cc_start: 0.7771 (t0) cc_final: 0.7526 (t70) REVERT: A 55 LEU cc_start: 0.8714 (mp) cc_final: 0.8503 (mm) REVERT: A 221 SER cc_start: 0.8056 (p) cc_final: 0.7744 (p) REVERT: A 242 LEU cc_start: 0.7967 (mp) cc_final: 0.7710 (mp) REVERT: A 280 ASN cc_start: 0.7414 (t0) cc_final: 0.7191 (t0) REVERT: A 281 GLU cc_start: 0.6561 (pp20) cc_final: 0.5846 (pp20) REVERT: A 317 ASN cc_start: 0.8274 (m-40) cc_final: 0.7875 (m110) REVERT: A 410 ILE cc_start: 0.5151 (OUTLIER) cc_final: 0.4900 (pt) REVERT: A 543 PHE cc_start: 0.8377 (m-10) cc_final: 0.8171 (m-10) REVERT: A 547 THR cc_start: 0.8142 (p) cc_final: 0.7887 (t) REVERT: A 586 ASP cc_start: 0.7957 (t0) cc_final: 0.7645 (t0) REVERT: A 619 GLU cc_start: 0.8434 (mp0) cc_final: 0.8213 (mp0) REVERT: A 642 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 787 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: A 904 TYR cc_start: 0.8442 (m-10) cc_final: 0.8160 (m-80) REVERT: A 976 VAL cc_start: 0.8608 (t) cc_final: 0.8255 (m) REVERT: A 984 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7731 (mp) REVERT: A 1139 ASP cc_start: 0.8165 (t70) cc_final: 0.7695 (p0) REVERT: G 70 MET cc_start: -0.2412 (mtp) cc_final: -0.3645 (mmt) REVERT: C 35 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7901 (mtp180) REVERT: C 54 ASP cc_start: 0.7217 (t0) cc_final: 0.7011 (t70) REVERT: C 127 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.7047 (m) REVERT: C 130 LYS cc_start: 0.7787 (tppt) cc_final: 0.7331 (tppt) REVERT: C 177 MET cc_start: 0.7020 (mpp) cc_final: 0.5953 (mmm) REVERT: C 190 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6532 (tpm-80) REVERT: C 239 GLN cc_start: 0.8197 (tp40) cc_final: 0.7663 (tm-30) REVERT: C 287 ASP cc_start: 0.7814 (p0) cc_final: 0.7492 (p0) REVERT: C 321 GLN cc_start: 0.7761 (mp10) cc_final: 0.7516 (mp10) REVERT: C 455 LEU cc_start: 0.2219 (OUTLIER) cc_final: 0.1894 (tp) REVERT: C 569 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8044 (mp) REVERT: C 591 SER cc_start: 0.8679 (t) cc_final: 0.8422 (p) REVERT: C 675 GLN cc_start: 0.7546 (tp40) cc_final: 0.7194 (tp40) REVERT: C 762 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7806 (mm-40) REVERT: C 779 GLN cc_start: 0.8479 (tp40) cc_final: 0.7998 (tp40) REVERT: C 821 LEU cc_start: 0.8209 (tt) cc_final: 0.7953 (tp) REVERT: C 856 ASN cc_start: 0.7623 (m110) cc_final: 0.7359 (m-40) REVERT: C 900 MET cc_start: 0.8374 (mtp) cc_final: 0.8133 (mtt) REVERT: C 921 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8347 (mmmm) REVERT: C 957 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8124 (tm-30) REVERT: C 964 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8482 (mtmm) REVERT: C 966 LEU cc_start: 0.8758 (mt) cc_final: 0.8482 (mp) REVERT: C 1019 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.7914 (ttp-110) REVERT: C 1036 GLN cc_start: 0.7905 (tp40) cc_final: 0.7333 (tt0) REVERT: C 1038 LYS cc_start: 0.8558 (mttp) cc_final: 0.8237 (mmmm) REVERT: C 1127 ASP cc_start: 0.7438 (m-30) cc_final: 0.7232 (m-30) REVERT: C 1136 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8492 (p) outliers start: 152 outliers final: 117 residues processed: 642 average time/residue: 0.4335 time to fit residues: 437.7215 Evaluate side-chains 657 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 524 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 106 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 374 optimal weight: 0.0270 chunk 352 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 299 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 114 optimal weight: 50.0000 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1010 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1074 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.226429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.159893 restraints weight = 50451.002| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.48 r_work: 0.3602 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32379 Z= 0.190 Angle : 0.587 12.868 44100 Z= 0.294 Chirality : 0.044 0.191 4960 Planarity : 0.005 0.060 5697 Dihedral : 6.182 63.404 4486 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.52 % Allowed : 15.51 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 4025 helix: 1.63 (0.21), residues: 635 sheet: -0.68 (0.17), residues: 935 loop : -2.03 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 112 HIS 0.009 0.001 HIS B 207 PHE 0.034 0.002 PHE A 797 TYR 0.018 0.001 TYR A 917 ARG 0.009 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 927) hydrogen bonds : angle 4.93405 ( 2625) SS BOND : bond 0.00296 ( 43) SS BOND : angle 1.38305 ( 86) covalent geometry : bond 0.00444 (32336) covalent geometry : angle 0.58464 (44014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 520 time to evaluate : 3.422 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: B 52 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8090 (p) REVERT: B 233 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6606 (tt) REVERT: B 280 ASN cc_start: 0.7727 (t0) cc_final: 0.7475 (t0) REVERT: B 281 GLU cc_start: 0.7352 (pp20) cc_final: 0.6909 (pp20) REVERT: B 305 SER cc_start: 0.8744 (p) cc_final: 0.8533 (m) REVERT: B 307 THR cc_start: 0.8510 (m) cc_final: 0.8212 (p) REVERT: B 543 PHE cc_start: 0.7218 (m-10) cc_final: 0.6578 (m-10) REVERT: B 703 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7246 (t0) REVERT: B 711 SER cc_start: 0.8196 (t) cc_final: 0.7992 (t) REVERT: B 737 ASP cc_start: 0.7696 (t0) cc_final: 0.7356 (m-30) REVERT: B 756 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 762 GLN cc_start: 0.7904 (mt0) cc_final: 0.7593 (mt0) REVERT: B 811 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7566 (mmtt) REVERT: B 814 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7732 (mmtt) REVERT: B 815 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7886 (mtm110) REVERT: B 904 TYR cc_start: 0.8235 (m-10) cc_final: 0.7993 (m-10) REVERT: B 933 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7823 (mtmm) REVERT: B 947 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8188 (mtpp) REVERT: B 957 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 983 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7748 (mtp-110) REVERT: B 1017 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7626 (tm-30) REVERT: B 1038 LYS cc_start: 0.8594 (mmmm) cc_final: 0.8369 (mmtp) REVERT: B 1084 ASP cc_start: 0.8190 (m-30) cc_final: 0.7971 (m-30) REVERT: B 1092 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: B 1127 ASP cc_start: 0.8048 (t0) cc_final: 0.7417 (t0) REVERT: E 37 VAL cc_start: 0.4783 (OUTLIER) cc_final: 0.4410 (t) REVERT: E 48 MET cc_start: 0.2043 (tpt) cc_final: 0.0989 (mpp) REVERT: A 54 ASP cc_start: 0.7572 (t0) cc_final: 0.7284 (t70) REVERT: A 130 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7391 (ttmt) REVERT: A 242 LEU cc_start: 0.7969 (mp) cc_final: 0.7701 (mp) REVERT: A 269 TYR cc_start: 0.7902 (m-10) cc_final: 0.7659 (m-10) REVERT: A 280 ASN cc_start: 0.7279 (t0) cc_final: 0.7051 (t0) REVERT: A 281 GLU cc_start: 0.6390 (pp20) cc_final: 0.5678 (pp20) REVERT: A 317 ASN cc_start: 0.8188 (m-40) cc_final: 0.7777 (m110) REVERT: A 410 ILE cc_start: 0.4853 (OUTLIER) cc_final: 0.4605 (pt) REVERT: A 543 PHE cc_start: 0.8284 (m-10) cc_final: 0.8074 (m-10) REVERT: A 547 THR cc_start: 0.8130 (p) cc_final: 0.7829 (t) REVERT: A 586 ASP cc_start: 0.7694 (t0) cc_final: 0.7383 (t0) REVERT: A 642 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 787 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: A 790 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8063 (mttp) REVERT: A 904 TYR cc_start: 0.8392 (m-10) cc_final: 0.8080 (m-80) REVERT: A 976 VAL cc_start: 0.8519 (t) cc_final: 0.8196 (m) REVERT: A 984 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 1039 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8391 (mtp180) REVERT: A 1073 LYS cc_start: 0.7819 (ttpp) cc_final: 0.7610 (ttpp) REVERT: A 1139 ASP cc_start: 0.7974 (t70) cc_final: 0.7529 (p0) REVERT: G 48 MET cc_start: 0.2917 (mtm) cc_final: 0.2162 (mtp) REVERT: G 70 MET cc_start: -0.2993 (mtp) cc_final: -0.3961 (mmt) REVERT: C 54 ASP cc_start: 0.6972 (t0) cc_final: 0.6593 (t70) REVERT: C 130 LYS cc_start: 0.7566 (tppt) cc_final: 0.7050 (tppt) REVERT: C 239 GLN cc_start: 0.8035 (tp40) cc_final: 0.7611 (tm-30) REVERT: C 281 GLU cc_start: 0.7558 (pp20) cc_final: 0.7155 (pp20) REVERT: C 287 ASP cc_start: 0.7402 (p0) cc_final: 0.7106 (p0) REVERT: C 321 GLN cc_start: 0.7504 (mp10) cc_final: 0.7233 (mp10) REVERT: C 455 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.1869 (tp) REVERT: C 535 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8451 (mmtt) REVERT: C 591 SER cc_start: 0.8582 (t) cc_final: 0.8287 (p) REVERT: C 675 GLN cc_start: 0.7255 (tp40) cc_final: 0.6923 (tp40) REVERT: C 726 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8469 (mt) REVERT: C 745 ASP cc_start: 0.7569 (m-30) cc_final: 0.7072 (p0) REVERT: C 779 GLN cc_start: 0.8384 (tp40) cc_final: 0.7816 (tp40) REVERT: C 856 ASN cc_start: 0.7454 (m110) cc_final: 0.7152 (m-40) REVERT: C 900 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7986 (mtt) REVERT: C 957 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7828 (tm-30) REVERT: C 964 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8350 (mtmm) REVERT: C 1019 ARG cc_start: 0.8054 (ttp-110) cc_final: 0.7731 (ttp-110) REVERT: C 1036 GLN cc_start: 0.7834 (tp40) cc_final: 0.7539 (tt0) REVERT: C 1038 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8054 (mmmm) REVERT: C 1072 GLU cc_start: 0.8105 (pm20) cc_final: 0.7892 (pm20) REVERT: C 1127 ASP cc_start: 0.7228 (m-30) cc_final: 0.6879 (m-30) REVERT: C 1136 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8408 (p) outliers start: 160 outliers final: 127 residues processed: 626 average time/residue: 0.4517 time to fit residues: 443.4072 Evaluate side-chains 662 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 519 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 397 optimal weight: 0.8980 chunk 281 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 321 optimal weight: 0.5980 chunk 214 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 344 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN A1074 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 992 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.227185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161092 restraints weight = 50238.602| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.37 r_work: 0.3625 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32379 Z= 0.134 Angle : 0.563 12.222 44100 Z= 0.280 Chirality : 0.043 0.156 4960 Planarity : 0.004 0.060 5697 Dihedral : 5.940 64.719 4479 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.44 % Allowed : 15.93 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 4025 helix: 1.83 (0.21), residues: 628 sheet: -0.56 (0.17), residues: 941 loop : -1.96 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 112 HIS 0.019 0.001 HIS B 207 PHE 0.043 0.002 PHE B 194 TYR 0.018 0.001 TYR B 92 ARG 0.009 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 927) hydrogen bonds : angle 4.83015 ( 2625) SS BOND : bond 0.00245 ( 43) SS BOND : angle 1.21495 ( 86) covalent geometry : bond 0.00313 (32336) covalent geometry : angle 0.56131 (44014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 519 time to evaluate : 3.190 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: B 52 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8101 (p) REVERT: B 233 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6528 (tt) REVERT: B 238 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7182 (t80) REVERT: B 281 GLU cc_start: 0.7439 (pp20) cc_final: 0.7161 (pp20) REVERT: B 305 SER cc_start: 0.8760 (p) cc_final: 0.8536 (m) REVERT: B 307 THR cc_start: 0.8460 (m) cc_final: 0.8150 (p) REVERT: B 695 TYR cc_start: 0.8191 (p90) cc_final: 0.7780 (p90) REVERT: B 737 ASP cc_start: 0.7638 (t0) cc_final: 0.7349 (m-30) REVERT: B 756 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 811 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7694 (mmtt) REVERT: B 814 LYS cc_start: 0.8332 (mmtp) cc_final: 0.7848 (mmtt) REVERT: B 815 ARG cc_start: 0.8412 (mtm110) cc_final: 0.7962 (mtm110) REVERT: B 904 TYR cc_start: 0.8210 (m-10) cc_final: 0.7978 (m-10) REVERT: B 933 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7707 (mtmm) REVERT: B 947 LYS cc_start: 0.8444 (ttmm) cc_final: 0.8124 (mtpp) REVERT: B 957 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 983 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7753 (mtp-110) REVERT: B 1038 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8351 (mmtp) REVERT: B 1084 ASP cc_start: 0.8160 (m-30) cc_final: 0.7925 (m-30) REVERT: B 1092 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: B 1127 ASP cc_start: 0.8023 (t0) cc_final: 0.7410 (t0) REVERT: E 37 VAL cc_start: 0.4777 (OUTLIER) cc_final: 0.4424 (t) REVERT: E 48 MET cc_start: 0.2196 (tpt) cc_final: 0.1027 (mpp) REVERT: A 31 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7101 (p0) REVERT: A 54 ASP cc_start: 0.7571 (t0) cc_final: 0.7284 (t70) REVERT: A 130 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7459 (ttmt) REVERT: A 242 LEU cc_start: 0.7919 (mp) cc_final: 0.7665 (mp) REVERT: A 269 TYR cc_start: 0.7827 (m-10) cc_final: 0.7541 (m-10) REVERT: A 280 ASN cc_start: 0.7247 (t0) cc_final: 0.7028 (t0) REVERT: A 281 GLU cc_start: 0.6369 (pp20) cc_final: 0.5657 (pp20) REVERT: A 317 ASN cc_start: 0.8090 (m-40) cc_final: 0.7671 (m110) REVERT: A 410 ILE cc_start: 0.4855 (OUTLIER) cc_final: 0.4601 (pt) REVERT: A 547 THR cc_start: 0.8039 (p) cc_final: 0.7779 (t) REVERT: A 586 ASP cc_start: 0.7675 (t0) cc_final: 0.7363 (t0) REVERT: A 723 THR cc_start: 0.8644 (t) cc_final: 0.8402 (p) REVERT: A 787 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: A 790 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8195 (mttp) REVERT: A 904 TYR cc_start: 0.8335 (m-10) cc_final: 0.8077 (m-80) REVERT: A 976 VAL cc_start: 0.8529 (t) cc_final: 0.8185 (m) REVERT: A 984 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7577 (mp) REVERT: A 1039 ARG cc_start: 0.8640 (mtp180) cc_final: 0.8385 (mtp180) REVERT: A 1139 ASP cc_start: 0.7958 (t70) cc_final: 0.7581 (p0) REVERT: G 48 MET cc_start: 0.2881 (mtm) cc_final: 0.2420 (mtt) REVERT: G 70 MET cc_start: -0.2635 (mtp) cc_final: -0.3778 (mmt) REVERT: C 54 ASP cc_start: 0.6940 (t0) cc_final: 0.6699 (m-30) REVERT: C 130 LYS cc_start: 0.7604 (tppt) cc_final: 0.7111 (tppt) REVERT: C 190 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6359 (tpm-80) REVERT: C 239 GLN cc_start: 0.7932 (tp40) cc_final: 0.7462 (tm-30) REVERT: C 281 GLU cc_start: 0.7565 (pp20) cc_final: 0.7147 (pp20) REVERT: C 287 ASP cc_start: 0.7375 (p0) cc_final: 0.7062 (p0) REVERT: C 321 GLN cc_start: 0.7532 (mp10) cc_final: 0.7273 (mp10) REVERT: C 455 LEU cc_start: 0.2334 (OUTLIER) cc_final: 0.1851 (tp) REVERT: C 535 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8416 (mmtt) REVERT: C 591 SER cc_start: 0.8609 (t) cc_final: 0.8293 (p) REVERT: C 675 GLN cc_start: 0.7224 (tp40) cc_final: 0.6891 (tp40) REVERT: C 726 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8446 (mt) REVERT: C 737 ASP cc_start: 0.7288 (t0) cc_final: 0.7083 (t0) REVERT: C 762 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7605 (mm-40) REVERT: C 779 GLN cc_start: 0.8341 (tp40) cc_final: 0.7803 (tp40) REVERT: C 821 LEU cc_start: 0.8126 (tt) cc_final: 0.7858 (tp) REVERT: C 856 ASN cc_start: 0.7428 (m110) cc_final: 0.7124 (m-40) REVERT: C 900 MET cc_start: 0.8155 (mtp) cc_final: 0.7919 (mtt) REVERT: C 957 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 964 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8361 (mtmm) REVERT: C 966 LEU cc_start: 0.8650 (mt) cc_final: 0.8343 (mp) REVERT: C 994 ASP cc_start: 0.8154 (t70) cc_final: 0.7816 (t0) REVERT: C 1019 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.7651 (ttp-110) REVERT: C 1036 GLN cc_start: 0.7717 (tp40) cc_final: 0.7490 (tt0) REVERT: C 1038 LYS cc_start: 0.8366 (mttp) cc_final: 0.8112 (mmmm) REVERT: C 1136 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8400 (p) outliers start: 157 outliers final: 125 residues processed: 629 average time/residue: 0.4532 time to fit residues: 446.8868 Evaluate side-chains 652 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 511 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 117 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 285 optimal weight: 40.0000 chunk 187 optimal weight: 0.8980 chunk 349 optimal weight: 1.9990 chunk 260 optimal weight: 0.0980 chunk 12 optimal weight: 0.0970 chunk 121 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 895 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.227138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161246 restraints weight = 50430.750| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.55 r_work: 0.3614 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32379 Z= 0.124 Angle : 0.562 11.687 44100 Z= 0.280 Chirality : 0.043 0.204 4960 Planarity : 0.004 0.060 5697 Dihedral : 5.906 65.458 4479 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.21 % Allowed : 16.44 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4025 helix: 1.94 (0.21), residues: 628 sheet: -0.39 (0.17), residues: 924 loop : -1.91 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 105 HIS 0.008 0.001 HIS B 207 PHE 0.041 0.002 PHE B 194 TYR 0.029 0.001 TYR E 35 ARG 0.011 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 927) hydrogen bonds : angle 4.75241 ( 2625) SS BOND : bond 0.00240 ( 43) SS BOND : angle 1.16660 ( 86) covalent geometry : bond 0.00289 (32336) covalent geometry : angle 0.56020 (44014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8050 Ramachandran restraints generated. 4025 Oldfield, 0 Emsley, 4025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 518 time to evaluate : 3.279 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: B 136 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5669 (m-10) REVERT: B 233 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6491 (tt) REVERT: B 238 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7171 (t80) REVERT: B 280 ASN cc_start: 0.7744 (t0) cc_final: 0.7515 (t0) REVERT: B 281 GLU cc_start: 0.7480 (pp20) cc_final: 0.7122 (pp20) REVERT: B 305 SER cc_start: 0.8723 (p) cc_final: 0.8491 (m) REVERT: B 307 THR cc_start: 0.8441 (m) cc_final: 0.8154 (p) REVERT: B 703 ASN cc_start: 0.7896 (t0) cc_final: 0.7611 (t0) REVERT: B 737 ASP cc_start: 0.7638 (t0) cc_final: 0.7346 (m-30) REVERT: B 756 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 811 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7639 (mmtt) REVERT: B 814 LYS cc_start: 0.8339 (mmtp) cc_final: 0.7830 (mmtt) REVERT: B 815 ARG cc_start: 0.8392 (mtm110) cc_final: 0.7952 (mtm110) REVERT: B 904 TYR cc_start: 0.8230 (m-10) cc_final: 0.7960 (m-10) REVERT: B 933 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7950 (mtmm) REVERT: B 947 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8156 (mtpp) REVERT: B 957 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 970 PHE cc_start: 0.8344 (m-80) cc_final: 0.7991 (m-80) REVERT: B 1038 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8382 (mmtp) REVERT: B 1084 ASP cc_start: 0.8183 (m-30) cc_final: 0.7958 (m-30) REVERT: B 1092 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: B 1127 ASP cc_start: 0.8023 (t0) cc_final: 0.7413 (t0) REVERT: E 37 VAL cc_start: 0.4739 (OUTLIER) cc_final: 0.4322 (t) REVERT: E 48 MET cc_start: 0.1451 (tpt) cc_final: 0.0690 (mpp) REVERT: D 35 TRP cc_start: 0.3797 (OUTLIER) cc_final: 0.3550 (m100) REVERT: A 31 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7005 (p0) REVERT: A 47 SER cc_start: 0.8522 (t) cc_final: 0.8317 (p) REVERT: A 130 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7336 (ttmt) REVERT: A 242 LEU cc_start: 0.7911 (mp) cc_final: 0.7630 (mp) REVERT: A 280 ASN cc_start: 0.7275 (t0) cc_final: 0.7047 (t0) REVERT: A 281 GLU cc_start: 0.6412 (pp20) cc_final: 0.5691 (pp20) REVERT: A 317 ASN cc_start: 0.8082 (m-40) cc_final: 0.7677 (m110) REVERT: A 410 ILE cc_start: 0.5228 (OUTLIER) cc_final: 0.4984 (pt) REVERT: A 547 THR cc_start: 0.8016 (p) cc_final: 0.7730 (t) REVERT: A 586 ASP cc_start: 0.7714 (t0) cc_final: 0.7386 (t0) REVERT: A 723 THR cc_start: 0.8666 (t) cc_final: 0.8431 (p) REVERT: A 787 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: A 790 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8192 (mttp) REVERT: A 904 TYR cc_start: 0.8326 (m-10) cc_final: 0.8015 (m-80) REVERT: A 976 VAL cc_start: 0.8578 (t) cc_final: 0.8231 (m) REVERT: A 984 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7564 (mp) REVERT: A 1139 ASP cc_start: 0.8009 (t70) cc_final: 0.7615 (p0) REVERT: A 1142 GLN cc_start: 0.7984 (mt0) cc_final: 0.6610 (mt0) REVERT: G 48 MET cc_start: 0.2732 (mtm) cc_final: 0.2383 (mtt) REVERT: G 70 MET cc_start: -0.2262 (mtp) cc_final: -0.3590 (mmt) REVERT: C 54 ASP cc_start: 0.6950 (t0) cc_final: 0.6728 (m-30) REVERT: C 130 LYS cc_start: 0.7612 (tppt) cc_final: 0.7068 (tppt) REVERT: C 168 PHE cc_start: 0.7790 (t80) cc_final: 0.7366 (t80) REVERT: C 190 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6459 (tpm-80) REVERT: C 239 GLN cc_start: 0.7968 (tp40) cc_final: 0.7483 (tm-30) REVERT: C 281 GLU cc_start: 0.7580 (pp20) cc_final: 0.7178 (pp20) REVERT: C 287 ASP cc_start: 0.7362 (p0) cc_final: 0.7043 (p0) REVERT: C 321 GLN cc_start: 0.7531 (mp10) cc_final: 0.7281 (mp10) REVERT: C 455 LEU cc_start: 0.2262 (OUTLIER) cc_final: 0.1942 (tp) REVERT: C 535 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8431 (mmtt) REVERT: C 591 SER cc_start: 0.8599 (t) cc_final: 0.8310 (p) REVERT: C 675 GLN cc_start: 0.7262 (tp40) cc_final: 0.6930 (tp40) REVERT: C 726 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 737 ASP cc_start: 0.7285 (t0) cc_final: 0.7078 (t0) REVERT: C 779 GLN cc_start: 0.8382 (tp40) cc_final: 0.7854 (tp40) REVERT: C 821 LEU cc_start: 0.8125 (tt) cc_final: 0.7852 (tp) REVERT: C 900 MET cc_start: 0.8151 (mtp) cc_final: 0.7934 (mtt) REVERT: C 957 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7940 (tm-30) REVERT: C 964 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8385 (mtmm) REVERT: C 966 LEU cc_start: 0.8645 (mt) cc_final: 0.8420 (mp) REVERT: C 994 ASP cc_start: 0.8181 (t70) cc_final: 0.7906 (t0) REVERT: C 1136 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8394 (p) outliers start: 149 outliers final: 123 residues processed: 625 average time/residue: 0.4465 time to fit residues: 437.5229 Evaluate side-chains 644 residues out of total 3540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 505 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 385 optimal weight: 4.9990 chunk 350 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 347 optimal weight: 0.8980 chunk 346 optimal weight: 0.0040 chunk 367 optimal weight: 0.8980 chunk 308 optimal weight: 0.6980 chunk 268 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 185 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 895 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.227796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162138 restraints weight = 50302.690| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.46 r_work: 0.3631 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32379 Z= 0.116 Angle : 0.562 11.605 44100 Z= 0.278 Chirality : 0.043 0.239 4960 Planarity : 0.004 0.060 5697 Dihedral : 5.887 65.951 4479 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.15 % Allowed : 16.81 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 4025 helix: 2.04 (0.21), residues: 628 sheet: -0.35 (0.17), residues: 949 loop : -1.89 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 105 HIS 0.018 0.001 HIS B 207 PHE 0.037 0.002 PHE C 194 TYR 0.022 0.001 TYR E 35 ARG 0.007 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 927) hydrogen bonds : angle 4.72242 ( 2625) SS BOND : bond 0.00224 ( 43) SS BOND : angle 1.03828 ( 86) covalent geometry : bond 0.00271 (32336) covalent geometry : angle 0.56051 (44014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28564.94 seconds wall clock time: 491 minutes 55.97 seconds (29515.97 seconds total)