Starting phenix.real_space_refine on Fri Jul 3 06:44:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8py4_18016/07_2026/8py4_18016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8py4_18016/07_2026/8py4_18016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8py4_18016/07_2026/8py4_18016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8py4_18016/07_2026/8py4_18016.map" model { file = "/net/cci-nas-00/data/ceres_data/8py4_18016/07_2026/8py4_18016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8py4_18016/07_2026/8py4_18016.cif" } resolution = 3.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8298 2.51 5 N 2042 2.21 5 O 2339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12747 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 208 Unusual residues: {'CLR': 5, 'I3O': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.08, per 1000 atoms: 0.24 Number of scatterers: 12747 At special positions: 0 Unit cell: (100.98, 103.62, 145.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2339 8.00 N 2042 7.00 C 8298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN B 596 " " NAG H 1 " - " ASN A 596 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 572.9 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 46.6% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.695A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.725A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.539A pdb=" N ALA B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.788A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 272 through 280 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.572A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 Processing helix chain 'B' and resid 391 through 413 removed outlier: 3.989A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'B' and resid 442 through 445 Processing helix chain 'B' and resid 446 through 451 removed outlier: 4.507A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 477 through 498 removed outlier: 3.518A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.987A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 Processing helix chain 'B' and resid 533 through 551 removed outlier: 4.252A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.437A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 587 removed outlier: 3.548A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 4.871A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.724A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.539A pdb=" N ALA A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.788A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.572A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 391 through 413 removed outlier: 3.988A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 441 Processing helix chain 'A' and resid 442 through 445 Processing helix chain 'A' and resid 446 through 451 removed outlier: 4.507A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 477 through 498 removed outlier: 3.518A pdb=" N MET A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.986A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 Processing helix chain 'A' and resid 533 through 551 removed outlier: 4.252A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.436A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 587 removed outlier: 3.548A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 4.871A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.695A pdb=" N VAL C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.678A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE D 41 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 46 " --> pdb=" O PHE D 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.281A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.457A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.457A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.678A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE F 41 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 46 " --> pdb=" O PHE F 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.281A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.656A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.252A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLY B 74 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 240 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.657A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.251A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLY A 74 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 240 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.456A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.456A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1893 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: 2.16 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2056 1.32 - 1.45: 3569 1.45 - 1.57: 7257 1.57 - 1.70: 36 1.70 - 1.83: 106 Bond restraints: 13024 Sorted by residual: bond pdb=" C10 I3O A 707 " pdb=" C18 I3O A 707 " ideal model delta sigma weight residual 1.521 1.640 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C10 I3O A 706 " pdb=" C18 I3O A 706 " ideal model delta sigma weight residual 1.521 1.639 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C17 I3O A 706 " pdb=" C19 I3O A 706 " ideal model delta sigma weight residual 1.521 1.634 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C17 I3O A 707 " pdb=" C19 I3O A 707 " ideal model delta sigma weight residual 1.521 1.633 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C10 I3O A 707 " pdb=" N02 I3O A 707 " ideal model delta sigma weight residual 1.471 1.569 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 13019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 17311 2.40 - 4.79: 339 4.79 - 7.19: 56 7.19 - 9.58: 12 9.58 - 11.98: 2 Bond angle restraints: 17720 Sorted by residual: angle pdb=" C21 I3O A 707 " pdb=" C22 I3O A 707 " pdb=" O04 I3O A 707 " ideal model delta sigma weight residual 110.17 122.15 -11.98 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C21 I3O A 706 " pdb=" C22 I3O A 706 " pdb=" O04 I3O A 706 " ideal model delta sigma weight residual 110.17 122.11 -11.94 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CB GLN A 126 " pdb=" CG GLN A 126 " pdb=" CD GLN A 126 " ideal model delta sigma weight residual 112.60 119.01 -6.41 1.70e+00 3.46e-01 1.42e+01 angle pdb=" CB GLN B 126 " pdb=" CG GLN B 126 " pdb=" CD GLN B 126 " ideal model delta sigma weight residual 112.60 118.98 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" CG GLN F 40 " pdb=" CD GLN F 40 " pdb=" NE2 GLN F 40 " ideal model delta sigma weight residual 116.40 111.63 4.77 1.50e+00 4.44e-01 1.01e+01 ... (remaining 17715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 7757 17.47 - 34.93: 354 34.93 - 52.40: 90 52.40 - 69.87: 20 69.87 - 87.33: 2 Dihedral angle restraints: 8223 sinusoidal: 3687 harmonic: 4536 Sorted by residual: dihedral pdb=" CA ASP F 32 " pdb=" C ASP F 32 " pdb=" N TYR F 33 " pdb=" CA TYR F 33 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASP D 32 " pdb=" C ASP D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLY F 43 " pdb=" C GLY F 43 " pdb=" N LYS F 44 " pdb=" CA LYS F 44 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 8220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1944 0.103 - 0.205: 66 0.205 - 0.308: 26 0.308 - 0.411: 12 0.411 - 0.513: 2 Chirality restraints: 2050 Sorted by residual: chirality pdb=" C10 I3O A 707 " pdb=" C11 I3O A 707 " pdb=" C18 I3O A 707 " pdb=" N02 I3O A 707 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" C10 I3O A 706 " pdb=" C11 I3O A 706 " pdb=" C18 I3O A 706 " pdb=" N02 I3O A 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" C19 I3O A 707 " pdb=" C17 I3O A 707 " pdb=" C20 I3O A 707 " pdb=" N03 I3O A 707 " both_signs ideal model delta sigma weight residual False 2.45 2.84 -0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 2047 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 I3O A 707 " 0.032 2.00e-02 2.50e+03 1.23e-01 1.89e+02 pdb=" C18 I3O A 707 " 0.028 2.00e-02 2.50e+03 pdb=" C19 I3O A 707 " -0.143 2.00e-02 2.50e+03 pdb=" N03 I3O A 707 " 0.199 2.00e-02 2.50e+03 pdb=" O02 I3O A 707 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 I3O A 706 " -0.032 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" C18 I3O A 706 " -0.028 2.00e-02 2.50e+03 pdb=" C19 I3O A 706 " 0.143 2.00e-02 2.50e+03 pdb=" N03 I3O A 706 " -0.199 2.00e-02 2.50e+03 pdb=" O02 I3O A 706 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C09 I3O A 707 " 0.096 2.00e-02 2.50e+03 1.06e-01 1.67e+02 pdb=" C10 I3O A 707 " -0.139 2.00e-02 2.50e+03 pdb=" C17 I3O A 707 " -0.003 2.00e-02 2.50e+03 pdb=" C19 I3O A 707 " 0.115 2.00e-02 2.50e+03 pdb=" N02 I3O A 707 " 0.072 2.00e-02 2.50e+03 pdb=" O03 I3O A 707 " -0.141 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 528 2.72 - 3.27: 12830 3.27 - 3.81: 20008 3.81 - 4.36: 25518 4.36 - 4.90: 44698 Nonbonded interactions: 103582 Sorted by model distance: nonbonded pdb=" O3 NAG H 1 " pdb=" O7 NAG H 1 " model vdw 2.178 3.040 nonbonded pdb=" O3 NAG G 1 " pdb=" O7 NAG G 1 " model vdw 2.178 3.040 nonbonded pdb=" O GLN F 16 " pdb=" OG SER F 17 " model vdw 2.184 3.040 nonbonded pdb=" O GLN D 16 " pdb=" OG SER D 17 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR A 613 " pdb=" O HOH A 801 " model vdw 2.213 3.040 ... (remaining 103577 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 35 through 705) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 5.740 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: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.110 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 : 0.010 0.289 13035 Z= 0.458 Angle : 0.817 11.977 17746 Z= 0.389 Chirality : 0.060 0.513 2050 Planarity : 0.006 0.123 2144 Dihedral : 11.008 87.335 5306 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.89 % Allowed : 4.15 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.21), residues: 1558 helix: 0.92 (0.21), residues: 652 sheet: -0.22 (0.30), residues: 276 loop : -1.63 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 378 TYR 0.014 0.001 TYR F 51 PHE 0.017 0.002 PHE F 79 TRP 0.013 0.002 TRP F 35 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.42 (13024) covalent geometry : angle 0.81017 / 0.39 (17720) SS BOND : bond 0.00771 / 0.35 ( 7) SS BOND : angle 1.26570 / 0.70 ( 14) hydrogen bonds : bond 0.15477 / 10.13 ( 651) hydrogen bonds : angle 5.98210 / 4.06 ( 1893) link_BETA1-4 : bond 0.00616 / 0.31 ( 2) link_BETA1-4 : angle 1.70941 / 0.85 ( 6) link_NAG-ASN : bond 0.28917 / 14.51 ( 2) link_NAG-ASN : angle 5.27978 / 2.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.469 Fit side-chains REVERT: B 173 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.7012 (p) outliers start: 12 outliers final: 8 residues processed: 226 average time/residue: 0.5718 time to fit residues: 140.4206 Evaluate side-chains 146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 631 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 ASN A 166 GLN A 271 GLN A 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096497 restraints weight = 17902.541| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.18 r_work: 0.3001 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13035 Z= 0.130 Angle : 0.585 7.405 17746 Z= 0.295 Chirality : 0.042 0.170 2050 Planarity : 0.003 0.031 2144 Dihedral : 7.296 107.526 2533 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.44 % Allowed : 11.63 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1558 helix: 1.54 (0.21), residues: 676 sheet: 0.17 (0.31), residues: 272 loop : -1.32 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.015 0.001 TYR B 336 PHE 0.017 0.001 PHE F 79 TRP 0.012 0.001 TRP B 379 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13024) covalent geometry : angle 0.58120 / 0.29 (17720) SS BOND : bond 0.00646 / 0.42 ( 7) SS BOND : angle 1.19835 / 0.65 ( 14) hydrogen bonds : bond 0.04787 / 3.12 ( 651) hydrogen bonds : angle 4.15170 / 2.81 ( 1893) link_BETA1-4 : bond 0.00240 / 0.12 ( 2) link_BETA1-4 : angle 2.27551 / 1.17 ( 6) link_NAG-ASN : bond 0.00971 / 0.48 ( 2) link_NAG-ASN : angle 2.70018 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.476 Fit side-chains REVERT: B 120 ASN cc_start: 0.7634 (m-40) cc_final: 0.7345 (t0) REVERT: B 163 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8016 (ptt-90) REVERT: B 166 GLN cc_start: 0.7923 (tt0) cc_final: 0.7494 (mt0) REVERT: B 173 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7260 (m) REVERT: B 272 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 338 ASN cc_start: 0.8274 (t0) cc_final: 0.7864 (t0) REVERT: B 374 CYS cc_start: 0.8272 (m) cc_final: 0.8056 (m) REVERT: B 475 LEU cc_start: 0.9001 (tp) cc_final: 0.8727 (mp) REVERT: B 514 MET cc_start: 0.8890 (mtp) cc_final: 0.8626 (mtm) REVERT: B 587 LEU cc_start: 0.8173 (mt) cc_final: 0.7826 (tp) REVERT: A 120 ASN cc_start: 0.7624 (m-40) cc_final: 0.7344 (t0) REVERT: A 163 ARG cc_start: 0.8329 (mtm180) cc_final: 0.8019 (ptt-90) REVERT: A 166 GLN cc_start: 0.8030 (tt0) cc_final: 0.7637 (mt0) REVERT: A 338 ASN cc_start: 0.8273 (t0) cc_final: 0.7875 (t0) REVERT: A 475 LEU cc_start: 0.9025 (tp) cc_final: 0.8713 (mp) REVERT: A 514 MET cc_start: 0.8883 (mtp) cc_final: 0.8624 (mtm) outliers start: 33 outliers final: 18 residues processed: 183 average time/residue: 0.5623 time to fit residues: 111.8886 Evaluate side-chains 149 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 40 GLN F 40 GLN B 375 HIS A 375 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089456 restraints weight = 18246.305| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.29 r_work: 0.2874 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13035 Z= 0.211 Angle : 0.630 8.228 17746 Z= 0.323 Chirality : 0.044 0.170 2050 Planarity : 0.004 0.035 2144 Dihedral : 6.548 52.341 2527 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.15 % Allowed : 12.00 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.21), residues: 1558 helix: 1.37 (0.20), residues: 694 sheet: 0.31 (0.31), residues: 272 loop : -1.31 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 147 TYR 0.015 0.002 TYR B 336 PHE 0.019 0.002 PHE D 79 TRP 0.016 0.002 TRP A 379 HIS 0.005 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (13024) covalent geometry : angle 0.62579 / 0.32 (17720) SS BOND : bond 0.00705 / 0.31 ( 7) SS BOND : angle 1.68740 / 0.92 ( 14) hydrogen bonds : bond 0.05717 / 3.71 ( 651) hydrogen bonds : angle 4.16348 / 2.82 ( 1893) link_BETA1-4 : bond 0.00567 / 0.29 ( 2) link_BETA1-4 : angle 1.96862 / 1.03 ( 6) link_NAG-ASN : bond 0.00501 / 0.25 ( 2) link_NAG-ASN : angle 2.55841 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 0.431 Fit side-chains REVERT: D 5 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: F 5 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: B 43 CYS cc_start: 0.7334 (m) cc_final: 0.6935 (t) REVERT: B 45 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6933 (mtp180) REVERT: B 120 ASN cc_start: 0.7743 (m-40) cc_final: 0.7349 (t0) REVERT: B 153 THR cc_start: 0.6656 (OUTLIER) cc_final: 0.6395 (p) REVERT: B 163 ARG cc_start: 0.8321 (mtm180) cc_final: 0.8038 (ptt-90) REVERT: B 173 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7532 (p) REVERT: B 246 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7537 (ttm170) REVERT: B 272 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 332 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5544 (mt) REVERT: B 338 ASN cc_start: 0.8358 (t0) cc_final: 0.8064 (m-40) REVERT: B 374 CYS cc_start: 0.8488 (m) cc_final: 0.8214 (m) REVERT: B 514 MET cc_start: 0.8945 (mtp) cc_final: 0.8684 (mtm) REVERT: B 533 VAL cc_start: 0.7849 (t) cc_final: 0.7614 (p) REVERT: A 43 CYS cc_start: 0.7294 (m) cc_final: 0.6916 (t) REVERT: A 45 ARG cc_start: 0.7195 (ttt-90) cc_final: 0.6981 (mtp180) REVERT: A 120 ASN cc_start: 0.7744 (m-40) cc_final: 0.7351 (t0) REVERT: A 153 THR cc_start: 0.6630 (OUTLIER) cc_final: 0.6371 (p) REVERT: A 163 ARG cc_start: 0.8347 (mtm180) cc_final: 0.8055 (ptt-90) REVERT: A 173 VAL cc_start: 0.7735 (OUTLIER) cc_final: 0.7460 (m) REVERT: A 332 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5580 (mt) REVERT: A 338 ASN cc_start: 0.8370 (t0) cc_final: 0.8086 (m-40) REVERT: A 514 MET cc_start: 0.8941 (mtp) cc_final: 0.8681 (mtm) REVERT: A 533 VAL cc_start: 0.7843 (t) cc_final: 0.7616 (p) outliers start: 56 outliers final: 22 residues processed: 195 average time/residue: 0.5146 time to fit residues: 109.9382 Evaluate side-chains 161 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 0.0670 chunk 152 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 111 GLN F 111 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN B 271 GLN ** A 40 HIS ** 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 = 0.3578 r_free = 0.3578 target = 0.124602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.091705 restraints weight = 18176.376| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.27 r_work: 0.2941 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13035 Z= 0.138 Angle : 0.549 7.029 17746 Z= 0.281 Chirality : 0.040 0.152 2050 Planarity : 0.003 0.036 2144 Dihedral : 6.040 53.156 2523 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.48 % Allowed : 15.56 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.22), residues: 1558 helix: 1.72 (0.20), residues: 694 sheet: 0.40 (0.30), residues: 272 loop : -1.13 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 45 TYR 0.012 0.001 TYR B 336 PHE 0.016 0.001 PHE D 79 TRP 0.013 0.001 TRP F 35 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13024) covalent geometry : angle 0.54461 / 0.28 (17720) SS BOND : bond 0.00389 / 0.17 ( 7) SS BOND : angle 1.54059 / 0.88 ( 14) hydrogen bonds : bond 0.04622 / 3.00 ( 651) hydrogen bonds : angle 3.94192 / 2.68 ( 1893) link_BETA1-4 : bond 0.00521 / 0.26 ( 2) link_BETA1-4 : angle 2.04327 / 1.05 ( 6) link_NAG-ASN : bond 0.00293 / 0.15 ( 2) link_NAG-ASN : angle 2.33835 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.505 Fit side-chains REVERT: D 5 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: D 81 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8943 (tp) REVERT: E 11 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7241 (t80) REVERT: F 5 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: F 81 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8942 (tp) REVERT: B 43 CYS cc_start: 0.7237 (m) cc_final: 0.6866 (t) REVERT: B 45 ARG cc_start: 0.7256 (ttt-90) cc_final: 0.6933 (mtp-110) REVERT: B 71 MET cc_start: 0.8549 (mtt) cc_final: 0.7393 (mtt) REVERT: B 120 ASN cc_start: 0.7771 (m-40) cc_final: 0.7411 (t0) REVERT: B 173 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7498 (p) REVERT: B 332 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5540 (mt) REVERT: B 374 CYS cc_start: 0.8461 (m) cc_final: 0.8191 (m) REVERT: B 514 MET cc_start: 0.8856 (mtp) cc_final: 0.8598 (mtm) REVERT: A 43 CYS cc_start: 0.7212 (m) cc_final: 0.6860 (t) REVERT: A 45 ARG cc_start: 0.7282 (ttt-90) cc_final: 0.6956 (mtp-110) REVERT: A 71 MET cc_start: 0.8565 (mtt) cc_final: 0.7423 (mtt) REVERT: A 120 ASN cc_start: 0.7770 (m-40) cc_final: 0.7420 (t0) REVERT: A 166 GLN cc_start: 0.7982 (tt0) cc_final: 0.7559 (mt0) REVERT: A 173 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7425 (m) REVERT: A 332 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5596 (mt) REVERT: A 514 MET cc_start: 0.8850 (mtp) cc_final: 0.8593 (mtm) REVERT: C 11 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7241 (t80) outliers start: 47 outliers final: 27 residues processed: 175 average time/residue: 0.5035 time to fit residues: 96.7426 Evaluate side-chains 170 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 636 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091542 restraints weight = 18281.182| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.29 r_work: 0.2924 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13035 Z= 0.170 Angle : 0.573 7.503 17746 Z= 0.294 Chirality : 0.041 0.154 2050 Planarity : 0.004 0.037 2144 Dihedral : 5.962 53.365 2523 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.52 % Allowed : 15.70 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1558 helix: 1.78 (0.20), residues: 694 sheet: 0.37 (0.30), residues: 272 loop : -1.17 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 45 TYR 0.012 0.002 TYR F 51 PHE 0.018 0.001 PHE D 79 TRP 0.012 0.001 TRP D 35 HIS 0.003 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (13024) covalent geometry : angle 0.56882 / 0.29 (17720) SS BOND : bond 0.00541 / 0.26 ( 7) SS BOND : angle 1.40635 / 0.76 ( 14) hydrogen bonds : bond 0.04962 / 3.22 ( 651) hydrogen bonds : angle 3.97245 / 2.70 ( 1893) link_BETA1-4 : bond 0.00501 / 0.25 ( 2) link_BETA1-4 : angle 1.96136 / 1.03 ( 6) link_NAG-ASN : bond 0.00337 / 0.17 ( 2) link_NAG-ASN : angle 2.51790 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 0.516 Fit side-chains REVERT: D 5 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: D 81 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8945 (tp) REVERT: E 11 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7245 (t80) REVERT: F 5 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: F 81 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8940 (tp) REVERT: B 43 CYS cc_start: 0.7259 (m) cc_final: 0.6887 (t) REVERT: B 45 ARG cc_start: 0.7309 (ttt-90) cc_final: 0.6975 (mtp-110) REVERT: B 105 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6459 (p0) REVERT: B 120 ASN cc_start: 0.7673 (m-40) cc_final: 0.7340 (t0) REVERT: B 166 GLN cc_start: 0.8061 (tt0) cc_final: 0.7684 (mt0) REVERT: B 172 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8002 (pptt) REVERT: B 173 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7654 (p) REVERT: B 332 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5654 (mt) REVERT: B 374 CYS cc_start: 0.8449 (m) cc_final: 0.8165 (m) REVERT: B 514 MET cc_start: 0.8868 (mtp) cc_final: 0.8613 (mtm) REVERT: A 43 CYS cc_start: 0.7243 (m) cc_final: 0.6885 (t) REVERT: A 45 ARG cc_start: 0.7333 (ttt-90) cc_final: 0.6998 (mtp-110) REVERT: A 105 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6475 (p0) REVERT: A 120 ASN cc_start: 0.7669 (m-40) cc_final: 0.7335 (t0) REVERT: A 173 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7516 (m) REVERT: A 332 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5680 (mt) REVERT: A 514 MET cc_start: 0.8859 (mtp) cc_final: 0.8603 (mtm) REVERT: A 587 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 11 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7235 (t80) outliers start: 61 outliers final: 37 residues processed: 177 average time/residue: 0.4474 time to fit residues: 87.3326 Evaluate side-chains 185 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 636 MET Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 90 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 111 GLN F 111 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.087468 restraints weight = 18281.187| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.19 r_work: 0.2905 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13035 Z= 0.193 Angle : 0.586 7.786 17746 Z= 0.300 Chirality : 0.042 0.159 2050 Planarity : 0.004 0.037 2144 Dihedral : 5.983 53.269 2523 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.96 % Allowed : 15.63 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.68 (0.21), residues: 1558 helix: 1.78 (0.20), residues: 696 sheet: 0.42 (0.30), residues: 272 loop : -1.18 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.012 0.002 TYR D 51 PHE 0.019 0.001 PHE D 79 TRP 0.013 0.002 TRP F 35 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (13024) covalent geometry : angle 0.58155 / 0.30 (17720) SS BOND : bond 0.00582 / 0.25 ( 7) SS BOND : angle 1.57836 / 0.86 ( 14) hydrogen bonds : bond 0.05165 / 3.35 ( 651) hydrogen bonds : angle 4.00030 / 2.72 ( 1893) link_BETA1-4 : bond 0.00582 / 0.30 ( 2) link_BETA1-4 : angle 1.98456 / 1.04 ( 6) link_NAG-ASN : bond 0.00373 / 0.19 ( 2) link_NAG-ASN : angle 2.60225 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 137 time to evaluate : 0.392 Fit side-chains REVERT: D 5 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: D 81 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8852 (tp) REVERT: E 11 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7072 (t80) REVERT: F 5 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: F 81 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8849 (tp) REVERT: B 43 CYS cc_start: 0.7179 (m) cc_final: 0.6738 (t) REVERT: B 45 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.6886 (mtp-110) REVERT: B 71 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7484 (mtt) REVERT: B 105 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6264 (p0) REVERT: B 120 ASN cc_start: 0.7800 (m-40) cc_final: 0.7410 (t0) REVERT: B 172 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7960 (pptt) REVERT: B 332 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5421 (mt) REVERT: B 374 CYS cc_start: 0.8657 (m) cc_final: 0.8329 (m) REVERT: B 514 MET cc_start: 0.8795 (mtp) cc_final: 0.8515 (mtm) REVERT: B 587 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8049 (tp) REVERT: A 43 CYS cc_start: 0.7190 (m) cc_final: 0.6761 (t) REVERT: A 45 ARG cc_start: 0.7323 (ttt-90) cc_final: 0.6899 (mtp-110) REVERT: A 71 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: A 105 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6264 (p0) REVERT: A 120 ASN cc_start: 0.7796 (m-40) cc_final: 0.7411 (t0) REVERT: A 173 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7362 (m) REVERT: A 332 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5525 (mt) REVERT: A 514 MET cc_start: 0.8791 (mtp) cc_final: 0.8511 (mtm) REVERT: A 587 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8118 (tp) REVERT: C 11 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7060 (t80) outliers start: 67 outliers final: 32 residues processed: 176 average time/residue: 0.4720 time to fit residues: 91.9501 Evaluate side-chains 181 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 153 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 111 GLN F 111 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** 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 = 0.3589 r_free = 0.3589 target = 0.125775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093572 restraints weight = 18110.236| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.32 r_work: 0.2957 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13035 Z= 0.111 Angle : 0.514 6.418 17746 Z= 0.264 Chirality : 0.039 0.141 2050 Planarity : 0.003 0.038 2144 Dihedral : 5.598 54.102 2522 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.56 % Allowed : 17.48 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.22), residues: 1558 helix: 2.13 (0.21), residues: 690 sheet: 0.58 (0.31), residues: 272 loop : -1.01 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.009 0.001 TYR A 336 PHE 0.015 0.001 PHE D 79 TRP 0.015 0.001 TRP D 35 HIS 0.001 0.000 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13024) covalent geometry : angle 0.51117 / 0.26 (17720) SS BOND : bond 0.00491 / 0.33 ( 7) SS BOND : angle 0.73458 / 0.39 ( 14) hydrogen bonds : bond 0.04048 / 2.63 ( 651) hydrogen bonds : angle 3.81832 / 2.60 ( 1893) link_BETA1-4 : bond 0.00603 / 0.31 ( 2) link_BETA1-4 : angle 2.01976 / 1.03 ( 6) link_NAG-ASN : bond 0.00275 / 0.14 ( 2) link_NAG-ASN : angle 2.37900 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.474 Fit side-chains REVERT: D 5 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: E 11 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7202 (t80) REVERT: F 5 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: B 43 CYS cc_start: 0.7271 (m) cc_final: 0.6931 (t) REVERT: B 45 ARG cc_start: 0.7382 (ttt-90) cc_final: 0.7057 (mtp-110) REVERT: B 71 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7320 (mtt) REVERT: B 120 ASN cc_start: 0.7691 (m-40) cc_final: 0.7363 (t0) REVERT: B 166 GLN cc_start: 0.8087 (tt0) cc_final: 0.7740 (mt0) REVERT: B 332 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5697 (mt) REVERT: B 374 CYS cc_start: 0.8477 (m) cc_final: 0.8196 (m) REVERT: B 489 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7871 (t80) REVERT: B 514 MET cc_start: 0.8859 (mtp) cc_final: 0.8610 (mtm) REVERT: A 43 CYS cc_start: 0.7242 (m) cc_final: 0.6921 (t) REVERT: A 45 ARG cc_start: 0.7404 (ttt-90) cc_final: 0.7059 (mtp-110) REVERT: A 71 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7342 (mtt) REVERT: A 120 ASN cc_start: 0.7683 (m-40) cc_final: 0.7351 (t0) REVERT: A 166 GLN cc_start: 0.8036 (tt0) cc_final: 0.7633 (mt0) REVERT: A 173 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7421 (m) REVERT: A 332 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5716 (mt) REVERT: A 489 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7891 (t80) REVERT: A 514 MET cc_start: 0.8842 (mtp) cc_final: 0.8591 (mtm) REVERT: A 540 LEU cc_start: 0.8382 (mt) cc_final: 0.8025 (mp) REVERT: C 11 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7199 (t80) outliers start: 48 outliers final: 23 residues processed: 174 average time/residue: 0.4707 time to fit residues: 90.3529 Evaluate side-chains 165 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 111 GLN F 111 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.089429 restraints weight = 17896.984| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.23 r_work: 0.2910 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13035 Z= 0.178 Angle : 0.570 10.089 17746 Z= 0.293 Chirality : 0.041 0.168 2050 Planarity : 0.004 0.038 2144 Dihedral : 5.806 54.311 2522 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.93 % Allowed : 17.56 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.22), residues: 1558 helix: 1.97 (0.20), residues: 696 sheet: 0.65 (0.31), residues: 272 loop : -0.97 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 45 TYR 0.012 0.002 TYR F 51 PHE 0.017 0.001 PHE D 79 TRP 0.011 0.001 TRP D 35 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (13024) covalent geometry : angle 0.56376 / 0.29 (17720) SS BOND : bond 0.00687 / 0.41 ( 7) SS BOND : angle 2.41063 / 1.37 ( 14) hydrogen bonds : bond 0.04910 / 3.18 ( 651) hydrogen bonds : angle 3.90963 / 2.67 ( 1893) link_BETA1-4 : bond 0.00688 / 0.34 ( 2) link_BETA1-4 : angle 1.90531 / 0.99 ( 6) link_NAG-ASN : bond 0.00383 / 0.19 ( 2) link_NAG-ASN : angle 2.59972 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.536 Fit side-chains REVERT: D 5 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: E 11 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7163 (t80) REVERT: F 5 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: B 43 CYS cc_start: 0.7225 (m) cc_final: 0.6824 (t) REVERT: B 45 ARG cc_start: 0.7412 (ttt-90) cc_final: 0.7001 (mtp-110) REVERT: B 71 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7243 (mtt) REVERT: B 120 ASN cc_start: 0.7818 (m-40) cc_final: 0.7400 (t0) REVERT: B 166 GLN cc_start: 0.8147 (tt0) cc_final: 0.7759 (mt0) REVERT: B 332 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5654 (mt) REVERT: B 374 CYS cc_start: 0.8639 (m) cc_final: 0.8325 (m) REVERT: B 489 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7910 (t80) REVERT: B 514 MET cc_start: 0.8871 (mtp) cc_final: 0.8607 (mtm) REVERT: B 587 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8208 (tp) REVERT: A 43 CYS cc_start: 0.7206 (m) cc_final: 0.6833 (t) REVERT: A 45 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6987 (mtp-110) REVERT: A 71 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7266 (mtt) REVERT: A 120 ASN cc_start: 0.7827 (m-40) cc_final: 0.7426 (t0) REVERT: A 166 GLN cc_start: 0.8122 (tt0) cc_final: 0.7744 (mt0) REVERT: A 173 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7401 (m) REVERT: A 332 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5669 (mt) REVERT: A 489 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7912 (t80) REVERT: A 514 MET cc_start: 0.8860 (mtp) cc_final: 0.8599 (mtm) REVERT: A 587 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8172 (tp) REVERT: C 11 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7178 (t80) outliers start: 53 outliers final: 30 residues processed: 163 average time/residue: 0.5029 time to fit residues: 90.4089 Evaluate side-chains 172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 111 GLN F 111 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** 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 = 0.3575 r_free = 0.3575 target = 0.124742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091616 restraints weight = 18205.561| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.32 r_work: 0.2932 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13035 Z= 0.134 Angle : 0.552 11.654 17746 Z= 0.281 Chirality : 0.040 0.149 2050 Planarity : 0.003 0.038 2144 Dihedral : 5.715 54.600 2522 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.70 % Allowed : 17.56 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.22), residues: 1558 helix: 2.13 (0.21), residues: 690 sheet: 0.73 (0.31), residues: 272 loop : -0.97 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 45 TYR 0.013 0.001 TYR F 100 PHE 0.016 0.001 PHE D 79 TRP 0.013 0.001 TRP F 35 HIS 0.002 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (13024) covalent geometry : angle 0.54823 / 0.28 (17720) SS BOND : bond 0.00421 / 0.20 ( 7) SS BOND : angle 1.36702 / 0.76 ( 14) hydrogen bonds : bond 0.04464 / 2.90 ( 651) hydrogen bonds : angle 3.85209 / 2.63 ( 1893) link_BETA1-4 : bond 0.00599 / 0.30 ( 2) link_BETA1-4 : angle 1.95448 / 1.01 ( 6) link_NAG-ASN : bond 0.00352 / 0.18 ( 2) link_NAG-ASN : angle 2.46091 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.503 Fit side-chains REVERT: D 5 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: E 11 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7174 (t80) REVERT: F 5 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: B 43 CYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6848 (t) REVERT: B 45 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.7045 (mtp-110) REVERT: B 71 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7196 (mtt) REVERT: B 120 ASN cc_start: 0.7771 (m-40) cc_final: 0.7383 (t0) REVERT: B 166 GLN cc_start: 0.8098 (tt0) cc_final: 0.7718 (mt0) REVERT: B 332 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5808 (mt) REVERT: B 374 CYS cc_start: 0.8528 (m) cc_final: 0.8228 (m) REVERT: B 489 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7916 (t80) REVERT: B 514 MET cc_start: 0.8847 (mtp) cc_final: 0.8598 (mtm) REVERT: A 43 CYS cc_start: 0.7227 (m) cc_final: 0.6862 (t) REVERT: A 45 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.7044 (mtp-110) REVERT: A 71 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7208 (mtt) REVERT: A 120 ASN cc_start: 0.7791 (m-40) cc_final: 0.7397 (t0) REVERT: A 166 GLN cc_start: 0.8076 (tt0) cc_final: 0.7706 (mt0) REVERT: A 173 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7400 (m) REVERT: A 332 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5759 (mt) REVERT: A 489 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7928 (t80) REVERT: A 514 MET cc_start: 0.8851 (mtp) cc_final: 0.8596 (mtm) REVERT: C 11 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7193 (t80) outliers start: 50 outliers final: 33 residues processed: 156 average time/residue: 0.5191 time to fit residues: 89.2723 Evaluate side-chains 170 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 636 MET Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 0.0050 chunk 76 optimal weight: 0.0050 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 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 = 0.3570 r_free = 0.3570 target = 0.124481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.091477 restraints weight = 18249.912| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.20 r_work: 0.2926 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13035 Z= 0.136 Angle : 0.544 10.913 17746 Z= 0.278 Chirality : 0.040 0.145 2050 Planarity : 0.003 0.038 2144 Dihedral : 5.690 54.767 2522 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.85 % Allowed : 17.41 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.22), residues: 1558 helix: 2.14 (0.21), residues: 690 sheet: 0.77 (0.31), residues: 272 loop : -0.93 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 45 TYR 0.011 0.001 TYR D 51 PHE 0.017 0.001 PHE D 79 TRP 0.012 0.001 TRP D 35 HIS 0.002 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13024) covalent geometry : angle 0.53999 / 0.28 (17720) SS BOND : bond 0.00402 / 0.17 ( 7) SS BOND : angle 1.25553 / 0.69 ( 14) hydrogen bonds : bond 0.04464 / 2.90 ( 651) hydrogen bonds : angle 3.83558 / 2.62 ( 1893) link_BETA1-4 : bond 0.00530 / 0.27 ( 2) link_BETA1-4 : angle 1.94401 / 1.01 ( 6) link_NAG-ASN : bond 0.00362 / 0.18 ( 2) link_NAG-ASN : angle 2.45619 / 1.41 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.389 Fit side-chains REVERT: D 5 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: D 81 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8850 (tp) REVERT: E 11 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7215 (t80) REVERT: F 5 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: F 81 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8852 (tp) REVERT: B 43 CYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6895 (t) REVERT: B 45 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7066 (mtp-110) REVERT: B 71 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7211 (mtt) REVERT: B 120 ASN cc_start: 0.7789 (m-40) cc_final: 0.7384 (t0) REVERT: B 166 GLN cc_start: 0.8097 (tt0) cc_final: 0.7728 (mt0) REVERT: B 332 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5870 (mt) REVERT: B 374 CYS cc_start: 0.8481 (m) cc_final: 0.8195 (m) REVERT: B 489 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7955 (t80) REVERT: B 514 MET cc_start: 0.8868 (mtp) cc_final: 0.8619 (mtm) REVERT: B 587 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 43 CYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6914 (t) REVERT: A 45 ARG cc_start: 0.7431 (ttt-90) cc_final: 0.7070 (mtp-110) REVERT: A 71 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7234 (mtt) REVERT: A 120 ASN cc_start: 0.7771 (m-40) cc_final: 0.7374 (t0) REVERT: A 166 GLN cc_start: 0.8081 (tt0) cc_final: 0.7727 (mt0) REVERT: A 173 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7415 (m) REVERT: A 332 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5859 (mt) REVERT: A 489 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7962 (t80) REVERT: A 514 MET cc_start: 0.8876 (mtp) cc_final: 0.8629 (mtm) REVERT: C 11 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7225 (t80) outliers start: 52 outliers final: 32 residues processed: 155 average time/residue: 0.4905 time to fit residues: 83.9744 Evaluate side-chains 175 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 636 MET Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 113 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** 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 = 0.3576 r_free = 0.3576 target = 0.124258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.089433 restraints weight = 18228.716| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.29 r_work: 0.2909 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13035 Z= 0.162 Angle : 0.573 11.358 17746 Z= 0.291 Chirality : 0.041 0.149 2050 Planarity : 0.004 0.038 2144 Dihedral : 5.795 54.738 2522 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.15 % Allowed : 17.19 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.22), residues: 1558 helix: 2.07 (0.20), residues: 690 sheet: 0.76 (0.31), residues: 272 loop : -0.94 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 45 TYR 0.014 0.002 TYR F 100 PHE 0.017 0.001 PHE F 79 TRP 0.011 0.001 TRP D 35 HIS 0.002 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (13024) covalent geometry : angle 0.56915 / 0.29 (17720) SS BOND : bond 0.00511 / 0.23 ( 7) SS BOND : angle 1.35171 / 0.73 ( 14) hydrogen bonds : bond 0.04797 / 3.12 ( 651) hydrogen bonds : angle 3.89362 / 2.66 ( 1893) link_BETA1-4 : bond 0.00570 / 0.29 ( 2) link_BETA1-4 : angle 1.86851 / 0.97 ( 6) link_NAG-ASN : bond 0.00375 / 0.19 ( 2) link_NAG-ASN : angle 2.55435 / 1.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.50 seconds wall clock time: 71 minutes 18.61 seconds (4278.61 seconds total)