Starting phenix.real_space_refine on Sat Oct 24 22:09:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9txl_56404/10_2026/9txl_56404.cif Found real_map, /net/cci-nas-00/data/ceres_data/9txl_56404/10_2026/9txl_56404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9txl_56404/10_2026/9txl_56404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9txl_56404/10_2026/9txl_56404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9txl_56404/10_2026/9txl_56404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9txl_56404/10_2026/9txl_56404.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 54 5.16 5 C 9051 2.51 5 N 2380 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14312 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3909 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 19, 'TRANS': 476} Chain breaks: 2 Chain: "B" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3859 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 3 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1552 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 190} Chain breaks: 2 Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "F" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1552 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 190} Chain breaks: 2 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' MG': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.60, per 1000 atoms: 0.25 Number of scatterers: 14312 At special positions: 0 Unit cell: (98.91, 147.58, 174.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 Mg 2 11.99 O 2825 8.00 N 2380 7.00 C 9051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 193 " distance=2.04 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 701 " - " ASN A 81 " " NAG A 702 " - " ASN A 207 " " NAG B 702 " - " ASN B 81 " " NAG H 1 " - " ASN A 577 " " NAG I 1 " - " ASN B 577 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 650.5 milliseconds 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 37 sheets defined 20.5% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 98 through 112 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.850A pdb=" N ASP A 234 " --> pdb=" O THR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.783A pdb=" N GLN A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.757A pdb=" N ALA A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.870A pdb=" N ILE A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.542A pdb=" N PHE A 540 " --> pdb=" O PRO A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 583 Processing helix chain 'B' and resid 98 through 112 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 303 removed outlier: 3.776A pdb=" N GLN B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 Processing helix chain 'B' and resid 351 through 369 removed outlier: 3.884A pdb=" N ALA B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 407 removed outlier: 3.884A pdb=" N ILE B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.517A pdb=" N GLN B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 561 removed outlier: 5.533A pdb=" N MET B 544 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU B 545 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 546 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 583 removed outlier: 3.555A pdb=" N ALA B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.685A pdb=" N LYS D 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.634A pdb=" N ASP D 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.940A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 126 Processing helix chain 'E' and resid 182 through 188 removed outlier: 3.738A pdb=" N HIS E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.535A pdb=" N LYS F 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.551A pdb=" N ASP F 89 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER F 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.811A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 126 Processing helix chain 'G' and resid 182 through 188 removed outlier: 3.761A pdb=" N HIS G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.561A pdb=" N THR A 141 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 147 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE A 79 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 149 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ALA A 77 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.006A pdb=" N VAL A 40 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N HIS A 177 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER A 42 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 179 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 44 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.671A pdb=" N MET A 591 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 96 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 128 removed outlier: 4.437A pdb=" N LYS A 162 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 128 removed outlier: 4.437A pdb=" N LYS A 162 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 321 removed outlier: 5.818A pdb=" N ASN A 274 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 381 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 276 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 383 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 278 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ARG A 438 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS A 414 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE A 440 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY A 416 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.645A pdb=" N ALA B 77 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 149 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE B 79 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU B 147 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 141 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 56 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER B 37 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 58 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE B 35 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLN B 173 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU B 38 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP B 175 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL B 40 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS B 177 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER B 42 " --> pdb=" O HIS B 177 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE B 179 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 44 " --> pdb=" O PHE B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 97 removed outlier: 8.719A pdb=" N THR B 589 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 120 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS B 162 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 94 through 97 removed outlier: 8.719A pdb=" N THR B 589 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 120 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS B 162 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 186 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 319 through 321 Processing sheet with id=AB3, first strand: chain 'B' and resid 319 through 321 removed outlier: 5.940A pdb=" N LYS B 273 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASN B 311 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 275 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE B 313 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE B 277 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE B 315 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 279 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASN B 274 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE B 381 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 276 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU B 383 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 278 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ARG B 438 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 414 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE B 440 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY B 416 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 10 removed outlier: 6.271A pdb=" N LYS D 37 " --> pdb=" O TRP D 46 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TRP D 46 " --> pdb=" O LYS D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 10 Processing sheet with id=AB7, first strand: chain 'D' and resid 122 through 126 removed outlier: 6.003A pdb=" N TYR D 177 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 126 removed outlier: 6.003A pdb=" N TYR D 177 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 13 through 14 removed outlier: 6.665A pdb=" N ALA E 13 " --> pdb=" O LYS E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.844A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.844A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 113 through 117 removed outlier: 3.695A pdb=" N VAL E 132 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR E 172 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 149 Processing sheet with id=AC8, first strand: chain 'F' and resid 2 through 5 Processing sheet with id=AC9, first strand: chain 'F' and resid 9 through 10 removed outlier: 6.789A pdb=" N GLU F 9 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS F 37 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP F 46 " --> pdb=" O LYS F 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 9 through 10 removed outlier: 6.789A pdb=" N GLU F 9 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 122 through 126 removed outlier: 5.981A pdb=" N TYR F 177 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 122 through 126 removed outlier: 5.981A pdb=" N TYR F 177 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AD5, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'G' and resid 13 through 14 removed outlier: 6.706A pdb=" N ALA G 13 " --> pdb=" O LYS G 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 48 removed outlier: 5.594A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN G 90 " --> pdb=" O THR G 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 113 through 117 removed outlier: 3.695A pdb=" N VAL G 132 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR G 172 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE1, first strand: chain 'G' and resid 144 through 149 702 hydrogen bonds defined for protein. 1869 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: 2.42 Time building geometry restraints manager: 1.50 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: 4562 1.34 - 1.46: 3318 1.46 - 1.58: 6636 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 14606 Sorted by residual: bond pdb=" CA ASP G 109 " pdb=" C ASP G 109 " ideal model delta sigma weight residual 1.522 1.545 -0.024 1.20e-02 6.94e+03 3.93e+00 bond pdb=" N ALA C 1 " pdb=" CA ALA C 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" N VAL F 1 " pdb=" CA VAL F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" C GLU B 180 " pdb=" N PRO B 181 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.70e+00 ... (remaining 14601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 19632 3.24 - 6.49: 181 6.49 - 9.73: 6 9.73 - 12.97: 0 12.97 - 16.22: 2 Bond angle restraints: 19821 Sorted by residual: angle pdb=" N GLY F 135 " pdb=" CA GLY F 135 " pdb=" C GLY F 135 " ideal model delta sigma weight residual 113.30 129.52 -16.22 2.90e+00 1.19e-01 3.13e+01 angle pdb=" N GLY D 135 " pdb=" CA GLY D 135 " pdb=" C GLY D 135 " ideal model delta sigma weight residual 113.30 129.11 -15.81 2.90e+00 1.19e-01 2.97e+01 angle pdb=" CA GLY F 135 " pdb=" C GLY F 135 " pdb=" N SER F 136 " ideal model delta sigma weight residual 116.20 124.11 -7.91 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N ILE E 105 " pdb=" CA ILE E 105 " pdb=" CB ILE E 105 " ideal model delta sigma weight residual 112.34 108.01 4.33 1.14e+00 7.69e-01 1.45e+01 angle pdb=" C TRP F 156 " pdb=" N ASN F 157 " pdb=" CA ASN F 157 " ideal model delta sigma weight residual 122.08 127.44 -5.36 1.47e+00 4.63e-01 1.33e+01 ... (remaining 19816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7869 17.92 - 35.84: 806 35.84 - 53.76: 185 53.76 - 71.68: 54 71.68 - 89.60: 20 Dihedral angle restraints: 8934 sinusoidal: 3631 harmonic: 5303 Sorted by residual: dihedral pdb=" CA SER F 158 " pdb=" C SER F 158 " pdb=" N GLY F 159 " pdb=" CA GLY F 159 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA THR A 317 " pdb=" C THR A 317 " pdb=" N GLU A 318 " pdb=" CA GLU A 318 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA GLU B 255 " pdb=" C GLU B 255 " pdb=" N ASN B 256 " pdb=" CA ASN B 256 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 8931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1788 0.047 - 0.095: 330 0.095 - 0.142: 154 0.142 - 0.189: 5 0.189 - 0.237: 4 Chirality restraints: 2281 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.43e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 577 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 207 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2278 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 180 " 0.037 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO B 181 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 586 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO B 587 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 587 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 587 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 586 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO A 587 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.026 5.00e-02 4.00e+02 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 12 2.46 - 3.07: 9330 3.07 - 3.68: 21904 3.68 - 4.29: 30797 4.29 - 4.90: 52885 Nonbonded interactions: 114928 Sorted by model distance: nonbonded pdb=" OE2 GLU A 370 " pdb="MG MG B 701 " model vdw 1.851 2.170 nonbonded pdb=" OE2 GLU C 2 " pdb="MG MG A 703 " model vdw 1.934 2.170 nonbonded pdb=" OG1 THR A 350 " pdb="MG MG A 703 " model vdw 1.978 2.170 nonbonded pdb=" OG SER B 282 " pdb="MG MG B 701 " model vdw 2.044 2.170 nonbonded pdb="MG MG A 703 " pdb=" O HOH A 801 " model vdw 2.057 2.170 ... (remaining 114923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 220 or resid 226 through 596)) selection = (chain 'B' and resid 30 through 596) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.750 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.004 0.048 14624 Z= 0.182 Angle : 0.758 16.216 19867 Z= 0.372 Chirality : 0.046 0.237 2281 Planarity : 0.005 0.057 2518 Dihedral : 16.137 89.600 5488 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.14 % Allowed : 18.93 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1787 helix: 0.87 (0.30), residues: 307 sheet: -0.49 (0.19), residues: 740 loop : -1.20 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 107 TYR 0.022 0.002 TYR G 185 PHE 0.017 0.001 PHE A 584 TRP 0.010 0.001 TRP G 147 HIS 0.005 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (14606) covalent geometry : angle 0.74034 / 0.37 (19821) SS BOND : bond 0.00507 / 0.21 ( 8) SS BOND : angle 0.74256 / 0.49 ( 16) hydrogen bonds : bond 0.10723 / 7.35 ( 623) hydrogen bonds : angle 5.84634 / 4.07 ( 1869) link_ALPHA1-3 : bond 0.00331 / 0.17 ( 1) link_ALPHA1-3 : angle 2.22596 / 1.17 ( 3) link_BETA1-4 : bond 0.01030 / 0.50 ( 4) link_BETA1-4 : angle 4.95633 / 2.34 ( 12) link_NAG-ASN : bond 0.00784 / 0.38 ( 5) link_NAG-ASN : angle 3.83695 / 2.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.8459 (m) cc_final: 0.7856 (p) REVERT: A 100 GLU cc_start: 0.7957 (tp30) cc_final: 0.7667 (tm-30) REVERT: A 119 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7502 (mtmm) REVERT: A 174 MET cc_start: 0.8408 (mtt) cc_final: 0.8201 (mtt) REVERT: B 75 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7905 (ptpp) REVERT: B 148 GLU cc_start: 0.6862 (tt0) cc_final: 0.5747 (tm-30) REVERT: B 164 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7797 (tmt-80) REVERT: B 278 VAL cc_start: 0.7942 (t) cc_final: 0.7644 (t) REVERT: B 290 ILE cc_start: 0.8605 (tp) cc_final: 0.8250 (tt) REVERT: B 347 LEU cc_start: 0.8116 (pt) cc_final: 0.7754 (tt) REVERT: B 547 LEU cc_start: 0.8342 (tm) cc_final: 0.7993 (tp) REVERT: B 555 GLN cc_start: 0.8549 (tm-30) cc_final: 0.7931 (tm-30) REVERT: B 565 ASP cc_start: 0.8694 (m-30) cc_final: 0.8460 (t70) REVERT: B 571 LEU cc_start: 0.8766 (mt) cc_final: 0.8538 (mt) REVERT: B 578 LEU cc_start: 0.9135 (mm) cc_final: 0.8930 (tp) REVERT: B 588 LEU cc_start: 0.8768 (mt) cc_final: 0.8364 (pp) REVERT: B 591 MET cc_start: 0.6072 (tpp) cc_final: 0.5357 (tpp) REVERT: D 55 ASP cc_start: 0.9018 (m-30) cc_final: 0.8781 (m-30) REVERT: D 179 MET cc_start: 0.8550 (ppp) cc_final: 0.8232 (ppp) REVERT: E 19 VAL cc_start: 0.8264 (t) cc_final: 0.7768 (p) REVERT: F 126 LEU cc_start: 0.8617 (mt) cc_final: 0.8354 (mp) REVERT: G 116 ILE cc_start: 0.7973 (tp) cc_final: 0.7683 (tp) REVERT: G 155 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8531 (mp-120) outliers start: 18 outliers final: 8 residues processed: 206 average time/residue: 0.1113 time to fit residues: 34.3336 Evaluate side-chains 132 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 HIS B 70 GLN B 212 HIS B 274 ASN D 38 GLN F 5 GLN F 157 ASN F 173 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.101174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.070269 restraints weight = 41845.417| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.74 r_work: 0.3259 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14624 Z= 0.217 Angle : 0.703 10.623 19867 Z= 0.355 Chirality : 0.046 0.269 2281 Planarity : 0.005 0.067 2518 Dihedral : 6.782 59.245 2162 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.04 % Allowed : 20.88 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1787 helix: 0.90 (0.29), residues: 316 sheet: -0.22 (0.19), residues: 729 loop : -1.16 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 438 TYR 0.021 0.002 TYR A 146 PHE 0.029 0.002 PHE A 584 TRP 0.031 0.002 TRP F 46 HIS 0.005 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (14606) covalent geometry : angle 0.68504 / 0.35 (19821) SS BOND : bond 0.00485 / 0.24 ( 8) SS BOND : angle 0.87152 / 0.69 ( 16) hydrogen bonds : bond 0.03488 / 2.30 ( 623) hydrogen bonds : angle 5.13840 / 3.50 ( 1869) link_ALPHA1-3 : bond 0.00088 / 0.05 ( 1) link_ALPHA1-3 : angle 2.42108 / 1.31 ( 3) link_BETA1-4 : bond 0.00419 / 0.21 ( 4) link_BETA1-4 : angle 4.34943 / 2.13 ( 12) link_NAG-ASN : bond 0.00711 / 0.37 ( 5) link_NAG-ASN : angle 4.20458 / 2.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7817 (tp30) cc_final: 0.7563 (tm-30) REVERT: B 75 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8408 (ptpp) REVERT: B 164 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7907 (tmt-80) REVERT: B 240 ARG cc_start: 0.9281 (mtt90) cc_final: 0.9037 (ptp90) REVERT: B 274 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8486 (m110) REVERT: B 555 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 571 LEU cc_start: 0.8991 (mt) cc_final: 0.8719 (mt) REVERT: B 578 LEU cc_start: 0.9151 (mm) cc_final: 0.8950 (tp) REVERT: D 3 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8427 (mm) REVERT: D 179 MET cc_start: 0.8420 (ppp) cc_final: 0.8126 (ppp) REVERT: E 5 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8889 (p) REVERT: E 10 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8712 (t) REVERT: E 120 SER cc_start: 0.5964 (OUTLIER) cc_final: 0.5368 (p) REVERT: F 59 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: F 179 MET cc_start: 0.8480 (ppp) cc_final: 0.7992 (ppp) REVERT: G 93 ASN cc_start: 0.8954 (t0) cc_final: 0.8630 (t0) REVERT: G 155 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8561 (mp-120) outliers start: 64 outliers final: 24 residues processed: 175 average time/residue: 0.0947 time to fit residues: 26.2885 Evaluate side-chains 131 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain G residue 36 TYR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 7, 72, 132, 9, 151, 130, 64, 59, 15, 119] chunk 98 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 554 GLN B 129 GLN B 166 GLN B 274 ASN B 433 ASN D 166 HIS F 5 GLN F 193 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.100928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.070443 restraints weight = 41758.534| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.63 r_work: 0.3263 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 14624 Z= 0.152 Angle : 0.592 9.953 19867 Z= 0.296 Chirality : 0.044 0.243 2281 Planarity : 0.004 0.052 2518 Dihedral : 6.275 58.903 2158 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.60 % Allowed : 21.58 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1787 helix: 1.50 (0.29), residues: 310 sheet: -0.10 (0.19), residues: 741 loop : -0.98 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 107 TYR 0.013 0.001 TYR D 49 PHE 0.016 0.001 PHE A 584 TRP 0.010 0.001 TRP G 35 HIS 0.004 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (14606) covalent geometry : angle 0.57425 / 0.29 (19821) SS BOND : bond 0.00351 / 0.14 ( 8) SS BOND : angle 0.78738 / 0.44 ( 16) hydrogen bonds : bond 0.03182 / 2.16 ( 623) hydrogen bonds : angle 4.86027 / 3.31 ( 1869) link_ALPHA1-3 : bond 0.00202 / 0.11 ( 1) link_ALPHA1-3 : angle 1.95010 / 1.05 ( 3) link_BETA1-4 : bond 0.00779 / 0.39 ( 4) link_BETA1-4 : angle 3.66006 / 1.76 ( 12) link_NAG-ASN : bond 0.00779 / 0.40 ( 5) link_NAG-ASN : angle 4.10651 / 2.77 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 101 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8207 (tp30) cc_final: 0.7759 (tm-30) REVERT: A 573 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8274 (t0) REVERT: B 75 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8495 (ptpp) REVERT: B 161 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 164 ARG cc_start: 0.8374 (ttm110) cc_final: 0.7760 (tmt-80) REVERT: B 240 ARG cc_start: 0.9450 (mtt90) cc_final: 0.9001 (ptp90) REVERT: B 274 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8732 (m110) REVERT: B 285 MET cc_start: 0.8906 (mmm) cc_final: 0.8668 (mmm) REVERT: B 555 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 3 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8459 (mm) REVERT: D 179 MET cc_start: 0.8401 (ppp) cc_final: 0.8138 (ppp) REVERT: E 10 SER cc_start: 0.9371 (OUTLIER) cc_final: 0.8843 (t) REVERT: E 83 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7585 (tp) REVERT: E 107 ARG cc_start: 0.6732 (mtm-85) cc_final: 0.6302 (mtm110) REVERT: F 179 MET cc_start: 0.8549 (ppp) cc_final: 0.7883 (ppp) REVERT: G 85 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8778 (p) REVERT: G 93 ASN cc_start: 0.9094 (t0) cc_final: 0.8812 (t0) REVERT: G 135 LEU cc_start: 0.8073 (mt) cc_final: 0.7467 (tp) REVERT: G 155 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8569 (mp-120) outliers start: 57 outliers final: 30 residues processed: 151 average time/residue: 0.1115 time to fit residues: 26.0966 Evaluate side-chains 130 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [179, 122, 81, 146, 18, 13, 75, 112, 1, 96, 62] chunk 179 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN B 274 ASN F 5 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.100481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.070222 restraints weight = 41078.021| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.62 r_work: 0.3277 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14624 Z= 0.149 Angle : 0.583 9.694 19867 Z= 0.292 Chirality : 0.043 0.242 2281 Planarity : 0.004 0.052 2518 Dihedral : 6.226 59.121 2157 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.22 % Allowed : 22.15 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1787 helix: 1.75 (0.30), residues: 309 sheet: 0.07 (0.19), residues: 714 loop : -0.98 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 187 TYR 0.014 0.001 TYR D 49 PHE 0.014 0.001 PHE A 584 TRP 0.016 0.001 TRP F 105 HIS 0.007 0.001 HIS D 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14606) covalent geometry : angle 0.56548 / 0.29 (19821) SS BOND : bond 0.00253 / 0.12 ( 8) SS BOND : angle 0.82214 / 0.45 ( 16) hydrogen bonds : bond 0.02946 / 1.98 ( 623) hydrogen bonds : angle 4.74656 / 3.23 ( 1869) link_ALPHA1-3 : bond 0.00136 / 0.07 ( 1) link_ALPHA1-3 : angle 2.04185 / 1.11 ( 3) link_BETA1-4 : bond 0.00735 / 0.36 ( 4) link_BETA1-4 : angle 3.66460 / 1.77 ( 12) link_NAG-ASN : bond 0.00729 / 0.37 ( 5) link_NAG-ASN : angle 3.99349 / 2.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 95 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8318 (tp30) cc_final: 0.7879 (tm-30) REVERT: A 573 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8295 (t0) REVERT: B 75 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8146 (ptpp) REVERT: B 161 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 164 ARG cc_start: 0.8408 (ttm110) cc_final: 0.7754 (tmt-80) REVERT: B 285 MET cc_start: 0.9004 (mmm) cc_final: 0.8799 (mmm) REVERT: B 555 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8223 (tm-30) REVERT: D 3 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8714 (mm) REVERT: D 22 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8280 (ttpp) REVERT: D 179 MET cc_start: 0.8482 (ppp) cc_final: 0.8160 (ppp) REVERT: E 10 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.8853 (t) REVERT: F 59 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: G 85 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8642 (p) REVERT: G 93 ASN cc_start: 0.9171 (t0) cc_final: 0.8947 (t0) REVERT: G 155 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8579 (mp-120) outliers start: 51 outliers final: 28 residues processed: 141 average time/residue: 0.0951 time to fit residues: 21.2605 Evaluate side-chains 123 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [138, 164, 159, 24, 101, 108, 133, 118, 145, 14, 60] chunk 138 optimal weight: 0.2980 chunk 164 optimal weight: 0.0870 chunk 159 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN E 6 GLN F 5 GLN F 157 ASN ** G 3 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 = 0.4000 r_free = 0.4000 target = 0.099201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068207 restraints weight = 41879.107| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.79 r_work: 0.3228 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14624 Z= 0.178 Angle : 0.617 9.229 19867 Z= 0.311 Chirality : 0.044 0.240 2281 Planarity : 0.004 0.057 2518 Dihedral : 6.281 57.428 2157 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.54 % Allowed : 21.96 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1787 helix: 1.77 (0.30), residues: 310 sheet: 0.09 (0.19), residues: 720 loop : -0.99 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 107 TYR 0.014 0.002 TYR A 146 PHE 0.015 0.002 PHE A 584 TRP 0.014 0.001 TRP F 105 HIS 0.007 0.001 HIS D 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (14606) covalent geometry : angle 0.60175 / 0.31 (19821) SS BOND : bond 0.00315 / 0.15 ( 8) SS BOND : angle 0.75764 / 0.41 ( 16) hydrogen bonds : bond 0.03052 / 2.04 ( 623) hydrogen bonds : angle 4.75636 / 3.25 ( 1869) link_ALPHA1-3 : bond 0.00222 / 0.12 ( 1) link_ALPHA1-3 : angle 1.96997 / 1.07 ( 3) link_BETA1-4 : bond 0.00854 / 0.43 ( 4) link_BETA1-4 : angle 3.44254 / 1.66 ( 12) link_NAG-ASN : bond 0.00751 / 0.38 ( 5) link_NAG-ASN : angle 3.82034 / 2.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 90 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9601 (tt) cc_final: 0.9381 (mm) REVERT: B 125 MET cc_start: 0.8557 (ttt) cc_final: 0.8312 (tmm) REVERT: B 161 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8449 (tt) REVERT: B 274 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8730 (m110) REVERT: B 285 MET cc_start: 0.9356 (mmm) cc_final: 0.8918 (mmm) REVERT: B 591 MET cc_start: 0.6310 (tpp) cc_final: 0.6048 (tpp) REVERT: D 22 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8401 (ttpp) REVERT: D 61 GLU cc_start: 0.8988 (tp30) cc_final: 0.8561 (tp30) REVERT: D 85 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7292 (pp) REVERT: D 179 MET cc_start: 0.8557 (ppp) cc_final: 0.8180 (ppp) REVERT: E 5 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8782 (p) REVERT: E 10 SER cc_start: 0.9438 (OUTLIER) cc_final: 0.8836 (t) REVERT: E 170 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6951 (p) REVERT: F 59 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: F 88 GLU cc_start: 0.8855 (tp30) cc_final: 0.8619 (tp30) REVERT: G 155 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8422 (mp-120) outliers start: 72 outliers final: 43 residues processed: 155 average time/residue: 0.0939 time to fit residues: 23.0525 Evaluate side-chains 132 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 81 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 183 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [113, 89, 112, 155, 99, 43, 124, 4, 123, 92, 56] chunk 113 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** G 3 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 = 0.3997 r_free = 0.3997 target = 0.100244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068822 restraints weight = 41131.434| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.72 r_work: 0.3225 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14624 Z= 0.170 Angle : 0.594 8.963 19867 Z= 0.299 Chirality : 0.044 0.246 2281 Planarity : 0.004 0.053 2518 Dihedral : 6.182 58.326 2153 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.60 % Allowed : 23.03 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1787 helix: 1.92 (0.30), residues: 309 sheet: 0.14 (0.19), residues: 719 loop : -0.93 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.015 0.002 TYR D 49 PHE 0.011 0.001 PHE B 48 TRP 0.013 0.001 TRP F 105 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (14606) covalent geometry : angle 0.57936 / 0.30 (19821) SS BOND : bond 0.00319 / 0.18 ( 8) SS BOND : angle 0.85918 / 0.51 ( 16) hydrogen bonds : bond 0.02959 / 1.99 ( 623) hydrogen bonds : angle 4.75049 / 3.24 ( 1869) link_ALPHA1-3 : bond 0.00151 / 0.08 ( 1) link_ALPHA1-3 : angle 1.93686 / 1.05 ( 3) link_BETA1-4 : bond 0.00761 / 0.38 ( 4) link_BETA1-4 : angle 3.37716 / 1.63 ( 12) link_NAG-ASN : bond 0.00706 / 0.36 ( 5) link_NAG-ASN : angle 3.68423 / 2.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 89 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9589 (tt) cc_final: 0.9366 (mm) REVERT: B 160 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 164 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8129 (tmt-80) REVERT: B 194 MET cc_start: 0.8323 (ptt) cc_final: 0.8096 (ptm) REVERT: B 271 MET cc_start: 0.9097 (mtp) cc_final: 0.8820 (ttt) REVERT: B 285 MET cc_start: 0.9409 (mmm) cc_final: 0.9020 (mmm) REVERT: B 591 MET cc_start: 0.6281 (tpp) cc_final: 0.5981 (tpp) REVERT: D 61 GLU cc_start: 0.9093 (tp30) cc_final: 0.8567 (tp30) REVERT: D 85 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7432 (pp) REVERT: D 179 MET cc_start: 0.8592 (ppp) cc_final: 0.8180 (ppp) REVERT: E 10 SER cc_start: 0.9413 (OUTLIER) cc_final: 0.8887 (t) REVERT: F 59 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: F 88 GLU cc_start: 0.8857 (tp30) cc_final: 0.8581 (tp30) REVERT: G 155 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8345 (mp-120) outliers start: 57 outliers final: 45 residues processed: 140 average time/residue: 0.0985 time to fit residues: 21.3064 Evaluate side-chains 129 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 80 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [113, 162, 74, 105, 73, 45, 77, 70, 36, 93, 125] chunk 113 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 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 = 0.4005 r_free = 0.4005 target = 0.099105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.068540 restraints weight = 40848.003| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.61 r_work: 0.3219 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14624 Z= 0.141 Angle : 0.578 8.815 19867 Z= 0.288 Chirality : 0.043 0.257 2281 Planarity : 0.004 0.050 2518 Dihedral : 6.087 59.435 2153 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.53 % Allowed : 22.71 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1787 helix: 1.77 (0.30), residues: 317 sheet: 0.20 (0.19), residues: 717 loop : -0.90 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 107 TYR 0.016 0.001 TYR D 49 PHE 0.010 0.001 PHE A 142 TRP 0.009 0.001 TRP D 46 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14606) covalent geometry : angle 0.56344 / 0.28 (19821) SS BOND : bond 0.00241 / 0.11 ( 8) SS BOND : angle 0.78482 / 0.45 ( 16) hydrogen bonds : bond 0.02864 / 1.92 ( 623) hydrogen bonds : angle 4.66528 / 3.19 ( 1869) link_ALPHA1-3 : bond 0.00189 / 0.10 ( 1) link_ALPHA1-3 : angle 1.94694 / 1.06 ( 3) link_BETA1-4 : bond 0.00789 / 0.39 ( 4) link_BETA1-4 : angle 3.37457 / 1.63 ( 12) link_NAG-ASN : bond 0.00667 / 0.34 ( 5) link_NAG-ASN : angle 3.54805 / 2.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 79 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 VAL cc_start: 0.7294 (t) cc_final: 0.7080 (p) REVERT: B 160 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8085 (pp) REVERT: B 164 ARG cc_start: 0.8588 (ttm110) cc_final: 0.8225 (tmt-80) REVERT: B 194 MET cc_start: 0.8372 (ptt) cc_final: 0.8148 (ptm) REVERT: B 271 MET cc_start: 0.9049 (mtp) cc_final: 0.8782 (ttt) REVERT: B 285 MET cc_start: 0.9392 (mmm) cc_final: 0.9051 (mmm) REVERT: B 544 MET cc_start: 0.9022 (tpt) cc_final: 0.8793 (mmm) REVERT: B 591 MET cc_start: 0.6403 (tpp) cc_final: 0.6029 (tpp) REVERT: D 61 GLU cc_start: 0.9008 (tp30) cc_final: 0.8484 (tp30) REVERT: D 85 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7472 (pp) REVERT: D 179 MET cc_start: 0.8664 (ppp) cc_final: 0.8246 (ppp) REVERT: E 10 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.8847 (t) REVERT: F 59 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: F 88 GLU cc_start: 0.8793 (tp30) cc_final: 0.8526 (tp30) REVERT: G 155 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8367 (mp-120) outliers start: 56 outliers final: 45 residues processed: 132 average time/residue: 0.0962 time to fit residues: 20.2693 Evaluate side-chains 126 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 77 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 145 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [158, 13, 127, 6, 116, 159, 114, 98, 71, 57, 144] chunk 158 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN A 292 GLN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** G 3 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 = 0.3944 r_free = 0.3944 target = 0.097345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.065613 restraints weight = 42378.700| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.80 r_work: 0.3141 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14624 Z= 0.292 Angle : 0.703 9.310 19867 Z= 0.359 Chirality : 0.046 0.228 2281 Planarity : 0.004 0.042 2518 Dihedral : 6.568 56.450 2153 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.29 % Allowed : 22.52 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1787 helix: 1.45 (0.29), residues: 317 sheet: 0.01 (0.19), residues: 745 loop : -0.98 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 61 TYR 0.021 0.002 TYR E 50 PHE 0.023 0.002 PHE A 584 TRP 0.023 0.002 TRP F 105 HIS 0.009 0.002 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.29 (14606) covalent geometry : angle 0.69083 / 0.36 (19821) SS BOND : bond 0.00350 / 0.17 ( 8) SS BOND : angle 1.20387 / 0.73 ( 16) hydrogen bonds : bond 0.03724 / 2.50 ( 623) hydrogen bonds : angle 5.17969 / 3.55 ( 1869) link_ALPHA1-3 : bond 0.00353 / 0.19 ( 1) link_ALPHA1-3 : angle 2.03815 / 1.12 ( 3) link_BETA1-4 : bond 0.00759 / 0.38 ( 4) link_BETA1-4 : angle 3.20525 / 1.55 ( 12) link_NAG-ASN : bond 0.00661 / 0.34 ( 5) link_NAG-ASN : angle 3.74711 / 2.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 76 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 THR cc_start: 0.7385 (m) cc_final: 0.6799 (p) REVERT: B 125 MET cc_start: 0.8479 (ttt) cc_final: 0.7907 (ttp) REVERT: B 160 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8172 (pp) REVERT: B 164 ARG cc_start: 0.8683 (ttm110) cc_final: 0.8247 (tmt-80) REVERT: B 285 MET cc_start: 0.9334 (mmm) cc_final: 0.8951 (mmm) REVERT: B 591 MET cc_start: 0.6062 (tpp) cc_final: 0.5656 (tpp) REVERT: D 61 GLU cc_start: 0.9145 (tp30) cc_final: 0.8746 (tp30) REVERT: D 85 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7673 (pp) REVERT: D 172 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6442 (tp) REVERT: D 179 MET cc_start: 0.8655 (ppp) cc_final: 0.8120 (ppp) REVERT: E 5 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8833 (p) REVERT: E 10 SER cc_start: 0.9498 (OUTLIER) cc_final: 0.9133 (t) REVERT: E 170 SER cc_start: 0.6848 (OUTLIER) cc_final: 0.6617 (p) REVERT: F 33 MET cc_start: 0.8880 (tpp) cc_final: 0.8652 (mmm) REVERT: F 59 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: G 109 ASP cc_start: 0.7471 (t0) cc_final: 0.7008 (t0) REVERT: G 155 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8345 (mp-120) outliers start: 68 outliers final: 48 residues processed: 140 average time/residue: 0.0927 time to fit residues: 20.9035 Evaluate side-chains 128 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 73 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 183 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [38, 35, 86, 84, 14, 139, 71, 9, 43, 4, 66] chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.098690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067395 restraints weight = 41428.376| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.73 r_work: 0.3213 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14624 Z= 0.129 Angle : 0.606 8.989 19867 Z= 0.302 Chirality : 0.044 0.270 2281 Planarity : 0.004 0.049 2518 Dihedral : 6.211 59.454 2153 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.03 % Allowed : 23.97 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1787 helix: 1.73 (0.30), residues: 316 sheet: 0.04 (0.19), residues: 747 loop : -0.85 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 107 TYR 0.015 0.001 TYR D 49 PHE 0.010 0.001 PHE A 142 TRP 0.013 0.001 TRP E 35 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14606) covalent geometry : angle 0.59248 / 0.30 (19821) SS BOND : bond 0.00205 / 0.09 ( 8) SS BOND : angle 0.80191 / 0.46 ( 16) hydrogen bonds : bond 0.02986 / 2.03 ( 623) hydrogen bonds : angle 4.77902 / 3.28 ( 1869) link_ALPHA1-3 : bond 0.00186 / 0.10 ( 1) link_ALPHA1-3 : angle 1.97362 / 1.07 ( 3) link_BETA1-4 : bond 0.00792 / 0.39 ( 4) link_BETA1-4 : angle 3.27263 / 1.57 ( 12) link_NAG-ASN : bond 0.00713 / 0.37 ( 5) link_NAG-ASN : angle 3.56694 / 2.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 81 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 THR cc_start: 0.7307 (m) cc_final: 0.6725 (p) REVERT: B 160 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8167 (pp) REVERT: B 194 MET cc_start: 0.7985 (ptt) cc_final: 0.7734 (ptm) REVERT: B 271 MET cc_start: 0.9064 (mtp) cc_final: 0.8645 (ttt) REVERT: B 285 MET cc_start: 0.9316 (mmm) cc_final: 0.8569 (mmm) REVERT: B 591 MET cc_start: 0.6032 (tpp) cc_final: 0.5697 (tpp) REVERT: D 9 GLU cc_start: 0.8067 (mp0) cc_final: 0.7676 (mp0) REVERT: D 61 GLU cc_start: 0.9084 (tp30) cc_final: 0.8650 (tp30) REVERT: D 85 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7721 (pp) REVERT: D 172 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6294 (tp) REVERT: D 179 MET cc_start: 0.8685 (ppp) cc_final: 0.8082 (ppp) REVERT: F 59 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: G 155 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8320 (mp-120) outliers start: 48 outliers final: 38 residues processed: 125 average time/residue: 0.0923 time to fit residues: 18.6737 Evaluate side-chains 117 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 75 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [170, 24, 138, 172, 126, 39, 65, 111, 13, 77, 160] chunk 170 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 138 optimal weight: 0.0040 chunk 172 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 0.0470 chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 160 optimal weight: 9.9990 overall best weight: 0.1828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 292 GLN A 568 GLN B 129 GLN B 554 GLN D 5 GLN E 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.099783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069465 restraints weight = 41800.454| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.73 r_work: 0.3267 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 14624 Z= 0.103 Angle : 0.599 8.931 19867 Z= 0.295 Chirality : 0.044 0.284 2281 Planarity : 0.004 0.053 2518 Dihedral : 5.943 59.133 2152 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.78 % Allowed : 24.35 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1787 helix: 1.83 (0.30), residues: 316 sheet: 0.24 (0.20), residues: 706 loop : -0.77 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 107 TYR 0.012 0.001 TYR D 49 PHE 0.021 0.001 PHE A 540 TRP 0.014 0.001 TRP E 35 HIS 0.003 0.001 HIS G 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (14606) covalent geometry : angle 0.58494 / 0.29 (19821) SS BOND : bond 0.00457 / 0.23 ( 8) SS BOND : angle 0.95670 / 0.53 ( 16) hydrogen bonds : bond 0.02807 / 1.92 ( 623) hydrogen bonds : angle 4.61779 / 3.15 ( 1869) link_ALPHA1-3 : bond 0.00201 / 0.11 ( 1) link_ALPHA1-3 : angle 1.94619 / 1.05 ( 3) link_BETA1-4 : bond 0.00805 / 0.40 ( 4) link_BETA1-4 : angle 3.32817 / 1.60 ( 12) link_NAG-ASN : bond 0.00735 / 0.39 ( 5) link_NAG-ASN : angle 3.45318 / 2.38 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.6681 (OUTLIER) cc_final: 0.6267 (p0) REVERT: B 39 THR cc_start: 0.7463 (m) cc_final: 0.6856 (p) REVERT: B 194 MET cc_start: 0.8006 (ptt) cc_final: 0.7754 (ptm) REVERT: B 271 MET cc_start: 0.9032 (mtp) cc_final: 0.8662 (ttt) REVERT: B 285 MET cc_start: 0.9274 (mmm) cc_final: 0.8691 (mmm) REVERT: B 554 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8811 (mt0) REVERT: B 591 MET cc_start: 0.6346 (tpp) cc_final: 0.6004 (tpp) REVERT: D 9 GLU cc_start: 0.8080 (mp0) cc_final: 0.7712 (mp0) REVERT: D 61 GLU cc_start: 0.8960 (tp30) cc_final: 0.8628 (tp30) REVERT: D 179 MET cc_start: 0.8708 (ppp) cc_final: 0.8073 (ppp) REVERT: F 33 MET cc_start: 0.8811 (tpp) cc_final: 0.8428 (tpp) REVERT: F 59 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: G 155 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8286 (mp10) outliers start: 44 outliers final: 36 residues processed: 120 average time/residue: 0.0974 time to fit residues: 18.5594 Evaluate side-chains 115 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [7, 128, 71, 147, 148, 138, 80, 23, 132, 137, 142] chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.100872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.069352 restraints weight = 41474.207| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.82 r_work: 0.3256 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.336 14624 Z= 0.288 Angle : 1.067 59.200 19867 Z= 0.644 Chirality : 0.054 1.241 2281 Planarity : 0.006 0.199 2518 Dihedral : 5.951 59.017 2152 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 2.52 % Allowed : 24.61 % Favored : 72.87 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1787 helix: 1.66 (0.30), residues: 316 sheet: 0.25 (0.20), residues: 706 loop : -0.76 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 107 TYR 0.013 0.001 TYR D 49 PHE 0.020 0.001 PHE A 540 TRP 0.012 0.001 TRP E 35 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.29 (14606) covalent geometry : angle 1.05970 / 0.64 (19821) SS BOND : bond 0.00263 / 0.12 ( 8) SS BOND : angle 0.87041 / 0.49 ( 16) hydrogen bonds : bond 0.02934 / 2.03 ( 623) hydrogen bonds : angle 4.62894 / 3.15 ( 1869) link_ALPHA1-3 : bond 0.00147 / 0.08 ( 1) link_ALPHA1-3 : angle 1.95020 / 1.05 ( 3) link_BETA1-4 : bond 0.00773 / 0.38 ( 4) link_BETA1-4 : angle 3.37531 / 1.63 ( 12) link_NAG-ASN : bond 0.00739 / 0.39 ( 5) link_NAG-ASN : angle 3.46467 / 2.39 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3876.31 seconds wall clock time: 67 minutes 10.99 seconds (4030.99 seconds total)