Starting phenix.real_space_refine on Mon May 19 00:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4c_41878/05_2025/8u4c_41878_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4c_41878/05_2025/8u4c_41878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4c_41878/05_2025/8u4c_41878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4c_41878/05_2025/8u4c_41878.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4c_41878/05_2025/8u4c_41878_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4c_41878/05_2025/8u4c_41878_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3510 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9324 2.51 5 N 2532 2.21 5 O 2730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14706 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6610 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6610 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 773} Chain breaks: 6 Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "F" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Time building chain proxies: 8.66, per 1000 atoms: 0.59 Number of scatterers: 14706 At special positions: 0 Unit cell: (135, 122.04, 170.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2730 8.00 N 2532 7.00 C 9324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.02 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 60 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 51 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.6 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 17.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.584A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.664A pdb=" N ARG A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.243A pdb=" N ASN A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.650A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.893A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.781A pdb=" N PHE A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 643' Processing helix chain 'A' and resid 692 through 714 Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.580A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.663A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.250A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.657A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.900A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.772A pdb=" N PHE B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 692 through 714 removed outlier: 3.562A pdb=" N LEU B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 881 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.518A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.805A pdb=" N THR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 3.863A pdb=" N ASP D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 52 through 58 removed outlier: 3.704A pdb=" N LEU D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.514A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.803A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 removed outlier: 3.879A pdb=" N ASP F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 52 through 58 removed outlier: 3.675A pdb=" N LEU F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 7.031A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 removed outlier: 3.625A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 321 removed outlier: 9.953A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 9.953A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'A' and resid 479 through 480 removed outlier: 4.053A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 486 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.551A pdb=" N LEU A 505 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.560A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 771 through 774 removed outlier: 3.666A pdb=" N GLU A 772 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 630 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 627 " --> pdb=" O CYS A 798 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 827 through 834 removed outlier: 5.092A pdb=" N GLN A 845 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 884 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 854 through 863 removed outlier: 3.724A pdb=" N GLY A 892 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 917 " --> pdb=" O GLY A 892 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 13 removed outlier: 7.031A pdb=" N GLN B 34 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG B 65 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC2, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.624A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 9.946A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321 removed outlier: 9.946A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC7, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.001A pdb=" N ARG B 479 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 486 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 530 through 533 removed outlier: 3.501A pdb=" N THR B 530 " --> pdb=" O TYR B 507 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 505 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 599 through 605 removed outlier: 5.554A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 771 through 774 removed outlier: 3.604A pdb=" N GLU B 772 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 630 " --> pdb=" O GLU B 772 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 834 removed outlier: 5.070A pdb=" N GLN B 845 " --> pdb=" O PRO B 829 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 854 through 863 removed outlier: 3.707A pdb=" N GLY B 892 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 917 " --> pdb=" O GLY B 892 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 861 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: 4.63 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4830 1.34 - 1.46: 3439 1.46 - 1.58: 6637 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 15048 Sorted by residual: bond pdb=" C CYS A 192 " pdb=" N PRO A 193 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.33e-02 5.65e+03 3.41e+00 bond pdb=" C CYS B 192 " pdb=" N PRO B 193 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.33e-02 5.65e+03 3.11e+00 bond pdb=" CB ARG F 38 " pdb=" CG ARG F 38 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.59e-02 3.96e+03 1.15e+00 bond pdb=" CB ASP D 52 " pdb=" CG ASP D 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 ... (remaining 15043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 20163 2.43 - 4.87: 180 4.87 - 7.30: 17 7.30 - 9.74: 12 9.74 - 12.17: 2 Bond angle restraints: 20374 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 113.53 108.38 5.15 9.80e-01 1.04e+00 2.77e+01 angle pdb=" CA ARG F 38 " pdb=" CB ARG F 38 " pdb=" CG ARG F 38 " ideal model delta sigma weight residual 114.10 123.50 -9.40 2.00e+00 2.50e-01 2.21e+01 angle pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " pdb=" CG ARG D 38 " ideal model delta sigma weight residual 114.10 123.12 -9.02 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CB MET B 843 " pdb=" CG MET B 843 " pdb=" SD MET B 843 " ideal model delta sigma weight residual 112.70 124.87 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB MET A 843 " pdb=" CG MET A 843 " pdb=" SD MET A 843 " ideal model delta sigma weight residual 112.70 124.32 -11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 20369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7713 17.74 - 35.48: 1094 35.48 - 53.22: 249 53.22 - 70.96: 43 70.96 - 88.70: 41 Dihedral angle restraints: 9140 sinusoidal: 3826 harmonic: 5314 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.51 84.51 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual -86.00 -163.27 77.27 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 9137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1378 0.031 - 0.061: 529 0.061 - 0.092: 168 0.092 - 0.122: 129 0.122 - 0.153: 12 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CA THR B 802 " pdb=" N THR B 802 " pdb=" C THR B 802 " pdb=" CB THR B 802 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA THR A 802 " pdb=" N THR A 802 " pdb=" C THR A 802 " pdb=" CB THR A 802 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE B 457 " pdb=" N ILE B 457 " pdb=" C ILE B 457 " pdb=" CB ILE B 457 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2213 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 632 " 0.017 2.00e-02 2.50e+03 1.53e-02 5.84e+00 pdb=" CG TRP B 632 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 632 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 632 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 632 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 632 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 632 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 632 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 911 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 912 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 912 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 912 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 911 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 912 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " -0.023 5.00e-02 4.00e+02 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 571 2.71 - 3.26: 14960 3.26 - 3.80: 23866 3.80 - 4.35: 28826 4.35 - 4.90: 47822 Nonbonded interactions: 116045 Sorted by model distance: nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.163 3.040 nonbonded pdb=" O PRO B 716 " pdb=" OH TYR D 27 " model vdw 2.183 3.040 nonbonded pdb=" O PRO A 716 " pdb=" OH TYR F 27 " model vdw 2.193 3.040 nonbonded pdb=" OG SER A 890 " pdb=" OH TYR A 894 " model vdw 2.198 3.040 ... (remaining 116040 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.900 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.005 0.341 15096 Z= 0.389 Angle : 0.609 12.171 20466 Z= 0.308 Chirality : 0.042 0.153 2216 Planarity : 0.003 0.043 2634 Dihedral : 17.057 88.702 5570 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 29.12 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1782 helix: 0.44 (0.38), residues: 192 sheet: -0.35 (0.28), residues: 352 loop : -1.32 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 632 HIS 0.008 0.000 HIS A 440 PHE 0.017 0.001 PHE A 572 TYR 0.015 0.001 TYR B 374 ARG 0.004 0.000 ARG A 882 Details of bonding type rmsd hydrogen bonds : bond 0.24102 ( 314) hydrogen bonds : angle 9.18251 ( 861) SS BOND : bond 0.00246 ( 46) SS BOND : angle 0.88504 ( 92) covalent geometry : bond 0.00296 (15048) covalent geometry : angle 0.60738 (20374) Misc. bond : bond 0.31750 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.8595 (tpp) cc_final: 0.7577 (mmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3259 time to fit residues: 30.9687 Evaluate side-chains 47 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.081807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.051258 restraints weight = 63055.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052903 restraints weight = 34307.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053934 restraints weight = 24479.216| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15096 Z= 0.201 Angle : 0.630 9.616 20466 Z= 0.322 Chirality : 0.044 0.145 2216 Planarity : 0.005 0.128 2634 Dihedral : 4.435 17.464 1996 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.18 % Favored : 92.59 % Rotamer: Outliers : 2.00 % Allowed : 26.51 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1782 helix: -0.02 (0.36), residues: 200 sheet: -0.60 (0.27), residues: 364 loop : -1.31 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 632 HIS 0.005 0.001 HIS A 440 PHE 0.017 0.001 PHE B 705 TYR 0.015 0.001 TYR A 374 ARG 0.015 0.001 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 314) hydrogen bonds : angle 7.13686 ( 861) SS BOND : bond 0.00338 ( 46) SS BOND : angle 0.98154 ( 92) covalent geometry : bond 0.00461 (15048) covalent geometry : angle 0.62805 (20374) Misc. bond : bond 0.00256 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9056 (tp) REVERT: A 843 MET cc_start: 0.8968 (tpp) cc_final: 0.7913 (mmm) REVERT: B 412 TRP cc_start: 0.8693 (OUTLIER) cc_final: 0.5792 (m-90) REVERT: B 442 MET cc_start: 0.9275 (mmm) cc_final: 0.8806 (mmm) outliers start: 33 outliers final: 14 residues processed: 84 average time/residue: 0.2583 time to fit residues: 34.1526 Evaluate side-chains 65 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 27 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 81 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 156 optimal weight: 40.0000 chunk 60 optimal weight: 0.0970 chunk 113 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.082021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052759 restraints weight = 61941.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054402 restraints weight = 32898.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.055437 restraints weight = 22899.936| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15096 Z= 0.123 Angle : 0.578 9.289 20466 Z= 0.295 Chirality : 0.043 0.145 2216 Planarity : 0.005 0.124 2634 Dihedral : 5.735 166.134 1996 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.51 % Favored : 93.27 % Rotamer: Outliers : 2.42 % Allowed : 26.63 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1782 helix: -0.15 (0.35), residues: 200 sheet: -0.59 (0.27), residues: 364 loop : -1.27 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 632 HIS 0.003 0.000 HIS A 440 PHE 0.015 0.001 PHE A 705 TYR 0.014 0.001 TYR A 374 ARG 0.017 0.001 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 314) hydrogen bonds : angle 6.61576 ( 861) SS BOND : bond 0.00177 ( 46) SS BOND : angle 0.77876 ( 92) covalent geometry : bond 0.00283 (15048) covalent geometry : angle 0.57698 (20374) Misc. bond : bond 0.00413 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9075 (tp) REVERT: A 843 MET cc_start: 0.8922 (tpp) cc_final: 0.7828 (mmm) REVERT: F 53 LEU cc_start: 0.9154 (tp) cc_final: 0.8950 (tt) outliers start: 40 outliers final: 23 residues processed: 96 average time/residue: 0.2555 time to fit residues: 38.2452 Evaluate side-chains 75 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.080677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050230 restraints weight = 63581.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051840 restraints weight = 34712.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052854 restraints weight = 24614.141| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 15096 Z= 0.261 Angle : 0.640 9.580 20466 Z= 0.326 Chirality : 0.045 0.277 2216 Planarity : 0.005 0.146 2634 Dihedral : 4.490 17.527 1996 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.30 % Favored : 92.48 % Rotamer: Outliers : 4.90 % Allowed : 24.64 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1782 helix: -0.18 (0.35), residues: 200 sheet: -0.59 (0.28), residues: 354 loop : -1.34 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 632 HIS 0.004 0.001 HIS B 710 PHE 0.017 0.002 PHE B 482 TYR 0.053 0.002 TYR B 708 ARG 0.024 0.001 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 314) hydrogen bonds : angle 6.48883 ( 861) SS BOND : bond 0.00259 ( 46) SS BOND : angle 0.98170 ( 92) covalent geometry : bond 0.00594 (15048) covalent geometry : angle 0.63822 (20374) Misc. bond : bond 0.01700 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 54 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8834 (OUTLIER) cc_final: 0.5879 (m-10) REVERT: A 442 MET cc_start: 0.8965 (tpp) cc_final: 0.8550 (tpp) REVERT: A 635 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8499 (mp-120) REVERT: A 843 MET cc_start: 0.8914 (tpp) cc_final: 0.7842 (mmm) REVERT: B 412 TRP cc_start: 0.8770 (OUTLIER) cc_final: 0.5785 (m-90) REVERT: B 477 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8720 (p90) REVERT: B 635 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8429 (mp-120) REVERT: B 843 MET cc_start: 0.8754 (tpp) cc_final: 0.8399 (tpp) REVERT: F 53 LEU cc_start: 0.9195 (tp) cc_final: 0.8956 (tt) outliers start: 81 outliers final: 40 residues processed: 130 average time/residue: 0.2108 time to fit residues: 44.7261 Evaluate side-chains 98 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 53 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 0.2980 chunk 170 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.080655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050201 restraints weight = 64065.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051824 restraints weight = 34385.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052861 restraints weight = 24252.822| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15096 Z= 0.201 Angle : 0.610 9.380 20466 Z= 0.310 Chirality : 0.044 0.249 2216 Planarity : 0.004 0.067 2634 Dihedral : 4.441 18.172 1996 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.30 % Favored : 92.48 % Rotamer: Outliers : 3.81 % Allowed : 25.79 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1782 helix: -0.03 (0.34), residues: 200 sheet: -0.77 (0.28), residues: 368 loop : -1.32 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 632 HIS 0.005 0.001 HIS A 185 PHE 0.017 0.001 PHE B 482 TYR 0.026 0.001 TYR A 708 ARG 0.005 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 314) hydrogen bonds : angle 6.25837 ( 861) SS BOND : bond 0.00256 ( 46) SS BOND : angle 0.95143 ( 92) covalent geometry : bond 0.00464 (15048) covalent geometry : angle 0.60796 (20374) Misc. bond : bond 0.00235 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 55 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9147 (p) REVERT: A 412 TRP cc_start: 0.8814 (OUTLIER) cc_final: 0.5922 (m-10) REVERT: A 442 MET cc_start: 0.8959 (tpp) cc_final: 0.8503 (tpp) REVERT: A 635 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8495 (mp-120) REVERT: A 843 MET cc_start: 0.8948 (tpp) cc_final: 0.7901 (mmm) REVERT: B 223 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9171 (p) REVERT: B 412 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.5652 (m-90) REVERT: B 477 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.8772 (p90) REVERT: B 635 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8403 (mp-120) REVERT: F 53 LEU cc_start: 0.9220 (tp) cc_final: 0.8985 (tt) outliers start: 63 outliers final: 37 residues processed: 116 average time/residue: 0.2136 time to fit residues: 39.8226 Evaluate side-chains 92 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 48 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.081508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051462 restraints weight = 63139.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.053148 restraints weight = 33202.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.054173 restraints weight = 23093.415| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15096 Z= 0.118 Angle : 0.587 13.841 20466 Z= 0.296 Chirality : 0.043 0.185 2216 Planarity : 0.006 0.251 2634 Dihedral : 4.448 38.073 1996 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.34 % Favored : 93.43 % Rotamer: Outliers : 3.09 % Allowed : 26.69 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.46 (0.20), residues: 1782 helix: -0.02 (0.35), residues: 198 sheet: -0.64 (0.28), residues: 358 loop : -1.29 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 632 HIS 0.003 0.000 HIS A 429 PHE 0.021 0.001 PHE C 28 TYR 0.019 0.001 TYR A 708 ARG 0.018 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 314) hydrogen bonds : angle 6.12147 ( 861) SS BOND : bond 0.00188 ( 46) SS BOND : angle 0.77994 ( 92) covalent geometry : bond 0.00266 (15048) covalent geometry : angle 0.58598 (20374) Misc. bond : bond 0.01067 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 53 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8786 (OUTLIER) cc_final: 0.5897 (m-10) REVERT: A 442 MET cc_start: 0.8956 (tpp) cc_final: 0.8492 (tpp) REVERT: A 582 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8171 (mttp) REVERT: A 635 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8469 (mp-120) REVERT: A 843 MET cc_start: 0.8987 (tpp) cc_final: 0.7726 (mmm) REVERT: B 223 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9167 (p) REVERT: B 412 TRP cc_start: 0.8744 (OUTLIER) cc_final: 0.5717 (m-10) REVERT: B 635 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8288 (mp-120) REVERT: F 53 LEU cc_start: 0.9183 (tp) cc_final: 0.8942 (tt) outliers start: 51 outliers final: 31 residues processed: 102 average time/residue: 0.2160 time to fit residues: 36.5307 Evaluate side-chains 87 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.080287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050352 restraints weight = 62316.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051928 restraints weight = 33150.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052958 restraints weight = 23203.816| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15096 Z= 0.206 Angle : 0.616 9.289 20466 Z= 0.309 Chirality : 0.044 0.197 2216 Planarity : 0.005 0.171 2634 Dihedral : 4.489 31.107 1996 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.35 % Favored : 92.42 % Rotamer: Outliers : 3.63 % Allowed : 26.76 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.54 (0.20), residues: 1782 helix: 0.09 (0.35), residues: 198 sheet: -0.78 (0.28), residues: 346 loop : -1.34 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 632 HIS 0.003 0.001 HIS A 440 PHE 0.018 0.001 PHE A 482 TYR 0.016 0.001 TYR A 708 ARG 0.007 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 314) hydrogen bonds : angle 5.98439 ( 861) SS BOND : bond 0.00250 ( 46) SS BOND : angle 0.97408 ( 92) covalent geometry : bond 0.00480 (15048) covalent geometry : angle 0.61396 (20374) Misc. bond : bond 0.00390 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 53 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 223 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9143 (p) REVERT: A 412 TRP cc_start: 0.8796 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: A 442 MET cc_start: 0.9049 (tpp) cc_final: 0.8515 (tpp) REVERT: A 477 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8673 (p90) REVERT: A 635 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8415 (mp-120) REVERT: A 843 MET cc_start: 0.8867 (tpp) cc_final: 0.7717 (mmm) REVERT: B 223 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9168 (p) REVERT: B 410 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8578 (pp30) REVERT: B 412 TRP cc_start: 0.8759 (OUTLIER) cc_final: 0.5774 (m-10) REVERT: B 482 PHE cc_start: 0.7437 (t80) cc_final: 0.7183 (t80) REVERT: B 635 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8283 (mp-120) REVERT: D 45 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: F 53 LEU cc_start: 0.9172 (tp) cc_final: 0.8903 (tt) outliers start: 60 outliers final: 44 residues processed: 111 average time/residue: 0.2313 time to fit residues: 40.9254 Evaluate side-chains 103 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 50 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 513 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 513 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.079412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048624 restraints weight = 64073.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050186 restraints weight = 35017.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051188 restraints weight = 24951.220| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 15096 Z= 0.299 Angle : 0.688 10.772 20466 Z= 0.347 Chirality : 0.046 0.183 2216 Planarity : 0.004 0.059 2634 Dihedral : 4.732 18.750 1996 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.14 % Favored : 91.64 % Rotamer: Outliers : 4.12 % Allowed : 26.63 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1782 helix: -0.56 (0.33), residues: 228 sheet: -0.80 (0.29), residues: 342 loop : -1.52 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 632 HIS 0.003 0.001 HIS B 548 PHE 0.025 0.002 PHE A 482 TYR 0.030 0.002 TYR A 708 ARG 0.014 0.001 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 314) hydrogen bonds : angle 6.04903 ( 861) SS BOND : bond 0.00308 ( 46) SS BOND : angle 1.15913 ( 92) covalent geometry : bond 0.00686 (15048) covalent geometry : angle 0.68546 (20374) Misc. bond : bond 0.01133 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 56 time to evaluate : 1.830 Fit side-chains revert: symmetry clash REVERT: A 223 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9181 (p) REVERT: A 412 TRP cc_start: 0.8798 (OUTLIER) cc_final: 0.6190 (m-10) REVERT: A 442 MET cc_start: 0.9089 (tpp) cc_final: 0.8537 (tpp) REVERT: A 477 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8635 (p90) REVERT: A 482 PHE cc_start: 0.7789 (t80) cc_final: 0.7557 (t80) REVERT: A 635 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8565 (mp-120) REVERT: A 843 MET cc_start: 0.8883 (tpp) cc_final: 0.7798 (mmm) REVERT: B 223 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9209 (p) REVERT: B 410 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8548 (pp30) REVERT: B 412 TRP cc_start: 0.8823 (OUTLIER) cc_final: 0.5747 (m-90) REVERT: B 477 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8570 (p90) REVERT: B 482 PHE cc_start: 0.7841 (t80) cc_final: 0.7594 (t80) REVERT: B 635 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8409 (mp-120) REVERT: D 45 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: F 53 LEU cc_start: 0.9184 (tp) cc_final: 0.8912 (tt) outliers start: 68 outliers final: 45 residues processed: 122 average time/residue: 0.2408 time to fit residues: 46.5010 Evaluate side-chains 106 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 51 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 120 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.0030 chunk 174 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.081425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.051403 restraints weight = 63027.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053083 restraints weight = 33506.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054161 restraints weight = 23425.301| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15096 Z= 0.110 Angle : 0.608 10.235 20466 Z= 0.305 Chirality : 0.044 0.197 2216 Planarity : 0.004 0.052 2634 Dihedral : 5.935 173.899 1996 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.12 % Favored : 93.66 % Rotamer: Outliers : 2.97 % Allowed : 27.72 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1782 helix: -0.38 (0.34), residues: 212 sheet: -0.72 (0.29), residues: 322 loop : -1.41 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 632 HIS 0.004 0.001 HIS A 429 PHE 0.024 0.001 PHE B 705 TYR 0.019 0.001 TYR B 507 ARG 0.006 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 314) hydrogen bonds : angle 5.93002 ( 861) SS BOND : bond 0.00216 ( 46) SS BOND : angle 0.84059 ( 92) covalent geometry : bond 0.00255 (15048) covalent geometry : angle 0.60712 (20374) Misc. bond : bond 0.00505 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 55 time to evaluate : 1.770 Fit side-chains REVERT: A 223 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9191 (p) REVERT: A 412 TRP cc_start: 0.8718 (OUTLIER) cc_final: 0.6076 (m-10) REVERT: A 442 MET cc_start: 0.9028 (tpp) cc_final: 0.8490 (tpp) REVERT: A 635 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8382 (mp-120) REVERT: A 843 MET cc_start: 0.8868 (tpp) cc_final: 0.7744 (mmm) REVERT: B 412 TRP cc_start: 0.8772 (OUTLIER) cc_final: 0.5852 (m-90) REVERT: B 553 MET cc_start: 0.7838 (mtp) cc_final: 0.7619 (mtt) REVERT: B 635 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8210 (mp-120) REVERT: F 53 LEU cc_start: 0.9090 (tp) cc_final: 0.8791 (tt) outliers start: 49 outliers final: 33 residues processed: 102 average time/residue: 0.2553 time to fit residues: 40.6050 Evaluate side-chains 88 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 50 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 79 optimal weight: 40.0000 chunk 15 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.079562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049491 restraints weight = 62781.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051038 restraints weight = 34050.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052018 restraints weight = 24082.126| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15096 Z= 0.275 Angle : 0.706 18.967 20466 Z= 0.355 Chirality : 0.047 0.342 2216 Planarity : 0.010 0.353 2634 Dihedral : 5.851 139.682 1996 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.91 % Favored : 91.86 % Rotamer: Outliers : 2.54 % Allowed : 28.15 % Favored : 69.31 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.88 (0.20), residues: 1782 helix: -0.81 (0.33), residues: 230 sheet: -0.82 (0.29), residues: 328 loop : -1.53 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 632 HIS 0.004 0.001 HIS A 710 PHE 0.022 0.002 PHE A 482 TYR 0.115 0.002 TYR A 708 ARG 0.031 0.001 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 314) hydrogen bonds : angle 6.04935 ( 861) SS BOND : bond 0.00255 ( 46) SS BOND : angle 1.12269 ( 92) covalent geometry : bond 0.00633 (15048) covalent geometry : angle 0.70398 (20374) Misc. bond : bond 0.01172 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 1.561 Fit side-chains REVERT: A 223 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9183 (p) REVERT: A 412 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.6164 (m-10) REVERT: A 442 MET cc_start: 0.9077 (tpp) cc_final: 0.8648 (mmm) REVERT: A 635 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8437 (mp-120) REVERT: A 843 MET cc_start: 0.8902 (tpp) cc_final: 0.7786 (mmm) REVERT: B 410 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8547 (pp30) REVERT: B 412 TRP cc_start: 0.8830 (OUTLIER) cc_final: 0.5789 (m-10) REVERT: B 504 MET cc_start: 0.8349 (mmp) cc_final: 0.8043 (mmm) REVERT: B 635 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8261 (mp-120) REVERT: D 45 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: F 53 LEU cc_start: 0.9169 (tp) cc_final: 0.8885 (tt) outliers start: 42 outliers final: 33 residues processed: 95 average time/residue: 0.2297 time to fit residues: 35.0547 Evaluate side-chains 92 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 52 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 149 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 34 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 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.081206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051627 restraints weight = 62278.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.053231 restraints weight = 33038.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.054263 restraints weight = 23125.333| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15096 Z= 0.120 Angle : 0.614 12.223 20466 Z= 0.310 Chirality : 0.045 0.271 2216 Planarity : 0.009 0.355 2634 Dihedral : 5.543 131.032 1996 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.68 % Favored : 93.10 % Rotamer: Outliers : 2.60 % Allowed : 27.97 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.69 (0.20), residues: 1782 helix: -0.44 (0.34), residues: 210 sheet: -0.66 (0.29), residues: 318 loop : -1.45 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 632 HIS 0.004 0.001 HIS A 429 PHE 0.023 0.001 PHE B 482 TYR 0.056 0.001 TYR A 708 ARG 0.022 0.001 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 314) hydrogen bonds : angle 5.88709 ( 861) SS BOND : bond 0.00190 ( 46) SS BOND : angle 0.84645 ( 92) covalent geometry : bond 0.00276 (15048) covalent geometry : angle 0.61279 (20374) Misc. bond : bond 0.01304 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5765.78 seconds wall clock time: 101 minutes 9.62 seconds (6069.62 seconds total)