Starting phenix.real_space_refine on Tue Sep 24 15:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/09_2024/7r4r_14315_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/09_2024/7r4r_14315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/09_2024/7r4r_14315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/09_2024/7r4r_14315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/09_2024/7r4r_14315_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4r_14315/09_2024/7r4r_14315_trim.cif" } resolution = 3.9 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= 0.001 sd= 0.026 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 119 5.16 5 C 16750 2.51 5 N 4337 2.21 5 O 5128 1.98 5 H 24171 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 1.93s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50505 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 16360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 16359 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 16359 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 bond proxies already assigned to first conformer: 16548 Chain: "B" Number of atoms: 16287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1054, 16267 Classifications: {'peptide': 1054} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1000} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1054, 16267 Classifications: {'peptide': 1054} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1000} Chain breaks: 8 bond proxies already assigned to first conformer: 16433 Chain: "C" Number of atoms: 16361 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 bond proxies already assigned to first conformer: 16549 Chain: "D" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 459 " occ=0.60 ... (20 atoms not shown) pdb=" HG BSER B 459 " occ=0.40 Time building chain proxies: 33.10, per 1000 atoms: 0.66 Number of scatterers: 50505 At special positions: 0 Unit cell: (149.6, 159.8, 202.3, 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 119 16.00 O 5128 8.00 N 4337 7.00 C 16750 6.00 H 24171 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.35 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.35 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.35 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1303 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 717 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 61 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG G 1 " - " ASN C 122 " " NAG I 1 " - " ASN C 234 " Time building additional restraints: 10.07 Conformation dependent library (CDL) restraints added in 5.2 seconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6158 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 50 sheets defined 23.0% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.983A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 898 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.867A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.994A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.059A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.510A pdb=" N ASN A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A1120 " --> pdb=" O THR A1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1120' Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.258A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.751A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.676A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 898 through 910 Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.868A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.993A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.059A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1116 through 1120 removed outlier: 3.509A pdb=" N ASN B1119 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B1120 " --> pdb=" O THR B1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1116 through 1120' Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 4.258A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1146' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.940A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.084A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 898 through 910 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.868A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.993A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.059A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1116 through 1120 removed outlier: 3.510A pdb=" N ASN C1119 " --> pdb=" O THR C1116 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C1120 " --> pdb=" O THR C1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1116 through 1120' Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 4.259A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1146' Processing helix chain 'D' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.939A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.535A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.426A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 316 removed outlier: 6.296A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.503A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 4.328A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 660 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 5.608A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.762A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.821A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.632A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.566A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1121 through 1122 removed outlier: 3.617A pdb=" N HIS A1088 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.939A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.535A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.427A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.512A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 316 removed outlier: 6.295A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.531A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD1, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AD2, first strand: chain 'B' and resid 659 through 660 Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 5.672A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.762A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.820A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B1060 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 735 removed outlier: 3.631A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1121 through 1122 removed outlier: 3.618A pdb=" N HIS B1088 " --> pdb=" O ILE B1081 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.939A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 49 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.536A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.427A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.512A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 309 through 316 removed outlier: 6.295A pdb=" N GLU C 309 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 601 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.277A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.080A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 659 through 660 Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.762A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.821A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.632A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1121 through 1122 removed outlier: 3.617A pdb=" N HIS C1088 " --> pdb=" O ILE C1081 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 4.379A pdb=" N ARG D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 10 through 13 966 hydrogen bonds defined for protein. 2640 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: 19.61 Time building geometry restraints manager: 12.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.50 - 0.85: 1190 0.85 - 1.21: 23012 1.21 - 1.56: 26520 1.56 - 1.92: 352 1.92 - 2.28: 16 Warning: very small bond lengths. Bond restraints: 51090 Sorted by residual: bond pdb=" CD ARG A 983 " pdb=" HD2 ARG A 983 " ideal model delta sigma weight residual 0.970 1.951 -0.981 2.00e-02 2.50e+03 2.41e+03 bond pdb=" CD ARG B 983 " pdb=" HD2 ARG B 983 " ideal model delta sigma weight residual 0.970 1.942 -0.972 2.00e-02 2.50e+03 2.36e+03 bond pdb=" CD ARG C 983 " pdb=" HD2 ARG C 983 " ideal model delta sigma weight residual 0.970 1.932 -0.962 2.00e-02 2.50e+03 2.31e+03 bond pdb=" CD ARG C 983 " pdb=" HD3 ARG C 983 " ideal model delta sigma weight residual 0.970 1.835 -0.865 2.00e-02 2.50e+03 1.87e+03 bond pdb=" CD ARG B 983 " pdb=" HD3 ARG B 983 " ideal model delta sigma weight residual 0.970 1.822 -0.852 2.00e-02 2.50e+03 1.81e+03 ... (remaining 51085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 18.31: 88274 18.31 - 36.61: 2224 36.61 - 54.92: 654 54.92 - 73.22: 174 73.22 - 91.53: 17 Bond angle restraints: 91343 Sorted by residual: angle pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " pdb=" NH1 ARG A 983 " ideal model delta sigma weight residual 121.50 57.47 64.03 1.00e+00 1.00e+00 4.10e+03 angle pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " pdb=" NH1 ARG C 983 " ideal model delta sigma weight residual 121.50 57.51 63.99 1.00e+00 1.00e+00 4.09e+03 angle pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " pdb=" NH1 ARG B 983 " ideal model delta sigma weight residual 121.50 57.57 63.93 1.00e+00 1.00e+00 4.09e+03 angle pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sigma weight residual 124.40 49.50 74.90 1.40e+00 5.10e-01 2.86e+03 angle pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sigma weight residual 124.40 49.51 74.89 1.40e+00 5.10e-01 2.86e+03 ... (remaining 91338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 23175 31.91 - 63.82: 1842 63.82 - 95.73: 182 95.73 - 127.64: 19 127.64 - 159.55: 6 Dihedral angle restraints: 25224 sinusoidal: 13784 harmonic: 11440 Sorted by residual: dihedral pdb=" CG HIS C1083 " pdb=" ND1 HIS C1083 " pdb=" CE1 HIS C1083 " pdb=" HE1 HIS C1083 " ideal model delta harmonic sigma weight residual -180.00 -20.45 -159.55 0 5.00e+00 4.00e-02 1.02e+03 dihedral pdb=" CG HIS B1083 " pdb=" ND1 HIS B1083 " pdb=" CE1 HIS B1083 " pdb=" HE1 HIS B1083 " ideal model delta harmonic sigma weight residual -180.00 -20.54 -159.46 0 5.00e+00 4.00e-02 1.02e+03 dihedral pdb=" CG HIS A1083 " pdb=" ND1 HIS A1083 " pdb=" CE1 HIS A1083 " pdb=" HE1 HIS A1083 " ideal model delta harmonic sigma weight residual -180.00 -20.68 -159.32 0 5.00e+00 4.00e-02 1.02e+03 ... (remaining 25221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.774: 4149 0.774 - 1.549: 79 1.549 - 2.323: 7 2.323 - 3.098: 12 3.098 - 3.872: 10 Chirality restraints: 4257 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 1.47 -3.87 2.00e-01 2.50e+01 3.75e+02 chirality pdb=" CB ILE A 923 " pdb=" CA ILE A 923 " pdb=" CG1 ILE A 923 " pdb=" CG2 ILE A 923 " both_signs ideal model delta sigma weight residual False 2.64 -0.95 3.59 2.00e-01 2.50e+01 3.23e+02 chirality pdb=" CB ILE C 923 " pdb=" CA ILE C 923 " pdb=" CG1 ILE C 923 " pdb=" CG2 ILE C 923 " both_signs ideal model delta sigma weight residual False 2.64 -0.95 3.59 2.00e-01 2.50e+01 3.23e+02 ... (remaining 4254 not shown) Planarity restraints: 7707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A1083 " 0.098 2.00e-02 2.50e+03 4.10e-01 3.79e+03 pdb=" CG HIS A1083 " 0.182 2.00e-02 2.50e+03 pdb=" ND1 HIS A1083 " 0.557 2.00e-02 2.50e+03 pdb=" CD2 HIS A1083 " -0.597 2.00e-02 2.50e+03 pdb=" CE1 HIS A1083 " 0.431 2.00e-02 2.50e+03 pdb=" NE2 HIS A1083 " -0.592 2.00e-02 2.50e+03 pdb=" HD2 HIS A1083 " -0.324 2.00e-02 2.50e+03 pdb=" HE1 HIS A1083 " 0.382 2.00e-02 2.50e+03 pdb=" HE2 HIS A1083 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B1083 " -0.098 2.00e-02 2.50e+03 4.10e-01 3.79e+03 pdb=" CG HIS B1083 " -0.182 2.00e-02 2.50e+03 pdb=" ND1 HIS B1083 " -0.557 2.00e-02 2.50e+03 pdb=" CD2 HIS B1083 " 0.598 2.00e-02 2.50e+03 pdb=" CE1 HIS B1083 " -0.432 2.00e-02 2.50e+03 pdb=" NE2 HIS B1083 " 0.591 2.00e-02 2.50e+03 pdb=" HD2 HIS B1083 " 0.324 2.00e-02 2.50e+03 pdb=" HE1 HIS B1083 " -0.380 2.00e-02 2.50e+03 pdb=" HE2 HIS B1083 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C1083 " -0.098 2.00e-02 2.50e+03 4.10e-01 3.78e+03 pdb=" CG HIS C1083 " -0.182 2.00e-02 2.50e+03 pdb=" ND1 HIS C1083 " -0.555 2.00e-02 2.50e+03 pdb=" CD2 HIS C1083 " 0.596 2.00e-02 2.50e+03 pdb=" CE1 HIS C1083 " -0.431 2.00e-02 2.50e+03 pdb=" NE2 HIS C1083 " 0.592 2.00e-02 2.50e+03 pdb=" HD2 HIS C1083 " 0.324 2.00e-02 2.50e+03 pdb=" HE1 HIS C1083 " -0.382 2.00e-02 2.50e+03 pdb=" HE2 HIS C1083 " 0.136 2.00e-02 2.50e+03 ... (remaining 7704 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 228 1.52 - 2.29: 16936 2.29 - 3.06: 151259 3.06 - 3.83: 213401 3.83 - 4.60: 334213 Warning: very small nonbonded interaction distances. Nonbonded interactions: 716037 Sorted by model distance: nonbonded pdb=" OE1 GLN B 954 " pdb="HE21 GLN B 954 " model vdw 0.749 1.960 nonbonded pdb=" OE1 GLN C 954 " pdb="HE21 GLN C 954 " model vdw 0.768 1.960 nonbonded pdb=" OE1 GLN A 954 " pdb="HE21 GLN A 954 " model vdw 0.768 1.960 nonbonded pdb=" OE1 GLN C 954 " pdb="HE22 GLN C 954 " model vdw 0.769 1.960 nonbonded pdb=" OE1 GLN A 954 " pdb="HE22 GLN A 954 " model vdw 0.769 1.960 ... (remaining 716032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 577 or (resid 584 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 o \ r name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) o \ r resid 585 through 1063 or (resid 1064 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 1065 through 1146 or resid 1301 through 1307)) selection = (chain 'B' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 656 or (resid 657 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or \ resid 658 through 1146 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 577 or (resid 584 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 o \ r name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) o \ r resid 585 through 656 or (resid 657 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 \ or name HB3)) or resid 658 through 1063 or (resid 1064 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or n \ ame NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or \ name HE2)) or resid 1065 through 1146 or resid 1301 through 1307)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.33 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: 7.540 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: 0.670 Extract box with map and model: 1.510 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 102.770 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.190 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4286 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 : 0.036 0.757 26919 Z= 2.366 Angle : 4.110 74.897 36614 Z= 2.248 Chirality : 0.315 3.872 4257 Planarity : 0.029 0.574 4684 Dihedral : 18.824 113.688 10311 Min Nonbonded Distance : 1.228 Molprobity Statistics. All-atom Clashscore : 59.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.52 % Favored : 91.27 % Rotamer: Outliers : 7.44 % Allowed : 31.12 % Favored : 61.44 % Cbeta Deviations : 4.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.91 % Twisted General : 1.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.13), residues: 3245 helix: -2.02 (0.17), residues: 640 sheet: -1.49 (0.20), residues: 628 loop : -2.48 (0.12), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.124 0.011 TRP C1102 HIS 0.407 0.035 HIS A1083 PHE 0.345 0.013 PHE A 318 TYR 0.178 0.006 TYR A 266 ARG 0.347 0.023 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 510 time to evaluate : 2.760 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 49 HIS cc_start: 0.4639 (OUTLIER) cc_final: 0.3616 (t-90) REVERT: A 118 LEU cc_start: 0.8087 (pt) cc_final: 0.7846 (pt) REVERT: A 151 SER cc_start: 0.8040 (t) cc_final: 0.7802 (p) REVERT: A 207 HIS cc_start: 0.5082 (p-80) cc_final: 0.4834 (p-80) REVERT: A 320 VAL cc_start: 0.5457 (OUTLIER) cc_final: 0.5205 (p) REVERT: A 377 PHE cc_start: 0.4313 (OUTLIER) cc_final: 0.3798 (p90) REVERT: A 389 ASP cc_start: 0.5500 (OUTLIER) cc_final: 0.5267 (p0) REVERT: A 398 ASP cc_start: 0.7964 (m-30) cc_final: 0.7738 (p0) REVERT: A 580 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.4819 (mm-40) REVERT: A 767 LEU cc_start: 0.5006 (pp) cc_final: 0.4396 (mp) REVERT: A 858 LEU cc_start: 0.8235 (mt) cc_final: 0.7816 (mm) REVERT: A 933 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7057 (tppp) REVERT: B 133 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: B 374 PHE cc_start: 0.2682 (OUTLIER) cc_final: -0.2149 (m-80) REVERT: B 393 THR cc_start: 0.5534 (p) cc_final: 0.4747 (p) REVERT: B 440 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6761 (p0) REVERT: B 456 PHE cc_start: 0.2835 (OUTLIER) cc_final: 0.1322 (m-80) REVERT: B 516 GLU cc_start: 0.4039 (OUTLIER) cc_final: 0.3162 (mp0) REVERT: B 613 GLN cc_start: 0.5498 (tp40) cc_final: 0.4881 (tp40) REVERT: B 619 GLU cc_start: 0.3124 (OUTLIER) cc_final: 0.2230 (mp0) REVERT: B 931 ILE cc_start: 0.3365 (mm) cc_final: 0.2685 (mm) REVERT: C 47 VAL cc_start: 0.3953 (t) cc_final: 0.3690 (t) REVERT: C 277 LEU cc_start: 0.5657 (mm) cc_final: 0.5166 (mt) REVERT: C 422 ASN cc_start: 0.6323 (OUTLIER) cc_final: 0.5115 (t0) REVERT: C 444 LYS cc_start: 0.3854 (OUTLIER) cc_final: 0.1545 (ttpp) REVERT: C 538 CYS cc_start: 0.1835 (OUTLIER) cc_final: 0.1191 (p) REVERT: C 740 MET cc_start: 0.6755 (ppp) cc_final: 0.6279 (ppp) REVERT: C 900 MET cc_start: 0.1447 (mmm) cc_final: 0.1110 (mmm) REVERT: C 1009 THR cc_start: 0.5703 (p) cc_final: 0.4449 (m) REVERT: C 1038 LYS cc_start: 0.7397 (mmtm) cc_final: 0.7179 (mmtm) REVERT: D 104 CYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5612 (m) outliers start: 211 outliers final: 123 residues processed: 683 average time/residue: 0.7938 time to fit residues: 827.6322 Evaluate side-chains 587 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 448 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1095 PHE Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1095 PHE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 116 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 257 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 297 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 388 ASN A 409 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 49 HIS B 196 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 414 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 955 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 394 ASN C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 658 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN D 73 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4504 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 26919 Z= 0.479 Angle : 1.817 42.594 36614 Z= 0.884 Chirality : 0.224 1.924 4257 Planarity : 0.014 0.351 4684 Dihedral : 15.241 140.652 4755 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 35.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.98 % Favored : 90.87 % Rotamer: Outliers : 11.93 % Allowed : 26.18 % Favored : 61.89 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.13), residues: 3245 helix: -1.81 (0.17), residues: 652 sheet: -1.56 (0.19), residues: 679 loop : -2.58 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C1102 HIS 0.023 0.004 HIS A1083 PHE 0.085 0.003 PHE C 43 TYR 0.041 0.002 TYR C 279 ARG 0.038 0.002 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 432 time to evaluate : 2.752 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 VAL cc_start: 0.5031 (OUTLIER) cc_final: 0.4805 (m) REVERT: A 47 VAL cc_start: 0.4815 (OUTLIER) cc_final: 0.4572 (t) REVERT: A 63 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8270 (t) REVERT: A 158 ARG cc_start: 0.6536 (ttp-170) cc_final: 0.6249 (ttm170) REVERT: A 207 HIS cc_start: 0.5612 (p-80) cc_final: 0.5376 (p-80) REVERT: A 212 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5483 (pt) REVERT: A 377 PHE cc_start: 0.4497 (OUTLIER) cc_final: 0.4040 (p90) REVERT: A 580 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.4980 (mm-40) REVERT: A 773 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.4964 (tm-30) REVERT: A 869 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7914 (ptp) REVERT: B 29 THR cc_start: 0.4984 (OUTLIER) cc_final: 0.4655 (p) REVERT: B 62 VAL cc_start: 0.6107 (OUTLIER) cc_final: 0.5691 (t) REVERT: B 113 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8971 (tptp) REVERT: B 157 PHE cc_start: 0.3016 (OUTLIER) cc_final: 0.2675 (m-80) REVERT: B 341 VAL cc_start: 0.3790 (OUTLIER) cc_final: 0.2958 (p) REVERT: B 374 PHE cc_start: 0.2797 (OUTLIER) cc_final: -0.2160 (m-80) REVERT: B 455 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.5368 (mt) REVERT: B 456 PHE cc_start: 0.3139 (OUTLIER) cc_final: 0.0686 (m-80) REVERT: B 490 PHE cc_start: 0.8600 (t80) cc_final: 0.8321 (t80) REVERT: B 611 LEU cc_start: 0.7283 (tt) cc_final: 0.6649 (tp) REVERT: B 613 GLN cc_start: 0.6194 (tp40) cc_final: 0.4875 (tm-30) REVERT: B 619 GLU cc_start: 0.3687 (OUTLIER) cc_final: 0.3221 (mp0) REVERT: B 710 ASN cc_start: 0.4155 (OUTLIER) cc_final: 0.3931 (p0) REVERT: B 872 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.5270 (pp30) REVERT: B 888 PHE cc_start: 0.8253 (p90) cc_final: 0.8014 (p90) REVERT: B 894 LEU cc_start: 0.4143 (mt) cc_final: 0.3203 (mt) REVERT: B 1145 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4332 (mt) REVERT: C 42 VAL cc_start: 0.4073 (OUTLIER) cc_final: 0.3862 (t) REVERT: C 65 PHE cc_start: 0.3086 (OUTLIER) cc_final: 0.2846 (m-80) REVERT: C 153 MET cc_start: 0.5311 (ptp) cc_final: 0.5017 (pmm) REVERT: C 157 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5445 (t80) REVERT: C 160 TYR cc_start: 0.5927 (p90) cc_final: 0.5600 (p90) REVERT: C 422 ASN cc_start: 0.6613 (OUTLIER) cc_final: 0.5415 (t0) REVERT: C 444 LYS cc_start: 0.3702 (OUTLIER) cc_final: 0.0733 (tttt) REVERT: C 448 ASN cc_start: 0.7667 (t0) cc_final: 0.7293 (m-40) REVERT: C 611 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6673 (tp) REVERT: C 646 ARG cc_start: 0.5419 (mmm160) cc_final: 0.5146 (mmp80) REVERT: C 900 MET cc_start: 0.2248 (mmm) cc_final: 0.1683 (mmm) REVERT: C 996 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7436 (tt) REVERT: C 1009 THR cc_start: 0.5995 (p) cc_final: 0.4643 (m) REVERT: C 1038 LYS cc_start: 0.7546 (mmtm) cc_final: 0.7317 (mmtm) REVERT: C 1050 MET cc_start: 0.5843 (tpp) cc_final: 0.5022 (tpp) REVERT: C 1145 LEU cc_start: 0.0529 (OUTLIER) cc_final: -0.0846 (tt) REVERT: D 104 CYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5885 (m) outliers start: 340 outliers final: 207 residues processed: 697 average time/residue: 0.6944 time to fit residues: 752.6283 Evaluate side-chains 646 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 410 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 104 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 322 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 925 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 388 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4666 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 26919 Z= 0.358 Angle : 1.509 37.147 36614 Z= 0.752 Chirality : 0.234 1.805 4257 Planarity : 0.010 0.371 4684 Dihedral : 13.072 158.113 4635 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 29.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.79 % Favored : 91.05 % Rotamer: Outliers : 9.14 % Allowed : 27.29 % Favored : 63.56 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.13), residues: 3245 helix: -1.43 (0.17), residues: 654 sheet: -1.59 (0.19), residues: 669 loop : -2.49 (0.12), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C1102 HIS 0.012 0.003 HIS B 245 PHE 0.048 0.002 PHE B 43 TYR 0.029 0.002 TYR B 37 ARG 0.039 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 419 time to evaluate : 2.766 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TRP cc_start: 0.8137 (t-100) cc_final: 0.7829 (t-100) REVERT: A 207 HIS cc_start: 0.5821 (p-80) cc_final: 0.5515 (p-80) REVERT: A 368 LEU cc_start: 0.2577 (OUTLIER) cc_final: 0.1341 (tp) REVERT: A 377 PHE cc_start: 0.4529 (OUTLIER) cc_final: 0.3966 (p90) REVERT: A 697 MET cc_start: 0.4848 (tpt) cc_final: 0.4039 (tpt) REVERT: A 752 LEU cc_start: 0.9292 (mt) cc_final: 0.9086 (mt) REVERT: A 773 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.4977 (tm-30) REVERT: A 925 ASN cc_start: 0.8734 (m-40) cc_final: 0.8531 (m-40) REVERT: A 947 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7741 (tppt) REVERT: A 1094 VAL cc_start: 0.4410 (m) cc_final: 0.3836 (t) REVERT: B 42 VAL cc_start: 0.1603 (OUTLIER) cc_final: 0.1342 (m) REVERT: B 62 VAL cc_start: 0.6293 (OUTLIER) cc_final: 0.5979 (t) REVERT: B 220 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.4110 (t80) REVERT: B 374 PHE cc_start: 0.2710 (OUTLIER) cc_final: -0.2208 (m-80) REVERT: B 455 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5180 (mt) REVERT: B 456 PHE cc_start: 0.2939 (OUTLIER) cc_final: 0.0871 (m-80) REVERT: B 473 TYR cc_start: 0.5599 (t80) cc_final: 0.5311 (t80) REVERT: B 490 PHE cc_start: 0.8600 (t80) cc_final: 0.8309 (t80) REVERT: B 539 VAL cc_start: 0.5223 (OUTLIER) cc_final: 0.5012 (m) REVERT: B 613 GLN cc_start: 0.6264 (tp40) cc_final: 0.5190 (tm-30) REVERT: B 619 GLU cc_start: 0.4253 (OUTLIER) cc_final: 0.4003 (mp0) REVERT: B 655 HIS cc_start: 0.7075 (t-90) cc_final: 0.6839 (m-70) REVERT: B 735 SER cc_start: 0.6658 (OUTLIER) cc_final: 0.6265 (p) REVERT: B 743 CYS cc_start: 0.3075 (OUTLIER) cc_final: 0.2795 (p) REVERT: B 872 GLN cc_start: 0.5726 (OUTLIER) cc_final: 0.5513 (pp30) REVERT: B 888 PHE cc_start: 0.8290 (p90) cc_final: 0.7956 (p90) REVERT: C 54 LEU cc_start: 0.4566 (mt) cc_final: 0.3532 (mt) REVERT: C 65 PHE cc_start: 0.3412 (OUTLIER) cc_final: 0.1595 (m-80) REVERT: C 77 LYS cc_start: 0.7420 (mmtm) cc_final: 0.7211 (mttt) REVERT: C 153 MET cc_start: 0.5001 (ptp) cc_final: 0.4617 (pmm) REVERT: C 160 TYR cc_start: 0.6146 (p90) cc_final: 0.5688 (p90) REVERT: C 177 MET cc_start: 0.1523 (mtm) cc_final: 0.1253 (mtm) REVERT: C 265 TYR cc_start: 0.8452 (p90) cc_final: 0.8195 (p90) REVERT: C 422 ASN cc_start: 0.6706 (OUTLIER) cc_final: 0.5496 (t0) REVERT: C 444 LYS cc_start: 0.3521 (OUTLIER) cc_final: 0.1004 (tttm) REVERT: C 448 ASN cc_start: 0.7858 (t0) cc_final: 0.7479 (m-40) REVERT: C 529 LYS cc_start: 0.2831 (OUTLIER) cc_final: 0.0483 (pptt) REVERT: C 646 ARG cc_start: 0.5569 (mmm160) cc_final: 0.5312 (mmp80) REVERT: C 658 ASN cc_start: 0.8500 (m-40) cc_final: 0.8209 (p0) REVERT: C 740 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5463 (ppp) REVERT: C 900 MET cc_start: 0.2172 (mmm) cc_final: 0.1603 (mmm) REVERT: C 996 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7399 (tt) REVERT: C 1038 LYS cc_start: 0.7704 (mmtm) cc_final: 0.7469 (mmtm) REVERT: C 1145 LEU cc_start: 0.0695 (OUTLIER) cc_final: -0.0088 (tt) outliers start: 260 outliers final: 195 residues processed: 617 average time/residue: 0.7265 time to fit residues: 690.9525 Evaluate side-chains 624 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 407 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1023 ASN Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 317 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 283 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 414 GLN C 564 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C 957 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26919 Z= 0.325 Angle : 1.418 38.087 36614 Z= 0.713 Chirality : 0.238 1.928 4257 Planarity : 0.006 0.077 4684 Dihedral : 11.514 171.859 4614 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.95 % Favored : 90.90 % Rotamer: Outliers : 8.03 % Allowed : 27.78 % Favored : 64.19 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.90 (0.13), residues: 3245 helix: -1.19 (0.18), residues: 651 sheet: -1.57 (0.19), residues: 654 loop : -2.41 (0.12), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.013 0.002 HIS A1064 PHE 0.036 0.002 PHE A 565 TYR 0.024 0.002 TYR C 279 ARG 0.009 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 430 time to evaluate : 2.755 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TRP cc_start: 0.8114 (t-100) cc_final: 0.7873 (t-100) REVERT: A 117 LEU cc_start: 0.7148 (pp) cc_final: 0.6944 (pt) REVERT: A 220 PHE cc_start: 0.5761 (OUTLIER) cc_final: 0.5172 (t80) REVERT: A 238 PHE cc_start: 0.7904 (p90) cc_final: 0.7699 (p90) REVERT: A 368 LEU cc_start: 0.2399 (OUTLIER) cc_final: 0.1203 (tp) REVERT: A 377 PHE cc_start: 0.4652 (OUTLIER) cc_final: 0.4188 (p90) REVERT: A 913 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: A 952 VAL cc_start: 0.7341 (m) cc_final: 0.6967 (t) REVERT: A 1094 VAL cc_start: 0.4999 (m) cc_final: 0.4484 (t) REVERT: B 220 PHE cc_start: 0.5422 (OUTLIER) cc_final: 0.4370 (t80) REVERT: B 374 PHE cc_start: 0.2813 (OUTLIER) cc_final: -0.2169 (m-80) REVERT: B 442 ASP cc_start: 0.6632 (t0) cc_final: 0.6118 (t0) REVERT: B 451 TYR cc_start: 0.7572 (m-10) cc_final: 0.7266 (m-10) REVERT: B 455 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.5509 (mt) REVERT: B 490 PHE cc_start: 0.8636 (t80) cc_final: 0.8358 (t80) REVERT: B 539 VAL cc_start: 0.5284 (OUTLIER) cc_final: 0.5073 (m) REVERT: B 560 LEU cc_start: -0.0002 (OUTLIER) cc_final: -0.0997 (mt) REVERT: B 613 GLN cc_start: 0.6569 (tp40) cc_final: 0.5658 (tm-30) REVERT: B 619 GLU cc_start: 0.4632 (OUTLIER) cc_final: 0.4415 (mp0) REVERT: B 735 SER cc_start: 0.6761 (OUTLIER) cc_final: 0.6372 (p) REVERT: B 743 CYS cc_start: 0.3613 (OUTLIER) cc_final: 0.3280 (p) REVERT: B 872 GLN cc_start: 0.5901 (OUTLIER) cc_final: 0.5677 (pp30) REVERT: B 888 PHE cc_start: 0.8286 (p90) cc_final: 0.7937 (p90) REVERT: B 1091 ARG cc_start: 0.1415 (OUTLIER) cc_final: -0.0883 (ptp-110) REVERT: C 54 LEU cc_start: 0.4444 (mt) cc_final: 0.3417 (mt) REVERT: C 65 PHE cc_start: 0.3850 (OUTLIER) cc_final: 0.0925 (m-80) REVERT: C 160 TYR cc_start: 0.6222 (p90) cc_final: 0.5765 (p90) REVERT: C 177 MET cc_start: 0.1848 (mtm) cc_final: 0.1501 (mtm) REVERT: C 265 TYR cc_start: 0.8520 (p90) cc_final: 0.8178 (p90) REVERT: C 444 LYS cc_start: 0.3737 (OUTLIER) cc_final: 0.1305 (tttm) REVERT: C 448 ASN cc_start: 0.7921 (t0) cc_final: 0.7540 (m-40) REVERT: C 529 LYS cc_start: 0.3585 (OUTLIER) cc_final: 0.1040 (pptt) REVERT: C 646 ARG cc_start: 0.6098 (mmm160) cc_final: 0.5828 (mmp80) REVERT: C 658 ASN cc_start: 0.8623 (m-40) cc_final: 0.8311 (p0) REVERT: C 900 MET cc_start: 0.2112 (mmm) cc_final: 0.1493 (mmm) REVERT: C 996 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7496 (tt) REVERT: C 1038 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7684 (mmtm) REVERT: C 1050 MET cc_start: 0.5768 (tpp) cc_final: 0.5321 (tpp) REVERT: C 1113 GLN cc_start: 0.2862 (OUTLIER) cc_final: 0.2487 (pm20) outliers start: 228 outliers final: 169 residues processed: 596 average time/residue: 0.7203 time to fit residues: 655.5624 Evaluate side-chains 599 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 411 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 236 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 284 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A 955 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN B 81 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 498 GLN C 540 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.181 26919 Z= 0.425 Angle : 1.452 36.385 36614 Z= 0.740 Chirality : 0.240 1.878 4257 Planarity : 0.007 0.080 4684 Dihedral : 11.156 179.445 4587 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 38.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.83 % Favored : 89.08 % Rotamer: Outliers : 7.96 % Allowed : 27.92 % Favored : 64.12 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.13), residues: 3245 helix: -1.46 (0.18), residues: 640 sheet: -1.83 (0.20), residues: 632 loop : -2.56 (0.12), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 64 HIS 0.011 0.003 HIS A1064 PHE 0.041 0.003 PHE B1089 TYR 0.028 0.002 TYR B 473 ARG 0.007 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 457 time to evaluate : 2.769 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TRP cc_start: 0.8340 (t60) cc_final: 0.8043 (t-100) REVERT: A 92 PHE cc_start: 0.7083 (t80) cc_final: 0.6670 (t80) REVERT: A 159 VAL cc_start: 0.6427 (OUTLIER) cc_final: 0.5225 (t) REVERT: A 207 HIS cc_start: 0.6495 (p-80) cc_final: 0.6182 (p-80) REVERT: A 220 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.6022 (t80) REVERT: A 368 LEU cc_start: 0.2309 (OUTLIER) cc_final: 0.1118 (tp) REVERT: A 377 PHE cc_start: 0.4826 (OUTLIER) cc_final: 0.4404 (p90) REVERT: A 953 ASN cc_start: 0.8068 (m110) cc_final: 0.7818 (m-40) REVERT: A 1144 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: B 220 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.5996 (t80) REVERT: B 374 PHE cc_start: 0.3006 (OUTLIER) cc_final: -0.1988 (m-80) REVERT: B 451 TYR cc_start: 0.7956 (m-10) cc_final: 0.7547 (m-10) REVERT: B 455 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.5519 (mt) REVERT: B 456 PHE cc_start: 0.3601 (OUTLIER) cc_final: 0.1474 (m-80) REVERT: B 490 PHE cc_start: 0.8680 (t80) cc_final: 0.8345 (t80) REVERT: B 726 ILE cc_start: 0.8177 (tp) cc_final: 0.7915 (tt) REVERT: B 735 SER cc_start: 0.7055 (OUTLIER) cc_final: 0.6479 (p) REVERT: B 749 CYS cc_start: 0.7470 (m) cc_final: 0.7141 (m) REVERT: B 868 GLU cc_start: 0.4372 (OUTLIER) cc_final: 0.3719 (mm-30) REVERT: B 888 PHE cc_start: 0.8499 (p90) cc_final: 0.8283 (p90) REVERT: B 913 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7720 (mm-40) REVERT: B 933 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6545 (ttpp) REVERT: B 983 ARG cc_start: 0.8056 (tmm-80) cc_final: 0.7597 (tmm-80) REVERT: B 1091 ARG cc_start: 0.3107 (OUTLIER) cc_final: 0.1463 (ptp-110) REVERT: C 160 TYR cc_start: 0.6630 (p90) cc_final: 0.6055 (p90) REVERT: C 177 MET cc_start: 0.1961 (mtm) cc_final: 0.1638 (mtm) REVERT: C 265 TYR cc_start: 0.8604 (p90) cc_final: 0.8383 (p90) REVERT: C 444 LYS cc_start: 0.4452 (OUTLIER) cc_final: 0.2009 (tttm) REVERT: C 448 ASN cc_start: 0.8246 (t0) cc_final: 0.7897 (m-40) REVERT: C 529 LYS cc_start: 0.4997 (OUTLIER) cc_final: 0.2480 (pptt) REVERT: C 568 ASP cc_start: 0.7062 (p0) cc_final: 0.6833 (p0) REVERT: C 646 ARG cc_start: 0.6870 (mmm160) cc_final: 0.6553 (mmp80) REVERT: C 658 ASN cc_start: 0.8879 (m-40) cc_final: 0.8397 (p0) REVERT: C 740 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6257 (ppp) REVERT: C 773 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: C 900 MET cc_start: 0.3105 (mmm) cc_final: 0.2486 (mmm) REVERT: C 991 VAL cc_start: 0.6453 (OUTLIER) cc_final: 0.5795 (t) REVERT: C 1007 TYR cc_start: 0.7428 (t80) cc_final: 0.6732 (t80) REVERT: C 1038 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7978 (mmtm) REVERT: C 1113 GLN cc_start: 0.3532 (OUTLIER) cc_final: 0.3283 (pm20) REVERT: C 1138 TYR cc_start: 0.7662 (t80) cc_final: 0.7401 (t80) outliers start: 226 outliers final: 180 residues processed: 620 average time/residue: 0.7516 time to fit residues: 711.9851 Evaluate side-chains 627 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 427 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 7.9990 chunk 285 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 186 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 317 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5321 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26919 Z= 0.301 Angle : 1.381 37.550 36614 Z= 0.696 Chirality : 0.239 1.763 4257 Planarity : 0.005 0.067 4684 Dihedral : 10.562 179.838 4584 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.01 % Favored : 90.87 % Rotamer: Outliers : 6.75 % Allowed : 29.14 % Favored : 64.12 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.13 % 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: -2.96 (0.13), residues: 3245 helix: -1.02 (0.19), residues: 647 sheet: -1.69 (0.20), residues: 620 loop : -2.49 (0.12), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 64 HIS 0.009 0.002 HIS B 66 PHE 0.026 0.002 PHE A 43 TYR 0.028 0.002 TYR A 269 ARG 0.006 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 438 time to evaluate : 2.872 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 58 PHE cc_start: 0.5763 (m-80) cc_final: 0.5349 (m-80) REVERT: A 64 TRP cc_start: 0.8309 (t60) cc_final: 0.7935 (t-100) REVERT: A 92 PHE cc_start: 0.7105 (t80) cc_final: 0.6658 (t80) REVERT: A 129 LYS cc_start: 0.8771 (mttt) cc_final: 0.8330 (mmtt) REVERT: A 159 VAL cc_start: 0.6648 (OUTLIER) cc_final: 0.5439 (t) REVERT: A 220 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5779 (t80) REVERT: A 368 LEU cc_start: 0.2446 (OUTLIER) cc_final: 0.1326 (tp) REVERT: A 377 PHE cc_start: 0.4879 (OUTLIER) cc_final: 0.4427 (p90) REVERT: A 1094 VAL cc_start: 0.5918 (OUTLIER) cc_final: 0.5399 (t) REVERT: B 328 ARG cc_start: 0.5924 (mmm160) cc_final: 0.5658 (mmm160) REVERT: B 374 PHE cc_start: 0.2746 (OUTLIER) cc_final: -0.1369 (m-80) REVERT: B 442 ASP cc_start: 0.6923 (t0) cc_final: 0.5766 (t0) REVERT: B 451 TYR cc_start: 0.7801 (m-10) cc_final: 0.7312 (m-80) REVERT: B 455 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.5012 (mp) REVERT: B 456 PHE cc_start: 0.3512 (OUTLIER) cc_final: 0.1272 (m-80) REVERT: B 490 PHE cc_start: 0.8597 (t80) cc_final: 0.8395 (t80) REVERT: B 613 GLN cc_start: 0.6840 (tp40) cc_final: 0.6000 (tm-30) REVERT: B 726 ILE cc_start: 0.8111 (tp) cc_final: 0.7810 (tt) REVERT: B 913 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7529 (mm-40) REVERT: B 983 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.7592 (tmm-80) REVERT: C 160 TYR cc_start: 0.6402 (p90) cc_final: 0.5892 (p90) REVERT: C 177 MET cc_start: 0.1993 (mtm) cc_final: 0.1656 (mtm) REVERT: C 265 TYR cc_start: 0.8506 (p90) cc_final: 0.8287 (p90) REVERT: C 444 LYS cc_start: 0.3757 (OUTLIER) cc_final: 0.1474 (tttm) REVERT: C 448 ASN cc_start: 0.8066 (t0) cc_final: 0.7693 (m-40) REVERT: C 529 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.2952 (pptt) REVERT: C 568 ASP cc_start: 0.6840 (p0) cc_final: 0.6591 (p0) REVERT: C 595 VAL cc_start: 0.8128 (t) cc_final: 0.7557 (t) REVERT: C 613 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: C 646 ARG cc_start: 0.6935 (mmm160) cc_final: 0.6645 (mmp80) REVERT: C 658 ASN cc_start: 0.8839 (m-40) cc_final: 0.8415 (p0) REVERT: C 773 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: C 900 MET cc_start: 0.2644 (mmm) cc_final: 0.1991 (mmm) REVERT: C 1007 TYR cc_start: 0.7242 (t80) cc_final: 0.6554 (t80) REVERT: C 1038 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7941 (mmtm) REVERT: C 1138 TYR cc_start: 0.7564 (t80) cc_final: 0.7269 (t80) REVERT: C 1145 LEU cc_start: 0.2590 (OUTLIER) cc_final: 0.2251 (tt) outliers start: 190 outliers final: 156 residues processed: 575 average time/residue: 0.7469 time to fit residues: 654.5297 Evaluate side-chains 600 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 430 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 180 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 316 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 192 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 414 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 474 GLN C 556 ASN C 658 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26919 Z= 0.279 Angle : 1.349 33.085 36614 Z= 0.682 Chirality : 0.239 1.896 4257 Planarity : 0.005 0.069 4684 Dihedral : 9.905 179.314 4572 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.23 % Favored : 90.68 % Rotamer: Outliers : 6.02 % Allowed : 29.55 % Favored : 64.43 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.10 % 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: -2.73 (0.13), residues: 3245 helix: -0.75 (0.19), residues: 654 sheet: -1.57 (0.20), residues: 631 loop : -2.37 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 64 HIS 0.007 0.001 HIS A 66 PHE 0.026 0.002 PHE A 43 TYR 0.020 0.001 TYR A 269 ARG 0.015 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 446 time to evaluate : 2.802 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 92 PHE cc_start: 0.7138 (t80) cc_final: 0.6717 (t80) REVERT: A 129 LYS cc_start: 0.8749 (mttt) cc_final: 0.8321 (mmtt) REVERT: A 133 PHE cc_start: 0.7982 (m-80) cc_final: 0.7401 (m-80) REVERT: A 159 VAL cc_start: 0.6679 (OUTLIER) cc_final: 0.5133 (t) REVERT: A 160 TYR cc_start: 0.8202 (p90) cc_final: 0.7800 (p90) REVERT: A 220 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5837 (t80) REVERT: A 302 THR cc_start: 0.7240 (p) cc_final: 0.6998 (p) REVERT: A 368 LEU cc_start: 0.2392 (OUTLIER) cc_final: 0.1180 (tt) REVERT: A 377 PHE cc_start: 0.4864 (OUTLIER) cc_final: 0.4475 (p90) REVERT: A 731 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7094 (ttp) REVERT: A 886 TRP cc_start: 0.6808 (OUTLIER) cc_final: 0.6601 (p90) REVERT: A 1051 SER cc_start: 0.8168 (m) cc_final: 0.7962 (p) REVERT: A 1092 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: B 64 TRP cc_start: 0.6413 (t-100) cc_final: 0.6148 (t-100) REVERT: B 357 ARG cc_start: 0.7590 (tmm-80) cc_final: 0.7353 (tmm-80) REVERT: B 374 PHE cc_start: 0.2509 (OUTLIER) cc_final: -0.1691 (m-80) REVERT: B 451 TYR cc_start: 0.7773 (m-10) cc_final: 0.7209 (m-80) REVERT: B 455 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.5444 (mp) REVERT: B 490 PHE cc_start: 0.8713 (t80) cc_final: 0.8411 (t80) REVERT: B 563 GLN cc_start: 0.3088 (OUTLIER) cc_final: 0.2286 (pt0) REVERT: B 613 GLN cc_start: 0.6530 (tp40) cc_final: 0.5945 (tm-30) REVERT: B 697 MET cc_start: 0.7818 (ppp) cc_final: 0.7281 (ppp) REVERT: B 726 ILE cc_start: 0.8066 (tp) cc_final: 0.7793 (tt) REVERT: B 749 CYS cc_start: 0.7180 (m) cc_final: 0.6980 (m) REVERT: B 983 ARG cc_start: 0.8009 (tmm-80) cc_final: 0.7558 (tmm-80) REVERT: C 246 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7970 (ptt180) REVERT: C 265 TYR cc_start: 0.8471 (p90) cc_final: 0.8269 (p90) REVERT: C 444 LYS cc_start: 0.3492 (OUTLIER) cc_final: 0.1556 (tttm) REVERT: C 448 ASN cc_start: 0.7965 (t0) cc_final: 0.7683 (m-40) REVERT: C 529 LYS cc_start: 0.5371 (OUTLIER) cc_final: 0.3410 (pptt) REVERT: C 595 VAL cc_start: 0.8156 (t) cc_final: 0.7611 (t) REVERT: C 613 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: C 658 ASN cc_start: 0.8826 (m110) cc_final: 0.8496 (p0) REVERT: C 731 MET cc_start: 0.5141 (tpp) cc_final: 0.4826 (tpp) REVERT: C 773 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: C 881 THR cc_start: 0.5369 (p) cc_final: 0.3949 (m) REVERT: C 900 MET cc_start: 0.2648 (mmm) cc_final: 0.1968 (mmm) REVERT: C 1007 TYR cc_start: 0.7157 (t80) cc_final: 0.6447 (t80) REVERT: C 1009 THR cc_start: 0.7072 (p) cc_final: 0.6106 (m) REVERT: C 1038 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7960 (mmtm) REVERT: C 1138 TYR cc_start: 0.7532 (t80) cc_final: 0.7237 (t80) REVERT: C 1145 LEU cc_start: 0.2650 (OUTLIER) cc_final: 0.2312 (tt) outliers start: 169 outliers final: 143 residues processed: 566 average time/residue: 0.7756 time to fit residues: 670.0788 Evaluate side-chains 589 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 431 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 0.4980 chunk 126 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26919 Z= 0.274 Angle : 1.330 33.127 36614 Z= 0.674 Chirality : 0.239 1.816 4257 Planarity : 0.005 0.068 4684 Dihedral : 9.457 179.446 4560 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.27 % Favored : 91.64 % Rotamer: Outliers : 5.84 % Allowed : 29.76 % Favored : 64.39 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % Twisted General : 0.06 % 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: -2.57 (0.13), residues: 3245 helix: -0.56 (0.19), residues: 656 sheet: -1.46 (0.20), residues: 623 loop : -2.29 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 353 HIS 0.007 0.001 HIS A1064 PHE 0.025 0.001 PHE A 43 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 445 time to evaluate : 2.769 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 92 PHE cc_start: 0.7242 (t80) cc_final: 0.6781 (t80) REVERT: A 129 LYS cc_start: 0.8811 (mttt) cc_final: 0.8287 (mmtm) REVERT: A 133 PHE cc_start: 0.7866 (m-80) cc_final: 0.7309 (m-80) REVERT: A 159 VAL cc_start: 0.6957 (OUTLIER) cc_final: 0.5385 (t) REVERT: A 160 TYR cc_start: 0.8208 (p90) cc_final: 0.7859 (p90) REVERT: A 220 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.6178 (t80) REVERT: A 368 LEU cc_start: 0.2365 (OUTLIER) cc_final: 0.1172 (tt) REVERT: A 377 PHE cc_start: 0.4771 (OUTLIER) cc_final: 0.4432 (p90) REVERT: A 731 MET cc_start: 0.7566 (ttm) cc_final: 0.7122 (ttp) REVERT: A 886 TRP cc_start: 0.6803 (OUTLIER) cc_final: 0.6601 (p90) REVERT: A 925 ASN cc_start: 0.9181 (m110) cc_final: 0.8903 (m110) REVERT: A 1051 SER cc_start: 0.8232 (m) cc_final: 0.7897 (p) REVERT: A 1094 VAL cc_start: 0.6045 (OUTLIER) cc_final: 0.5530 (t) REVERT: B 64 TRP cc_start: 0.6447 (t-100) cc_final: 0.6104 (t-100) REVERT: B 357 ARG cc_start: 0.7576 (tmm-80) cc_final: 0.7324 (tmm-80) REVERT: B 374 PHE cc_start: 0.2615 (OUTLIER) cc_final: -0.1558 (m-80) REVERT: B 451 TYR cc_start: 0.7856 (m-10) cc_final: 0.7348 (m-80) REVERT: B 455 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.5499 (mt) REVERT: B 456 PHE cc_start: 0.3457 (OUTLIER) cc_final: 0.2413 (m-80) REVERT: B 563 GLN cc_start: 0.2864 (OUTLIER) cc_final: 0.2138 (pt0) REVERT: B 613 GLN cc_start: 0.6653 (tp40) cc_final: 0.6181 (tm-30) REVERT: B 697 MET cc_start: 0.7889 (ppp) cc_final: 0.7155 (ppp) REVERT: B 726 ILE cc_start: 0.8111 (tp) cc_final: 0.7842 (tt) REVERT: B 776 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8490 (ptpp) REVERT: B 983 ARG cc_start: 0.8071 (tmm-80) cc_final: 0.7608 (tmm-80) REVERT: C 444 LYS cc_start: 0.3292 (OUTLIER) cc_final: 0.1316 (tttm) REVERT: C 448 ASN cc_start: 0.7923 (t0) cc_final: 0.7573 (m-40) REVERT: C 529 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.3890 (pptt) REVERT: C 646 ARG cc_start: 0.7064 (mmm160) cc_final: 0.6768 (mmp80) REVERT: C 658 ASN cc_start: 0.8647 (m110) cc_final: 0.8393 (p0) REVERT: C 731 MET cc_start: 0.5347 (tpp) cc_final: 0.5050 (tpp) REVERT: C 773 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: C 878 LEU cc_start: 0.6755 (mt) cc_final: 0.6068 (mt) REVERT: C 881 THR cc_start: 0.5431 (p) cc_final: 0.3804 (m) REVERT: C 900 MET cc_start: 0.2730 (mmm) cc_final: 0.2075 (mmm) REVERT: C 1007 TYR cc_start: 0.7246 (t80) cc_final: 0.6510 (t80) REVERT: C 1009 THR cc_start: 0.7113 (p) cc_final: 0.6171 (m) REVERT: C 1038 LYS cc_start: 0.8258 (mmtm) cc_final: 0.8002 (mmtm) REVERT: C 1138 TYR cc_start: 0.7469 (t80) cc_final: 0.7187 (t80) REVERT: C 1145 LEU cc_start: 0.3184 (OUTLIER) cc_final: 0.2867 (tt) outliers start: 164 outliers final: 133 residues processed: 566 average time/residue: 0.7763 time to fit residues: 669.1548 Evaluate side-chains 579 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 432 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 276 optimal weight: 0.0670 chunk 294 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 266 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.7421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26919 Z= 0.272 Angle : 1.325 33.477 36614 Z= 0.673 Chirality : 0.239 1.793 4257 Planarity : 0.005 0.068 4684 Dihedral : 9.251 179.183 4551 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.76 % Favored : 91.14 % Rotamer: Outliers : 5.35 % Allowed : 30.29 % Favored : 64.36 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % 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: -2.53 (0.14), residues: 3245 helix: -0.49 (0.19), residues: 650 sheet: -1.46 (0.20), residues: 630 loop : -2.27 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.007 0.001 HIS C1064 PHE 0.029 0.001 PHE A 318 TYR 0.013 0.001 TYR B 160 ARG 0.008 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 452 time to evaluate : 2.772 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 92 PHE cc_start: 0.7274 (t80) cc_final: 0.6814 (t80) REVERT: A 129 LYS cc_start: 0.8771 (mttt) cc_final: 0.8296 (mmtm) REVERT: A 159 VAL cc_start: 0.7080 (OUTLIER) cc_final: 0.5554 (t) REVERT: A 160 TYR cc_start: 0.8211 (p90) cc_final: 0.7859 (p90) REVERT: A 368 LEU cc_start: 0.2274 (OUTLIER) cc_final: 0.1088 (tt) REVERT: A 377 PHE cc_start: 0.4794 (OUTLIER) cc_final: 0.4463 (p90) REVERT: A 925 ASN cc_start: 0.9187 (m110) cc_final: 0.8936 (m110) REVERT: A 1051 SER cc_start: 0.8224 (m) cc_final: 0.7896 (p) REVERT: A 1094 VAL cc_start: 0.6125 (OUTLIER) cc_final: 0.5613 (t) REVERT: B 64 TRP cc_start: 0.6474 (t-100) cc_final: 0.6132 (t-100) REVERT: B 309 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: B 357 ARG cc_start: 0.7567 (tmm-80) cc_final: 0.7310 (tmm-80) REVERT: B 374 PHE cc_start: 0.2554 (OUTLIER) cc_final: -0.1644 (m-80) REVERT: B 442 ASP cc_start: 0.6980 (t0) cc_final: 0.5897 (t0) REVERT: B 451 TYR cc_start: 0.7868 (m-10) cc_final: 0.7475 (m-80) REVERT: B 455 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.5523 (mt) REVERT: B 456 PHE cc_start: 0.3481 (OUTLIER) cc_final: 0.2442 (m-80) REVERT: B 563 GLN cc_start: 0.2830 (OUTLIER) cc_final: 0.2056 (pt0) REVERT: B 613 GLN cc_start: 0.6669 (tp40) cc_final: 0.6179 (tm-30) REVERT: B 697 MET cc_start: 0.7951 (ppp) cc_final: 0.7252 (ppp) REVERT: B 726 ILE cc_start: 0.8144 (tp) cc_final: 0.7886 (tt) REVERT: B 776 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8482 (ptpp) REVERT: B 983 ARG cc_start: 0.8086 (tmm-80) cc_final: 0.7616 (tmm-80) REVERT: C 444 LYS cc_start: 0.3281 (OUTLIER) cc_final: 0.1356 (ttmt) REVERT: C 529 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.4275 (pptt) REVERT: C 646 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6801 (mmp80) REVERT: C 658 ASN cc_start: 0.8688 (m110) cc_final: 0.8443 (p0) REVERT: C 773 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: C 878 LEU cc_start: 0.6844 (mt) cc_final: 0.6162 (mt) REVERT: C 881 THR cc_start: 0.5488 (p) cc_final: 0.3884 (m) REVERT: C 900 MET cc_start: 0.2732 (mmm) cc_final: 0.2090 (mmm) REVERT: C 1007 TYR cc_start: 0.7267 (t80) cc_final: 0.6552 (t80) REVERT: C 1009 THR cc_start: 0.7199 (p) cc_final: 0.6264 (m) REVERT: C 1038 LYS cc_start: 0.8243 (mmtm) cc_final: 0.8001 (mmtm) REVERT: C 1138 TYR cc_start: 0.7477 (t80) cc_final: 0.7189 (t80) REVERT: C 1145 LEU cc_start: 0.3252 (OUTLIER) cc_final: 0.2942 (tt) outliers start: 150 outliers final: 133 residues processed: 562 average time/residue: 0.7597 time to fit residues: 651.2456 Evaluate side-chains 587 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 441 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 1.9990 chunk 311 optimal weight: 0.0980 chunk 190 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 326 optimal weight: 20.0000 chunk 300 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26919 Z= 0.270 Angle : 1.323 34.904 36614 Z= 0.671 Chirality : 0.239 1.795 4257 Planarity : 0.005 0.068 4684 Dihedral : 9.136 179.023 4550 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.33 % Rotamer: Outliers : 5.25 % Allowed : 30.22 % Favored : 64.53 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % 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: -2.49 (0.14), residues: 3245 helix: -0.45 (0.19), residues: 650 sheet: -1.43 (0.20), residues: 630 loop : -2.25 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.011 0.001 HIS C1064 PHE 0.025 0.001 PHE A 43 TYR 0.015 0.001 TYR C 37 ARG 0.009 0.001 ARG B 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 456 time to evaluate : 2.799 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 129 LYS cc_start: 0.8779 (mttt) cc_final: 0.8307 (mmtm) REVERT: A 368 LEU cc_start: 0.2282 (OUTLIER) cc_final: 0.1091 (tt) REVERT: A 925 ASN cc_start: 0.9204 (m110) cc_final: 0.8979 (m110) REVERT: A 947 LYS cc_start: 0.8469 (tppt) cc_final: 0.7700 (tppt) REVERT: A 1051 SER cc_start: 0.8286 (m) cc_final: 0.7881 (p) REVERT: A 1094 VAL cc_start: 0.6216 (OUTLIER) cc_final: 0.5718 (t) REVERT: B 64 TRP cc_start: 0.6502 (t-100) cc_final: 0.6157 (t-100) REVERT: B 309 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: B 374 PHE cc_start: 0.2593 (OUTLIER) cc_final: -0.1587 (m-80) REVERT: B 442 ASP cc_start: 0.6944 (t0) cc_final: 0.5866 (t0) REVERT: B 451 TYR cc_start: 0.7877 (m-10) cc_final: 0.7501 (m-80) REVERT: B 456 PHE cc_start: 0.3503 (OUTLIER) cc_final: 0.2625 (m-80) REVERT: B 563 GLN cc_start: 0.3028 (OUTLIER) cc_final: 0.2218 (pt0) REVERT: B 613 GLN cc_start: 0.6642 (tp40) cc_final: 0.6188 (tm-30) REVERT: B 697 MET cc_start: 0.7909 (ppp) cc_final: 0.7269 (ppp) REVERT: B 726 ILE cc_start: 0.8176 (tp) cc_final: 0.7959 (tt) REVERT: B 776 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8486 (ptpp) REVERT: B 983 ARG cc_start: 0.8097 (tmm-80) cc_final: 0.7638 (tmm-80) REVERT: C 334 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7617 (p0) REVERT: C 444 LYS cc_start: 0.2960 (OUTLIER) cc_final: 0.1013 (tttm) REVERT: C 529 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.4501 (pptt) REVERT: C 646 ARG cc_start: 0.7130 (mmm160) cc_final: 0.6843 (mmp80) REVERT: C 658 ASN cc_start: 0.8684 (m110) cc_final: 0.8449 (p0) REVERT: C 725 GLU cc_start: 0.6043 (mp0) cc_final: 0.5823 (mp0) REVERT: C 773 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: C 878 LEU cc_start: 0.6858 (mt) cc_final: 0.6236 (mt) REVERT: C 881 THR cc_start: 0.5495 (p) cc_final: 0.3863 (m) REVERT: C 953 ASN cc_start: 0.7880 (m-40) cc_final: 0.7488 (m-40) REVERT: C 1007 TYR cc_start: 0.7298 (t80) cc_final: 0.6605 (t80) REVERT: C 1038 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7995 (mmtm) REVERT: C 1138 TYR cc_start: 0.7464 (t80) cc_final: 0.7175 (t80) REVERT: C 1145 LEU cc_start: 0.3397 (OUTLIER) cc_final: 0.3093 (tt) outliers start: 147 outliers final: 132 residues processed: 562 average time/residue: 0.7650 time to fit residues: 656.0813 Evaluate side-chains 592 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 449 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 72 optimal weight: 0.3980 chunk 260 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.114124 restraints weight = 212111.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.121343 restraints weight = 118011.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.126540 restraints weight = 73484.361| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 26919 Z= 0.290 Angle : 1.387 59.115 36614 Z= 0.718 Chirality : 0.239 1.788 4257 Planarity : 0.005 0.068 4684 Dihedral : 9.050 179.044 4540 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.24 % Rotamer: Outliers : 5.15 % Allowed : 30.42 % Favored : 64.43 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.64 % 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: -2.49 (0.14), residues: 3245 helix: -0.45 (0.19), residues: 650 sheet: -1.43 (0.20), residues: 630 loop : -2.25 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.010 0.001 HIS C1064 PHE 0.034 0.001 PHE A 201 TYR 0.015 0.001 TYR B 396 ARG 0.011 0.001 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12295.07 seconds wall clock time: 210 minutes 25.88 seconds (12625.88 seconds total)