Starting phenix.real_space_refine on Mon Sep 30 07:20:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5r_16441/09_2024/8c5r_16441.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5r_16441/09_2024/8c5r_16441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5r_16441/09_2024/8c5r_16441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5r_16441/09_2024/8c5r_16441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5r_16441/09_2024/8c5r_16441.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5r_16441/09_2024/8c5r_16441.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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 114 5.16 5 C 15984 2.51 5 N 4158 2.21 5 O 4713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24969 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8328 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 6 Chain: "B" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8328 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8313 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Time building chain proxies: 16.34, per 1000 atoms: 0.65 Number of scatterers: 24969 At special positions: 0 Unit cell: (144.768, 155.584, 193.024, 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 114 16.00 O 4713 8.00 N 4158 7.00 C 15984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 6.56 Conformation dependent library (CDL) restraints added in 3.3 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 44 sheets defined 23.9% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.561A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.634A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.502A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 4.498A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.540A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.043A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.663A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.978A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.552A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER B 443 " --> pdb=" O LYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.605A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.163A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.534A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.667A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.250A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.904A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.232A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.697A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.543A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.625A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.739A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.782A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.525A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.638A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.638A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 4.028A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.663A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.848A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.066A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 263 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.655A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.517A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.333A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.397A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.380A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 327 removed outlier: 5.200A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.503A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.246A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.117A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.965A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.532A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.331A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 154 through 157 removed outlier: 6.482A pdb=" N ASP B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR B 259 " --> pdb=" O HIS B 245 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.502A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.551A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.539A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.538A pdb=" N TYR B 453 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.945A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 4.901A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.121A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 263 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.514A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.425A pdb=" N ASP C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.416A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.541A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.624A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.339A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.525A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.573A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 941 hydrogen bonds defined for protein. 2607 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: 12.27 Time building geometry restraints manager: 7.66 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: 8004 1.34 - 1.46: 6148 1.46 - 1.58: 11261 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25557 Sorted by residual: bond pdb=" N PRO B 373 " pdb=" CD PRO B 373 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO C 213 " pdb=" CD PRO C 213 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO A 213 " pdb=" CD PRO A 213 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO A 373 " pdb=" CD PRO A 373 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 ... (remaining 25552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 34513 2.59 - 5.19: 226 5.19 - 7.78: 7 7.78 - 10.37: 4 10.37 - 12.96: 7 Bond angle restraints: 34757 Sorted by residual: angle pdb=" CA PRO A 213 " pdb=" N PRO A 213 " pdb=" CD PRO A 213 " ideal model delta sigma weight residual 112.00 99.04 12.96 1.40e+00 5.10e-01 8.57e+01 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 99.20 12.80 1.40e+00 5.10e-01 8.36e+01 angle pdb=" CA PRO C 213 " pdb=" N PRO C 213 " pdb=" CD PRO C 213 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" CD PRO A 373 " ideal model delta sigma weight residual 112.00 99.23 12.77 1.40e+00 5.10e-01 8.32e+01 angle pdb=" CA PRO B 213 " pdb=" N PRO B 213 " pdb=" CD PRO B 213 " ideal model delta sigma weight residual 112.00 99.26 12.74 1.40e+00 5.10e-01 8.29e+01 ... (remaining 34752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14856 17.99 - 35.99: 308 35.99 - 53.98: 62 53.98 - 71.98: 11 71.98 - 89.97: 10 Dihedral angle restraints: 15247 sinusoidal: 5974 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.81 -49.81 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.72 -49.72 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 15244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2879 0.039 - 0.078: 671 0.078 - 0.118: 290 0.118 - 0.157: 80 0.157 - 0.196: 5 Chirality restraints: 3925 Sorted by residual: chirality pdb=" CA ILE A 211 " pdb=" N ILE A 211 " pdb=" C ILE A 211 " pdb=" CB ILE A 211 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA ILE C 211 " pdb=" N ILE C 211 " pdb=" C ILE C 211 " pdb=" CB ILE C 211 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 3922 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.055 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO A 373 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 212 " -0.053 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO C 213 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 213 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 213 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.050 5.00e-02 4.00e+02 6.96e-02 7.74e+00 pdb=" N PRO C 373 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.037 5.00e-02 4.00e+02 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.43: 36 1.43 - 2.30: 174 2.30 - 3.17: 21411 3.17 - 4.03: 64916 4.03 - 4.90: 120700 Warning: very small nonbonded interaction distances. Nonbonded interactions: 207237 Sorted by model distance: nonbonded pdb=" CG PHE B 643 " pdb=" CZ TYR B 655 " model vdw 0.567 3.480 nonbonded pdb=" CD2 PHE B 643 " pdb=" CE1 TYR B 655 " model vdw 0.618 3.640 nonbonded pdb=" CG PHE C 643 " pdb=" CZ TYR C 655 " model vdw 0.632 3.480 nonbonded pdb=" CB PHE C 643 " pdb=" CE2 TYR C 655 " model vdw 0.773 3.740 nonbonded pdb=" CD1 LEU B 455 " pdb=" NE ARG B 493 " model vdw 0.806 3.540 ... (remaining 207232 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.710 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.380 Process input model: 61.740 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:3.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3687 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 0.058 25557 Z= 0.202 Angle : 0.587 12.964 34757 Z= 0.327 Chirality : 0.044 0.196 3925 Planarity : 0.003 0.076 4495 Dihedral : 8.088 89.972 9161 Min Nonbonded Distance : 0.567 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.09 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -3.20 (0.12), residues: 3136 helix: -1.45 (0.15), residues: 666 sheet: -1.97 (0.17), residues: 694 loop : -2.52 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.004 0.001 HIS A1048 PHE 0.014 0.001 PHE C 490 TYR 0.014 0.001 TYR C 873 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 LEU cc_start: 0.7602 (mt) cc_final: 0.7355 (mt) REVERT: A 800 PHE cc_start: 0.6179 (m-80) cc_final: 0.4410 (m-80) REVERT: A 874 THR cc_start: 0.6447 (p) cc_final: 0.6116 (p) REVERT: A 904 TYR cc_start: 0.5590 (t80) cc_final: 0.4982 (t80) REVERT: A 1049 LEU cc_start: 0.7539 (mt) cc_final: 0.7280 (mt) REVERT: B 882 ILE cc_start: 0.7097 (mt) cc_final: 0.6848 (mt) REVERT: B 1009 THR cc_start: 0.7656 (m) cc_final: 0.7219 (m) REVERT: B 1039 ARG cc_start: 0.7977 (mtp180) cc_final: 0.6931 (mmm-85) REVERT: C 962 LEU cc_start: 0.5773 (tp) cc_final: 0.5431 (tt) REVERT: C 1110 TYR cc_start: 0.6515 (t80) cc_final: 0.6121 (t80) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.3776 time to fit residues: 325.5626 Evaluate side-chains 273 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 872 GLN A1011 GLN A1071 GLN B 49 HIS B 99 ASN B 388 ASN B 437 ASN B 901 GLN B 955 ASN B 957 GLN B1125 ASN B1134 ASN C 506 GLN C 762 GLN C 935 GLN C 954 HIS C1002 GLN C1005 GLN C1054 GLN C1106 GLN C1135 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4918 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 25557 Z= 0.400 Angle : 0.758 10.485 34757 Z= 0.399 Chirality : 0.050 0.232 3925 Planarity : 0.005 0.069 4495 Dihedral : 4.661 28.735 3412 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.58 % Allowed : 6.10 % Favored : 91.32 % 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: -2.25 (0.13), residues: 3136 helix: -0.31 (0.18), residues: 659 sheet: -1.44 (0.17), residues: 735 loop : -2.02 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 886 HIS 0.014 0.002 HIS C1064 PHE 0.049 0.003 PHE B 643 TYR 0.025 0.002 TYR B 873 ARG 0.010 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 315 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLN cc_start: 0.7589 (tp40) cc_final: 0.7342 (tt0) REVERT: A 873 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7416 (m-10) REVERT: B 1097 SER cc_start: 0.8630 (t) cc_final: 0.8154 (p) REVERT: B 1102 TRP cc_start: 0.8375 (m100) cc_final: 0.7683 (m100) REVERT: C 697 MET cc_start: 0.7091 (tmm) cc_final: 0.6821 (ttt) REVERT: C 887 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8063 (m) REVERT: C 1110 TYR cc_start: 0.7946 (t80) cc_final: 0.7658 (t80) outliers start: 72 outliers final: 40 residues processed: 377 average time/residue: 0.3624 time to fit residues: 215.7027 Evaluate side-chains 253 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 211 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 239 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 288 optimal weight: 2.9990 chunk 311 optimal weight: 0.2980 chunk 256 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 231 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1071 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 321 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1113 GLN B1119 ASN C 506 GLN C 955 ASN C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4893 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25557 Z= 0.188 Angle : 0.531 8.595 34757 Z= 0.277 Chirality : 0.044 0.221 3925 Planarity : 0.004 0.056 4495 Dihedral : 3.993 22.439 3412 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.76 % Allowed : 9.47 % Favored : 88.77 % 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: -1.55 (0.14), residues: 3136 helix: 0.73 (0.19), residues: 654 sheet: -1.00 (0.18), residues: 700 loop : -1.78 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.004 0.001 HIS C 519 PHE 0.022 0.001 PHE A1121 TYR 0.018 0.001 TYR B 265 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 239 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLN cc_start: 0.7482 (tp40) cc_final: 0.7144 (tt0) REVERT: A 873 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: A 896 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8512 (mt) REVERT: B 646 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.6181 (mmt90) REVERT: B 664 ILE cc_start: 0.7711 (mp) cc_final: 0.7342 (mt) REVERT: B 962 LEU cc_start: 0.8291 (mm) cc_final: 0.7949 (mm) REVERT: B 1102 TRP cc_start: 0.8301 (m100) cc_final: 0.8050 (m-10) REVERT: C 697 MET cc_start: 0.7097 (tmm) cc_final: 0.6854 (ttt) outliers start: 49 outliers final: 31 residues processed: 280 average time/residue: 0.3676 time to fit residues: 167.7298 Evaluate side-chains 228 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 149 optimal weight: 0.0000 chunk 31 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 289 optimal weight: 0.0040 chunk 306 optimal weight: 0.6980 chunk 151 optimal weight: 40.0000 chunk 274 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 901 GLN B1005 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4909 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25557 Z= 0.157 Angle : 0.493 7.844 34757 Z= 0.256 Chirality : 0.044 0.149 3925 Planarity : 0.003 0.056 4495 Dihedral : 3.849 21.735 3412 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.47 % Allowed : 10.76 % Favored : 87.77 % 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: -1.26 (0.14), residues: 3136 helix: 1.02 (0.20), residues: 663 sheet: -0.82 (0.18), residues: 689 loop : -1.61 (0.13), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 64 HIS 0.003 0.001 HIS A 66 PHE 0.018 0.001 PHE A1121 TYR 0.023 0.001 TYR C 91 ARG 0.005 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLN cc_start: 0.7537 (tp40) cc_final: 0.7011 (tt0) REVERT: A 896 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 646 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.6131 (mmt90) REVERT: B 664 ILE cc_start: 0.7871 (mp) cc_final: 0.7532 (mt) REVERT: B 1002 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: B 1102 TRP cc_start: 0.8273 (m100) cc_final: 0.7998 (m-10) outliers start: 41 outliers final: 30 residues processed: 262 average time/residue: 0.3188 time to fit residues: 138.3198 Evaluate side-chains 225 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1006 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 126 optimal weight: 0.0970 chunk 261 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 156 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1071 GLN A1101 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 901 GLN B1119 ASN C 207 HIS C 474 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25557 Z= 0.354 Angle : 0.627 11.344 34757 Z= 0.332 Chirality : 0.048 0.195 3925 Planarity : 0.004 0.067 4495 Dihedral : 4.521 22.503 3412 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.65 % Allowed : 10.83 % Favored : 86.51 % 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: -1.52 (0.14), residues: 3136 helix: 0.39 (0.19), residues: 665 sheet: -0.84 (0.18), residues: 689 loop : -1.66 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 64 HIS 0.012 0.002 HIS C1064 PHE 0.018 0.002 PHE C1121 TYR 0.024 0.002 TYR B 789 ARG 0.005 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 240 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 664 ILE cc_start: 0.8363 (mp) cc_final: 0.7926 (mt) REVERT: C 28 TYR cc_start: 0.4563 (m-80) cc_final: 0.4175 (m-80) REVERT: C 204 TYR cc_start: 0.4790 (m-80) cc_final: 0.2827 (m-80) outliers start: 74 outliers final: 48 residues processed: 299 average time/residue: 0.3361 time to fit residues: 166.3154 Evaluate side-chains 247 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1006 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 179 optimal weight: 0.0570 chunk 75 optimal weight: 0.9980 chunk 306 optimal weight: 0.0870 chunk 254 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 161 optimal weight: 0.3980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A1005 GLN A1071 GLN B 49 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 901 GLN B1119 ASN C 564 GLN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5138 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25557 Z= 0.164 Angle : 0.510 8.936 34757 Z= 0.266 Chirality : 0.044 0.194 3925 Planarity : 0.004 0.065 4495 Dihedral : 4.067 23.529 3412 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.08 % Allowed : 12.52 % Favored : 85.40 % 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: -1.21 (0.14), residues: 3136 helix: 0.87 (0.20), residues: 664 sheet: -0.70 (0.19), residues: 669 loop : -1.54 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.007 0.001 HIS B 49 PHE 0.028 0.001 PHE C 759 TYR 0.020 0.001 TYR C 91 ARG 0.006 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8673 (mt) REVERT: A 1118 ASP cc_start: 0.6035 (t0) cc_final: 0.5749 (t0) REVERT: B 664 ILE cc_start: 0.8371 (mp) cc_final: 0.7879 (mt) REVERT: B 1121 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.5736 (t80) outliers start: 58 outliers final: 35 residues processed: 275 average time/residue: 0.3277 time to fit residues: 148.7738 Evaluate side-chains 240 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 967 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 0.0570 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 901 GLN B1119 ASN C 519 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 moved from start: 0.8127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25557 Z= 0.283 Angle : 0.579 10.381 34757 Z= 0.303 Chirality : 0.046 0.241 3925 Planarity : 0.004 0.063 4495 Dihedral : 4.344 24.507 3412 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.01 % Allowed : 13.09 % Favored : 84.90 % 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: -1.31 (0.14), residues: 3136 helix: 0.62 (0.19), residues: 661 sheet: -0.73 (0.19), residues: 684 loop : -1.53 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1102 HIS 0.009 0.001 HIS C1064 PHE 0.021 0.002 PHE A 65 TYR 0.017 0.001 TYR C 91 ARG 0.006 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8772 (mt) REVERT: B 129 LYS cc_start: 0.4159 (mmtt) cc_final: 0.3567 (mtpt) REVERT: B 1119 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 1121 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.5753 (t80) REVERT: C 204 TYR cc_start: 0.5132 (m-80) cc_final: 0.4603 (m-80) REVERT: C 305 SER cc_start: 0.7377 (t) cc_final: 0.6958 (m) outliers start: 56 outliers final: 46 residues processed: 269 average time/residue: 0.3290 time to fit residues: 146.3497 Evaluate side-chains 254 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 205 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 967 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 50.0000 chunk 28 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B1119 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 0.8440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25557 Z= 0.231 Angle : 0.549 9.436 34757 Z= 0.287 Chirality : 0.045 0.239 3925 Planarity : 0.004 0.062 4495 Dihedral : 4.225 23.052 3412 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.08 % Allowed : 13.63 % Favored : 84.29 % 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: -1.21 (0.14), residues: 3136 helix: 0.77 (0.20), residues: 659 sheet: -0.65 (0.19), residues: 674 loop : -1.50 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 104 HIS 0.006 0.001 HIS C1064 PHE 0.024 0.002 PHE A 759 TYR 0.018 0.001 TYR C 91 ARG 0.006 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 227 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 896 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 664 ILE cc_start: 0.8440 (mp) cc_final: 0.8024 (mt) REVERT: B 1121 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.5964 (t80) REVERT: C 153 MET cc_start: 0.3080 (tpp) cc_final: 0.2664 (tpt) REVERT: C 204 TYR cc_start: 0.5163 (m-80) cc_final: 0.4587 (m-80) REVERT: C 305 SER cc_start: 0.7557 (t) cc_final: 0.7131 (m) outliers start: 58 outliers final: 43 residues processed: 272 average time/residue: 0.3352 time to fit residues: 151.7914 Evaluate side-chains 254 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 209 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1006 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 0.5980 chunk 292 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 257 optimal weight: 0.0670 chunk 269 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 755 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 moved from start: 0.8736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25557 Z= 0.206 Angle : 0.556 12.723 34757 Z= 0.285 Chirality : 0.045 0.257 3925 Planarity : 0.004 0.060 4495 Dihedral : 4.117 22.485 3412 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.94 % Allowed : 13.92 % Favored : 84.15 % 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: -1.16 (0.14), residues: 3136 helix: 0.81 (0.20), residues: 654 sheet: -0.60 (0.19), residues: 670 loop : -1.47 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 104 HIS 0.005 0.001 HIS C1064 PHE 0.023 0.001 PHE A 43 TYR 0.027 0.001 TYR B1007 ARG 0.010 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 TRP cc_start: 0.6316 (p90) cc_final: 0.5790 (p90) REVERT: A 896 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8700 (mt) REVERT: B 664 ILE cc_start: 0.8464 (mp) cc_final: 0.8093 (mt) REVERT: B 1121 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.5911 (t80) REVERT: C 153 MET cc_start: 0.3137 (tpp) cc_final: 0.2819 (tpt) REVERT: C 204 TYR cc_start: 0.5310 (m-80) cc_final: 0.4979 (m-80) outliers start: 54 outliers final: 46 residues processed: 278 average time/residue: 0.3299 time to fit residues: 152.1094 Evaluate side-chains 261 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 0.4980 chunk 301 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 251 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 194 optimal weight: 0.0770 chunk 154 optimal weight: 5.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1002 GLN B 99 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5277 moved from start: 0.8902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25557 Z= 0.180 Angle : 0.553 10.466 34757 Z= 0.283 Chirality : 0.044 0.201 3925 Planarity : 0.004 0.112 4495 Dihedral : 4.023 21.275 3412 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.65 % Allowed : 14.56 % Favored : 83.79 % 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: -1.06 (0.14), residues: 3136 helix: 0.94 (0.20), residues: 659 sheet: -0.60 (0.19), residues: 696 loop : -1.41 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 104 HIS 0.004 0.001 HIS A1088 PHE 0.030 0.001 PHE A 43 TYR 0.038 0.001 TYR B1007 ARG 0.009 0.000 ARG B 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 TRP cc_start: 0.6575 (p90) cc_final: 0.5930 (p90) REVERT: A 896 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8673 (mt) REVERT: A 1132 ILE cc_start: 0.8900 (tt) cc_final: 0.8681 (tt) REVERT: B 664 ILE cc_start: 0.8416 (mp) cc_final: 0.8066 (mt) REVERT: B 1121 PHE cc_start: 0.6842 (t80) cc_final: 0.5858 (t80) REVERT: C 153 MET cc_start: 0.3142 (tpp) cc_final: 0.2870 (tpt) REVERT: C 204 TYR cc_start: 0.5337 (m-80) cc_final: 0.4776 (m-80) REVERT: C 305 SER cc_start: 0.7660 (t) cc_final: 0.7413 (m) outliers start: 46 outliers final: 41 residues processed: 265 average time/residue: 0.3278 time to fit residues: 145.4192 Evaluate side-chains 256 residues out of total 2788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A1106 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.213308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.171073 restraints weight = 43236.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164251 restraints weight = 65703.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158472 restraints weight = 47889.698| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.9339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25557 Z= 0.270 Angle : 0.598 9.999 34757 Z= 0.309 Chirality : 0.046 0.214 3925 Planarity : 0.004 0.065 4495 Dihedral : 4.273 22.333 3412 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.87 % Allowed : 14.60 % Favored : 83.54 % 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: -1.21 (0.14), residues: 3136 helix: 0.64 (0.20), residues: 671 sheet: -0.66 (0.19), residues: 702 loop : -1.47 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 104 HIS 0.007 0.001 HIS C1064 PHE 0.027 0.002 PHE A 43 TYR 0.026 0.001 TYR A 655 ARG 0.008 0.001 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5041.59 seconds wall clock time: 91 minutes 38.93 seconds (5498.93 seconds total)