Starting phenix.real_space_refine on Mon Dec 30 05:50:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4f_36904/12_2024/8w4f_36904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4f_36904/12_2024/8w4f_36904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w4f_36904/12_2024/8w4f_36904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4f_36904/12_2024/8w4f_36904.map" model { file = "/net/cci-nas-00/data/ceres_data/8w4f_36904/12_2024/8w4f_36904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4f_36904/12_2024/8w4f_36904.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.116 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: 5 Type Number sf(0) Gaussians S 135 5.16 5 C 19431 2.51 5 N 5157 2.21 5 O 5865 1.98 5 H 29841 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 60429 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 17237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 17237 Classifications: {'peptide': 1120} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1061} Chain: "B" Number of atoms: 17237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 17237 Classifications: {'peptide': 1120} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1061} Chain: "C" Number of atoms: 17237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 17237 Classifications: {'peptide': 1120} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1061} Chain: "D" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 2906 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "E" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 2906 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "F" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 2906 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 185} Time building chain proxies: 21.03, per 1000 atoms: 0.35 Number of scatterers: 60429 At special positions: 0 Unit cell: (153.86, 146.01, 183.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 O 5865 8.00 N 5157 7.00 C 19431 6.00 H 29841 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.22 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.11 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.08 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=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.12 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.10 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.10 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=2.13 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.08 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.08 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=2.04 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=2.07 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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: 12.06 Conformation dependent library (CDL) restraints added in 3.9 seconds 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7302 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 19.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.581A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.745A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.639A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 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 removed outlier: 4.390A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.037A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.809A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.950A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 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 965 removed outlier: 4.166A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.293A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.874A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.623A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.850A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.503A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.505A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.597A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.765A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.774A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1145 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 143 through 151 removed outlier: 4.002A pdb=" N LYS D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 149 through 152 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 143 through 150 Processing helix chain 'F' and resid 193 through 197 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.347A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.820A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.528A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR A 114 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 133 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.937A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.214A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.555A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 543 removed outlier: 4.533A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.444A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.298A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.298A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB4, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.311A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.743A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.519A pdb=" N ILE B 68 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG B 78 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.940A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 126 " --> pdb=" O PRO B 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.570A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 313 removed outlier: 4.289A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC2, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.320A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.201A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.644A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.436A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.436A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.645A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.571A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.717A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.631A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 175 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 128 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN C 173 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.072A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.693A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.207A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE1, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.706A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.418A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.418A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.811A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.284A pdb=" N GLY D 16 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.720A pdb=" N ALA D 97 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AE9, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AF1, first strand: chain 'E' and resid 5 through 7 removed outlier: 6.714A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.933A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA E 40 " --> pdb=" O GLU E 44 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.862A pdb=" N PHE E 168 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 5 through 8 removed outlier: 3.813A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU F 81 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N CYS F 22 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.593A pdb=" N TRP F 36 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU F 47 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG F 38 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG F 45 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 158 through 162 1061 hydrogen bonds defined for protein. 2877 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: 25.33 Time building geometry restraints manager: 14.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.15: 29826 1.15 - 1.34: 7021 1.34 - 1.53: 19564 1.53 - 1.72: 4561 1.72 - 1.91: 177 Bond restraints: 61149 Sorted by residual: bond pdb=" CA ASP A 215 " pdb=" C ASP A 215 " ideal model delta sigma weight residual 1.523 1.380 0.144 1.18e-02 7.18e+03 1.48e+02 bond pdb=" C ALA B 713 " pdb=" N ILE B 714 " ideal model delta sigma weight residual 1.329 1.417 -0.089 7.30e-03 1.88e+04 1.47e+02 bond pdb=" CA ILE A 896 " pdb=" C ILE A 896 " ideal model delta sigma weight residual 1.524 1.428 0.096 8.30e-03 1.45e+04 1.34e+02 bond pdb=" CA ILE B1018 " pdb=" C ILE B1018 " ideal model delta sigma weight residual 1.524 1.379 0.145 1.30e-02 5.92e+03 1.24e+02 bond pdb=" CA VAL E 154 " pdb=" C VAL E 154 " ideal model delta sigma weight residual 1.527 1.422 0.105 9.70e-03 1.06e+04 1.16e+02 ... (remaining 61144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 95629 4.23 - 8.46: 12026 8.46 - 12.68: 2149 12.68 - 16.91: 363 16.91 - 21.14: 26 Bond angle restraints: 110193 Sorted by residual: angle pdb=" N PRO B 862 " pdb=" CA PRO B 862 " pdb=" CB PRO B 862 " ideal model delta sigma weight residual 103.22 110.48 -7.26 5.20e-01 3.70e+00 1.95e+02 angle pdb=" CA PHE A 497 " pdb=" CB PHE A 497 " pdb=" CG PHE A 497 " ideal model delta sigma weight residual 113.80 127.58 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" CA PRO D 193 " pdb=" C PRO D 193 " pdb=" N PRO D 194 " ideal model delta sigma weight residual 117.93 134.32 -16.39 1.20e+00 6.94e-01 1.87e+02 angle pdb=" CA PRO E 192 " pdb=" C PRO E 192 " pdb=" N PRO E 193 " ideal model delta sigma weight residual 117.93 134.32 -16.39 1.20e+00 6.94e-01 1.86e+02 angle pdb=" N PRO F 193 " pdb=" CA PRO F 193 " pdb=" C PRO F 193 " ideal model delta sigma weight residual 110.70 127.10 -16.40 1.22e+00 6.72e-01 1.81e+02 ... (remaining 110188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 27373 17.99 - 35.98: 1126 35.98 - 53.98: 569 53.98 - 71.97: 234 71.97 - 89.96: 41 Dihedral angle restraints: 29343 sinusoidal: 15741 harmonic: 13602 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 178.78 -85.78 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" N ALA C 123 " pdb=" C ALA C 123 " pdb=" CA ALA C 123 " pdb=" CB ALA C 123 " ideal model delta harmonic sigma weight residual 122.90 143.57 -20.67 0 2.50e+00 1.60e-01 6.84e+01 dihedral pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CA PRO A 986 " pdb=" CB PRO A 986 " ideal model delta harmonic sigma weight residual 115.10 135.42 -20.32 0 2.50e+00 1.60e-01 6.61e+01 ... (remaining 29340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4328 0.188 - 0.377: 412 0.377 - 0.565: 27 0.565 - 0.753: 4 0.753 - 0.942: 2 Chirality restraints: 4773 Sorted by residual: chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 1.78 0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ASP A 571 " pdb=" N ASP A 571 " pdb=" C ASP A 571 " pdb=" CB ASP A 571 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA ALA C 123 " pdb=" N ALA C 123 " pdb=" C ALA C 123 " pdb=" CB ALA C 123 " both_signs ideal model delta sigma weight residual False 2.48 1.76 0.73 2.00e-01 2.50e+01 1.31e+01 ... (remaining 4770 not shown) Planarity restraints: 9315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 695 " 0.340 2.00e-02 2.50e+03 1.63e-01 8.01e+02 pdb=" CG TYR B 695 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR B 695 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR B 695 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR B 695 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 695 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 695 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR B 695 " 0.274 2.00e-02 2.50e+03 pdb=" HD1 TYR B 695 " -0.233 2.00e-02 2.50e+03 pdb=" HD2 TYR B 695 " -0.191 2.00e-02 2.50e+03 pdb=" HE1 TYR B 695 " -0.106 2.00e-02 2.50e+03 pdb=" HE2 TYR B 695 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 695 " 0.233 2.00e-02 2.50e+03 1.61e-01 7.81e+02 pdb=" CG TYR A 695 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 695 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR A 695 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 695 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 695 " -0.100 2.00e-02 2.50e+03 pdb=" CZ TYR A 695 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR A 695 " 0.292 2.00e-02 2.50e+03 pdb=" HD1 TYR A 695 " -0.235 2.00e-02 2.50e+03 pdb=" HD2 TYR A 695 " 0.080 2.00e-02 2.50e+03 pdb=" HE1 TYR A 695 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 695 " -0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " -0.125 2.00e-02 2.50e+03 1.34e-01 7.22e+02 pdb=" CG TRP C 64 " 0.100 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.153 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " 0.168 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " 0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " -0.094 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " -0.022 2.00e-02 2.50e+03 pdb=" HD1 TRP C 64 " -0.164 2.00e-02 2.50e+03 pdb=" HE1 TRP C 64 " -0.100 2.00e-02 2.50e+03 pdb=" HE3 TRP C 64 " 0.213 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 64 " 0.087 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 64 " -0.302 2.00e-02 2.50e+03 pdb=" HH2 TRP C 64 " -0.048 2.00e-02 2.50e+03 ... (remaining 9312 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 767 1.85 - 2.53: 52036 2.53 - 3.22: 189266 3.22 - 3.91: 253602 3.91 - 4.60: 394130 Nonbonded interactions: 889801 Sorted by model distance: nonbonded pdb=" H SER B 810 " pdb=" H LYS B 811 " model vdw 1.157 2.100 nonbonded pdb=" HG SER A 659 " pdb=" HG SER A 698 " model vdw 1.159 2.100 nonbonded pdb=" HG CYS C 136 " pdb=" H ASP C 138 " model vdw 1.179 2.270 nonbonded pdb=" HG SER A 514 " pdb=" HH TYR C 200 " model vdw 1.183 2.100 nonbonded pdb=" H ALA A 852 " pdb=" H GLN A 853 " model vdw 1.184 2.100 ... (remaining 889796 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.830 Extract box with map and model: 1.870 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 102.790 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 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 : 0.026 0.145 31308 Z= 1.709 Angle : 2.676 16.478 42621 Z= 1.946 Chirality : 0.115 0.942 4773 Planarity : 0.014 0.140 5577 Dihedral : 11.764 89.960 11235 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 1.19 % Allowed : 6.50 % Favored : 92.31 % Rotamer: Outliers : 0.12 % Allowed : 0.92 % Favored : 98.96 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.80 (0.12), residues: 3939 helix: -0.30 (0.18), residues: 679 sheet: 0.20 (0.18), residues: 717 loop : -2.00 (0.11), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.013 TRP C 633 HIS 0.040 0.001 HIS C 146 PHE 0.136 0.006 PHE B1075 TYR 0.231 0.008 TYR B 695 ARG 0.051 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 309 GLU cc_start: 0.9499 (mt-10) cc_final: 0.9124 (mp0) REVERT: A 697 MET cc_start: 0.8744 (ptm) cc_final: 0.7590 (ppp) REVERT: B 151 SER cc_start: 0.9427 (t) cc_final: 0.9193 (p) REVERT: B 988 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8811 (pt0) REVERT: C 1041 ASP cc_start: 0.6727 (m-30) cc_final: 0.6300 (m-30) REVERT: C 1142 GLN cc_start: 0.9484 (tt0) cc_final: 0.8971 (tp-100) outliers start: 4 outliers final: 3 residues processed: 186 average time/residue: 1.1171 time to fit residues: 297.4463 Evaluate side-chains 133 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 6.9990 chunk 297 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 188 ASN C 493 GLN C 556 ASN C 625 HIS C 658 ASN C 777 ASN D 32 ASN D 149 GLN E 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 31308 Z= 0.327 Angle : 0.731 7.494 42621 Z= 0.416 Chirality : 0.047 0.184 4773 Planarity : 0.005 0.058 5577 Dihedral : 6.791 76.604 4272 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.56 % Favored : 93.75 % Rotamer: Outliers : 0.03 % Allowed : 0.74 % Favored : 99.23 % 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: -1.40 (0.12), residues: 3939 helix: 0.76 (0.20), residues: 664 sheet: 0.08 (0.18), residues: 694 loop : -1.80 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 436 HIS 0.010 0.002 HIS A 655 PHE 0.042 0.002 PHE C 490 TYR 0.028 0.002 TYR D 161 ARG 0.006 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 697 MET cc_start: 0.8631 (ptm) cc_final: 0.8071 (ppp) REVERT: A 792 PRO cc_start: 0.6105 (Cg_exo) cc_final: 0.5884 (Cg_endo) REVERT: B 1029 MET cc_start: 0.8702 (tpp) cc_final: 0.8482 (tpp) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 1.0549 time to fit residues: 218.0754 Evaluate side-chains 108 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 9.9990 chunk 110 optimal weight: 0.0970 chunk 297 optimal weight: 0.9980 chunk 243 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 357 optimal weight: 20.0000 chunk 386 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 chunk 354 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 overall best weight: 3.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN A 914 ASN A 935 GLN B 218 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 31308 Z= 0.206 Angle : 0.596 7.208 42621 Z= 0.337 Chirality : 0.044 0.217 4773 Planarity : 0.004 0.093 5577 Dihedral : 6.035 75.030 4272 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.25 % Favored : 93.12 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.41 % 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: -1.37 (0.13), residues: 3939 helix: 1.13 (0.20), residues: 679 sheet: -0.22 (0.19), residues: 646 loop : -1.76 (0.11), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 176 HIS 0.007 0.001 HIS C 146 PHE 0.030 0.001 PHE C 718 TYR 0.023 0.001 TYR C1067 ARG 0.010 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 177 MET cc_start: 0.5807 (mpp) cc_final: 0.5501 (mpp) REVERT: A 309 GLU cc_start: 0.9173 (mp0) cc_final: 0.8959 (mp0) REVERT: A 697 MET cc_start: 0.8705 (ptm) cc_final: 0.8112 (ppp) REVERT: A 792 PRO cc_start: 0.6262 (Cg_exo) cc_final: 0.6057 (Cg_endo) REVERT: C 1142 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9089 (tp-100) REVERT: D 144 MET cc_start: 0.9278 (mmp) cc_final: 0.8970 (tpp) REVERT: D 148 LEU cc_start: 0.9357 (mt) cc_final: 0.8771 (mm) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 1.1941 time to fit residues: 223.4493 Evaluate side-chains 101 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 379 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 460 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 856 ASN A 965 GLN A1088 HIS B 334 ASN B1088 HIS C 125 ASN C 234 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1101 HIS F 82 GLN F 84 ASN F 143 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 31308 Z= 0.315 Angle : 0.675 11.321 42621 Z= 0.377 Chirality : 0.044 0.212 4773 Planarity : 0.005 0.059 5577 Dihedral : 5.951 75.862 4272 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.21 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.12), residues: 3939 helix: 0.64 (0.20), residues: 685 sheet: -0.67 (0.19), residues: 685 loop : -1.97 (0.11), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 258 HIS 0.009 0.002 HIS A1048 PHE 0.054 0.002 PHE C 456 TYR 0.043 0.002 TYR A 365 ARG 0.009 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6258 (mpp) cc_final: 0.5986 (mpp) REVERT: A 697 MET cc_start: 0.8685 (ptm) cc_final: 0.8431 (ppp) REVERT: B 1029 MET cc_start: 0.8873 (tpp) cc_final: 0.8493 (tpp) REVERT: C 697 MET cc_start: 0.9279 (ttp) cc_final: 0.8686 (ptm) REVERT: C 1002 GLN cc_start: 0.9557 (tp40) cc_final: 0.9342 (tp-100) REVERT: D 148 LEU cc_start: 0.9412 (mt) cc_final: 0.9146 (tt) REVERT: E 147 MET cc_start: 0.7494 (ttm) cc_final: 0.6846 (ttm) REVERT: F 34 MET cc_start: 0.6088 (tmm) cc_final: 0.5536 (tmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 1.1446 time to fit residues: 188.7897 Evaluate side-chains 93 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 324 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 193 optimal weight: 30.0000 chunk 340 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 173 GLN A 218 GLN A 343 ASN A 354 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 370 ASN B 460 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 901 GLN B1101 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 935 GLN ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS D 3 GLN D 74 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.161 31308 Z= 0.447 Angle : 0.839 19.632 42621 Z= 0.468 Chirality : 0.048 0.190 4773 Planarity : 0.007 0.107 5577 Dihedral : 6.477 72.591 4272 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 30.57 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.48 % Favored : 88.93 % Rotamer: Outliers : 0.12 % Allowed : 2.28 % Favored : 97.60 % 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: -2.79 (0.12), residues: 3939 helix: -0.51 (0.18), residues: 703 sheet: -1.27 (0.20), residues: 610 loop : -2.55 (0.10), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 152 HIS 0.015 0.003 HIS C1064 PHE 0.038 0.003 PHE C 306 TYR 0.057 0.003 TYR F 60 ARG 0.016 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1041 ASP cc_start: 0.8050 (m-30) cc_final: 0.7834 (m-30) REVERT: B 1029 MET cc_start: 0.9058 (tpp) cc_final: 0.8699 (tpp) REVERT: C 1002 GLN cc_start: 0.9476 (tp40) cc_final: 0.9232 (tp-100) REVERT: D 83 MET cc_start: 0.1838 (mpp) cc_final: 0.1452 (mpp) outliers start: 4 outliers final: 3 residues processed: 104 average time/residue: 1.1688 time to fit residues: 181.9328 Evaluate side-chains 88 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 380 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 199 optimal weight: 10.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 784 GLN B 836 GLN B1023 ASN C 409 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 762 GLN C 764 ASN C 777 ASN C 804 GLN C 965 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN D 82 GLN F 3 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 31308 Z= 0.273 Angle : 0.643 7.961 42621 Z= 0.358 Chirality : 0.044 0.158 4773 Planarity : 0.005 0.058 5577 Dihedral : 6.225 75.878 4272 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.42 % Favored : 90.20 % Rotamer: Outliers : 0.03 % Allowed : 0.98 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.60 (0.12), residues: 3939 helix: 0.20 (0.19), residues: 709 sheet: -1.37 (0.20), residues: 652 loop : -2.56 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.009 0.002 HIS C 49 PHE 0.033 0.002 PHE F 68 TYR 0.024 0.002 TYR A 365 ARG 0.012 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6578 (mpp) cc_final: 0.6350 (mpp) REVERT: A 394 ASN cc_start: 0.8701 (p0) cc_final: 0.8489 (t0) REVERT: A 697 MET cc_start: 0.8987 (ppp) cc_final: 0.8541 (ppp) REVERT: A 1041 ASP cc_start: 0.8176 (m-30) cc_final: 0.7907 (m-30) REVERT: C 697 MET cc_start: 0.9480 (ttp) cc_final: 0.9146 (ptp) REVERT: C 1002 GLN cc_start: 0.9460 (tp40) cc_final: 0.9225 (tp-100) REVERT: D 83 MET cc_start: 0.1655 (mpp) cc_final: 0.1209 (mpp) REVERT: D 144 MET cc_start: 0.9560 (mmp) cc_final: 0.9240 (tpp) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 1.0990 time to fit residues: 152.2637 Evaluate side-chains 82 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 320 optimal weight: 0.2980 chunk 212 optimal weight: 3.9990 chunk 378 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 174 optimal weight: 30.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 764 ASN C 777 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31308 Z= 0.193 Angle : 0.567 5.829 42621 Z= 0.313 Chirality : 0.044 0.149 4773 Planarity : 0.004 0.050 5577 Dihedral : 5.872 78.886 4272 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.75 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.33 (0.12), residues: 3939 helix: 0.88 (0.20), residues: 715 sheet: -1.42 (0.19), residues: 656 loop : -2.47 (0.11), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 258 HIS 0.007 0.001 HIS B1083 PHE 0.021 0.002 PHE B 970 TYR 0.021 0.002 TYR A 365 ARG 0.007 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6572 (mpp) cc_final: 0.6033 (mmt) REVERT: A 697 MET cc_start: 0.8795 (ppp) cc_final: 0.8224 (ppp) REVERT: A 1041 ASP cc_start: 0.8247 (m-30) cc_final: 0.7978 (m-30) REVERT: B 1002 GLN cc_start: 0.9355 (tt0) cc_final: 0.9032 (tp40) REVERT: C 1002 GLN cc_start: 0.9465 (tp40) cc_final: 0.9219 (tp-100) REVERT: D 83 MET cc_start: 0.1254 (mpp) cc_final: 0.0852 (mpp) REVERT: D 144 MET cc_start: 0.9539 (mmp) cc_final: 0.9101 (tpp) REVERT: D 178 LYS cc_start: 0.7586 (mmpt) cc_final: 0.7211 (mmpt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 1.1109 time to fit residues: 149.4058 Evaluate side-chains 79 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 354 ASN A 422 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN B 218 GLN B 343 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 657 ASN B 777 ASN B 824 ASN C 125 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN C 751 ASN C 764 ASN C 777 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 31308 Z= 0.386 Angle : 0.736 8.762 42621 Z= 0.414 Chirality : 0.045 0.314 4773 Planarity : 0.006 0.062 5577 Dihedral : 6.330 78.130 4272 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.59 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.91 (0.12), residues: 3939 helix: 0.07 (0.19), residues: 706 sheet: -1.75 (0.20), residues: 591 loop : -2.74 (0.10), residues: 2642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 152 HIS 0.010 0.002 HIS B 655 PHE 0.032 0.003 PHE F 68 TYR 0.029 0.003 TYR D 161 ARG 0.008 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.9275 (ppp) cc_final: 0.8810 (ppp) REVERT: A 978 ASN cc_start: 0.9017 (m-40) cc_final: 0.8805 (t0) REVERT: C 1002 GLN cc_start: 0.9553 (tp40) cc_final: 0.9229 (tp-100) REVERT: D 144 MET cc_start: 0.9589 (mmp) cc_final: 0.9216 (tpp) REVERT: F 34 MET cc_start: 0.6219 (tmm) cc_final: 0.5922 (tmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 1.1065 time to fit residues: 146.1594 Evaluate side-chains 79 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 7.9990 chunk 362 optimal weight: 9.9990 chunk 331 optimal weight: 0.8980 chunk 352 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 277 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 333 optimal weight: 0.9990 chunk 351 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1005 GLN D 3 GLN D 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.8164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31308 Z= 0.224 Angle : 0.598 6.618 42621 Z= 0.332 Chirality : 0.044 0.245 4773 Planarity : 0.005 0.056 5577 Dihedral : 6.115 80.904 4272 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.48 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -2.68 (0.12), residues: 3939 helix: 0.67 (0.20), residues: 710 sheet: -1.82 (0.19), residues: 612 loop : -2.66 (0.11), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 258 HIS 0.006 0.001 HIS C 49 PHE 0.032 0.002 PHE C 565 TYR 0.025 0.002 TYR A 365 ARG 0.006 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6534 (mpp) cc_final: 0.5932 (mmt) REVERT: B 1002 GLN cc_start: 0.9412 (tt0) cc_final: 0.9145 (tp40) REVERT: C 1002 GLN cc_start: 0.9508 (tp40) cc_final: 0.9141 (tp-100) REVERT: D 144 MET cc_start: 0.9550 (mmp) cc_final: 0.9177 (tpp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 1.1713 time to fit residues: 155.5838 Evaluate side-chains 82 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 20.0000 chunk 373 optimal weight: 9.9990 chunk 227 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 391 optimal weight: 4.9990 chunk 360 optimal weight: 20.0000 chunk 311 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 965 GLN B 218 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.8447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31308 Z= 0.247 Angle : 0.599 13.211 42621 Z= 0.332 Chirality : 0.044 0.312 4773 Planarity : 0.005 0.077 5577 Dihedral : 5.993 82.841 4272 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.55 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -2.62 (0.12), residues: 3939 helix: 0.81 (0.20), residues: 710 sheet: -1.77 (0.20), residues: 610 loop : -2.65 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 258 HIS 0.006 0.001 HIS C 49 PHE 0.023 0.002 PHE A 374 TYR 0.026 0.002 TYR A 365 ARG 0.006 0.001 ARG B 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 177 MET cc_start: 0.6749 (mpp) cc_final: 0.6192 (mmt) REVERT: A 697 MET cc_start: 0.9196 (ppp) cc_final: 0.8978 (ppp) REVERT: B 1002 GLN cc_start: 0.9471 (tt0) cc_final: 0.9183 (tm-30) REVERT: C 1002 GLN cc_start: 0.9528 (tp40) cc_final: 0.9165 (tp-100) REVERT: D 83 MET cc_start: -0.0741 (mpp) cc_final: -0.0950 (mpp) REVERT: D 144 MET cc_start: 0.9588 (mmp) cc_final: 0.9182 (tpp) REVERT: F 34 MET cc_start: 0.6183 (tmm) cc_final: 0.5871 (tmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 1.1626 time to fit residues: 154.6553 Evaluate side-chains 83 residues out of total 3372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 287 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 320 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 5.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 218 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 777 ASN C 928 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.038801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.026907 restraints weight = 1588009.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.027555 restraints weight = 1332222.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.028099 restraints weight = 1153632.370| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.8871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 31308 Z= 0.255 Angle : 0.610 6.464 42621 Z= 0.339 Chirality : 0.044 0.167 4773 Planarity : 0.005 0.062 5577 Dihedral : 6.030 83.136 4272 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.32 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.71 (0.12), residues: 3939 helix: 0.74 (0.20), residues: 705 sheet: -1.83 (0.19), residues: 621 loop : -2.71 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 258 HIS 0.007 0.001 HIS C 49 PHE 0.025 0.002 PHE C 194 TYR 0.028 0.002 TYR A 365 ARG 0.005 0.001 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7512.13 seconds wall clock time: 133 minutes 2.99 seconds (7982.99 seconds total)