Starting phenix.real_space_refine on Wed Jul 30 19:17:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7b_18210/07_2025/8q7b_18210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7b_18210/07_2025/8q7b_18210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7b_18210/07_2025/8q7b_18210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7b_18210/07_2025/8q7b_18210.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7b_18210/07_2025/8q7b_18210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7b_18210/07_2025/8q7b_18210.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 8306 2.51 5 N 2042 2.21 5 O 2354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12770 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: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'BWQ': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'BWQ': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.66, per 1000 atoms: 0.68 Number of scatterers: 12770 At special positions: 0 Unit cell: (99.66, 96.36, 145.2, 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 2354 8.00 N 2042 7.00 C 8306 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=2.05 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 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 18 sheets defined 46.3% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.535A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.877A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) 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: 3.578A 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 187 through 198 removed outlier: 3.668A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.982A pdb=" N THR B 202 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.622A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) 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 removed outlier: 3.623A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.586A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 Processing helix chain 'B' and resid 392 through 413 removed outlier: 4.630A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.644A 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 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.838A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (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: 3.533A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.993A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.915A 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: 4.210A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.424A 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: 4.005A 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: 5.168A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.858A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.744A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.560A 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 187 through 198 removed outlier: 3.701A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.993A pdb=" N THR A 202 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.630A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) 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 removed outlier: 3.597A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.645A pdb=" N LEU A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.661A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.690A 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 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.853A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (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: 3.514A pdb=" N MET A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.965A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.881A 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: 4.179A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.429A 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: 4.017A 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: 5.181A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.535A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.359A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.359A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.541A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.332A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.332A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.372A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.372A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.681A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.408A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.714A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.422A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.541A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2001 1.32 - 1.45: 3607 1.45 - 1.57: 7320 1.57 - 1.70: 0 1.70 - 1.83: 106 Bond restraints: 13034 Sorted by residual: bond pdb=" C VAL A 638 " pdb=" O VAL A 638 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.35e+01 bond pdb=" C SER A 467 " pdb=" O SER A 467 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.15e-02 7.56e+03 9.43e+00 bond pdb=" C05 BWQ A1301 " pdb=" N38 BWQ A1301 " ideal model delta sigma weight residual 1.479 1.418 0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" C05 BWQ B 706 " pdb=" N38 BWQ B 706 " ideal model delta sigma weight residual 1.479 1.421 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" C12 BWQ B 706 " pdb=" O11 BWQ B 706 " ideal model delta sigma weight residual 1.416 1.358 0.058 2.00e-02 2.50e+03 8.42e+00 ... (remaining 13029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16990 1.99 - 3.98: 575 3.98 - 5.96: 127 5.96 - 7.95: 33 7.95 - 9.94: 9 Bond angle restraints: 17734 Sorted by residual: angle pdb=" C CYS A 603 " pdb=" N ASN A 604 " pdb=" CA ASN A 604 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C CYS B 603 " pdb=" N ASN B 604 " pdb=" CA ASN B 604 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" N ASP F 32 " pdb=" CA ASP F 32 " pdb=" C ASP F 32 " ideal model delta sigma weight residual 110.80 118.99 -8.19 2.13e+00 2.20e-01 1.48e+01 angle pdb=" N ASP D 32 " pdb=" CA ASP D 32 " pdb=" C ASP D 32 " ideal model delta sigma weight residual 110.80 118.44 -7.64 2.13e+00 2.20e-01 1.29e+01 angle pdb=" N ASN A 604 " pdb=" CA ASN A 604 " pdb=" C ASN A 604 " ideal model delta sigma weight residual 110.80 118.43 -7.63 2.13e+00 2.20e-01 1.28e+01 ... (remaining 17729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.45: 7986 29.45 - 58.90: 215 58.90 - 88.35: 20 88.35 - 117.80: 4 117.80 - 147.24: 4 Dihedral angle restraints: 8229 sinusoidal: 3693 harmonic: 4536 Sorted by residual: 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 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 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 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CB CYS B 603 " pdb=" SG CYS B 603 " pdb=" SG CYS A 603 " pdb=" CB CYS A 603 " ideal model delta sinusoidal sigma weight residual 93.00 53.22 39.78 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 8226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1740 0.072 - 0.144: 266 0.144 - 0.215: 22 0.215 - 0.287: 16 0.287 - 0.359: 8 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C13 CLR B 705 " pdb=" C12 CLR B 705 " pdb=" C14 CLR B 705 " pdb=" C17 CLR B 705 " both_signs ideal model delta sigma weight residual False -2.93 -2.57 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C13 CLR A1306 " pdb=" C12 CLR A1306 " pdb=" C14 CLR A1306 " pdb=" C17 CLR A1306 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C13 CLR B 701 " pdb=" C12 CLR B 701 " pdb=" C14 CLR B 701 " pdb=" C17 CLR B 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2049 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 330 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLU A 330 " -0.064 2.00e-02 2.50e+03 pdb=" O GLU A 330 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS A 331 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 330 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C GLU B 330 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU B 330 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS B 331 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 641 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU B 641 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU B 641 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 642 " 0.021 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 524 2.71 - 3.26: 12414 3.26 - 3.81: 20306 3.81 - 4.35: 27456 4.35 - 4.90: 45597 Nonbonded interactions: 106297 Sorted by model distance: nonbonded pdb=" O LEU B 168 " pdb=" NH2 ARG B 193 " model vdw 2.165 3.120 nonbonded pdb=" O TYR A 336 " pdb=" OG SER A 339 " model vdw 2.174 3.040 nonbonded pdb=" O TYR B 336 " pdb=" OG SER B 339 " model vdw 2.179 3.040 nonbonded pdb=" O LEU A 168 " pdb=" NH2 ARG A 193 " model vdw 2.187 3.120 nonbonded pdb=" O ALA A 529 " pdb=" NZ LYS A 647 " model vdw 2.189 3.120 ... (remaining 106292 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 654 or resid 1302 through 1305)) selection = (chain 'B' and (resid 35 through 654 or resid 702 through 705)) } 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: 7.750 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 32.690 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.007 0.061 13045 Z= 0.322 Angle : 0.958 13.129 17760 Z= 0.465 Chirality : 0.059 0.359 2052 Planarity : 0.005 0.044 2144 Dihedral : 13.885 147.244 5312 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 1.48 % Allowed : 6.89 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.18), residues: 1558 helix: -1.00 (0.18), residues: 652 sheet: -1.23 (0.28), residues: 288 loop : -2.31 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 35 HIS 0.005 0.002 HIS A 583 PHE 0.024 0.003 PHE D 54 TYR 0.023 0.003 TYR A 369 ARG 0.004 0.001 ARG A 575 Details of bonding type rmsd link_NAG-ASN : bond 0.01256 ( 2) link_NAG-ASN : angle 10.70547 ( 6) link_BETA1-4 : bond 0.00203 ( 2) link_BETA1-4 : angle 4.11970 ( 6) hydrogen bonds : bond 0.15786 ( 628) hydrogen bonds : angle 6.34841 ( 1908) SS BOND : bond 0.00895 ( 7) SS BOND : angle 1.55870 ( 14) covalent geometry : bond 0.00723 (13034) covalent geometry : angle 0.93442 (17734) *********************** 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 251 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 1.548 Fit side-chains REVERT: F 3 GLN cc_start: 0.7373 (tp-100) cc_final: 0.7080 (tm-30) REVERT: F 6 GLU cc_start: 0.8027 (mp0) cc_final: 0.7767 (mp0) REVERT: B 138 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6907 (mt-10) REVERT: B 152 MET cc_start: 0.7672 (mtp) cc_final: 0.7435 (mtm) REVERT: B 158 ASN cc_start: 0.7360 (m-40) cc_final: 0.7023 (m-40) REVERT: B 198 MET cc_start: 0.8398 (mtp) cc_final: 0.8162 (mtp) REVERT: B 236 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6688 (ttm110) REVERT: B 243 HIS cc_start: 0.7518 (t70) cc_final: 0.6817 (t70) REVERT: B 244 GLN cc_start: 0.7951 (pt0) cc_final: 0.7546 (pt0) REVERT: B 489 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.7929 (t80) REVERT: B 515 MET cc_start: 0.8500 (mmm) cc_final: 0.8251 (mmm) REVERT: A 152 MET cc_start: 0.7538 (mtp) cc_final: 0.7196 (mtm) REVERT: A 158 ASN cc_start: 0.7285 (m-40) cc_final: 0.7032 (m-40) REVERT: A 198 MET cc_start: 0.8403 (mtp) cc_final: 0.8143 (mtp) REVERT: A 214 THR cc_start: 0.8048 (m) cc_final: 0.7677 (m) REVERT: A 243 HIS cc_start: 0.7410 (t70) cc_final: 0.6757 (t70) REVERT: A 244 GLN cc_start: 0.7917 (pt0) cc_final: 0.7612 (pt0) REVERT: A 489 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.7945 (t80) outliers start: 20 outliers final: 9 residues processed: 249 average time/residue: 1.3250 time to fit residues: 358.3817 Evaluate side-chains 168 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 GLN D 16 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 77 ASN E 6 GLN E 79 GLN F 3 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 77 ASN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 109 ASN B 418 ASN B 425 ASN B 457 HIS B 531 GLN B 582 GLN B 583 HIS B 589 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 418 ASN A 425 ASN A 457 HIS A 531 GLN A 583 HIS A 589 GLN C 6 GLN C 79 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102882 restraints weight = 15945.230| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.88 r_work: 0.3087 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13045 Z= 0.138 Angle : 0.652 8.315 17760 Z= 0.320 Chirality : 0.043 0.176 2052 Planarity : 0.004 0.049 2144 Dihedral : 11.277 135.335 2549 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.33 % Allowed : 12.22 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1558 helix: 0.76 (0.20), residues: 670 sheet: -0.73 (0.30), residues: 278 loop : -1.72 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35 HIS 0.003 0.001 HIS B 630 PHE 0.019 0.002 PHE F 79 TYR 0.013 0.002 TYR B 336 ARG 0.006 0.000 ARG B 163 Details of bonding type rmsd link_NAG-ASN : bond 0.01155 ( 2) link_NAG-ASN : angle 6.81084 ( 6) link_BETA1-4 : bond 0.00227 ( 2) link_BETA1-4 : angle 2.51197 ( 6) hydrogen bonds : bond 0.04387 ( 628) hydrogen bonds : angle 4.59123 ( 1908) SS BOND : bond 0.00471 ( 7) SS BOND : angle 0.82004 ( 14) covalent geometry : bond 0.00307 (13034) covalent geometry : angle 0.63869 (17734) *********************** 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 218 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.415 Fit side-chains REVERT: F 3 GLN cc_start: 0.7935 (tp40) cc_final: 0.7500 (mm-40) REVERT: B 71 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6813 (mtp) REVERT: B 152 MET cc_start: 0.7557 (mtp) cc_final: 0.7305 (mtm) REVERT: B 158 ASN cc_start: 0.7329 (m-40) cc_final: 0.7018 (m-40) REVERT: B 198 MET cc_start: 0.8467 (mtp) cc_final: 0.8235 (mtp) REVERT: B 243 HIS cc_start: 0.7657 (t70) cc_final: 0.6789 (t70) REVERT: B 244 GLN cc_start: 0.8106 (pt0) cc_final: 0.7647 (pt0) REVERT: B 398 GLN cc_start: 0.7998 (mm110) cc_final: 0.7785 (mm110) REVERT: B 479 LEU cc_start: 0.8384 (tp) cc_final: 0.8067 (mp) REVERT: B 489 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 515 MET cc_start: 0.9188 (mmm) cc_final: 0.8803 (mmm) REVERT: A 152 MET cc_start: 0.7454 (mtp) cc_final: 0.7088 (mtm) REVERT: A 158 ASN cc_start: 0.7253 (m-40) cc_final: 0.7052 (m-40) REVERT: A 236 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7355 (ttm110) REVERT: A 243 HIS cc_start: 0.7485 (t70) cc_final: 0.6742 (t70) REVERT: A 244 GLN cc_start: 0.7946 (pt0) cc_final: 0.7522 (pt0) REVERT: A 393 GLN cc_start: 0.7284 (mp10) cc_final: 0.6780 (mm-40) REVERT: A 477 ASP cc_start: 0.8094 (m-30) cc_final: 0.7876 (m-30) REVERT: A 489 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8106 (t80) REVERT: C 15 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7290 (mp) outliers start: 45 outliers final: 11 residues processed: 203 average time/residue: 1.2080 time to fit residues: 269.2453 Evaluate side-chains 161 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 109 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099854 restraints weight = 16032.600| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.86 r_work: 0.3042 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13045 Z= 0.249 Angle : 0.748 8.408 17760 Z= 0.373 Chirality : 0.048 0.218 2052 Planarity : 0.005 0.052 2144 Dihedral : 10.886 130.139 2534 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.67 % Allowed : 13.78 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1558 helix: 0.97 (0.20), residues: 674 sheet: -0.64 (0.30), residues: 278 loop : -1.63 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 35 HIS 0.004 0.002 HIS B 630 PHE 0.023 0.002 PHE D 79 TYR 0.018 0.003 TYR B 605 ARG 0.010 0.001 ARG A 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 2) link_NAG-ASN : angle 3.92261 ( 6) link_BETA1-4 : bond 0.00090 ( 2) link_BETA1-4 : angle 2.99489 ( 6) hydrogen bonds : bond 0.05274 ( 628) hydrogen bonds : angle 4.72075 ( 1908) SS BOND : bond 0.00872 ( 7) SS BOND : angle 1.58657 ( 14) covalent geometry : bond 0.00592 (13034) covalent geometry : angle 0.74164 (17734) *********************** 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 217 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.354 Fit side-chains REVERT: D 3 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7683 (mm-40) REVERT: D 111 GLN cc_start: 0.7940 (pm20) cc_final: 0.7703 (pm20) REVERT: F 3 GLN cc_start: 0.8001 (tp40) cc_final: 0.7551 (mm-40) REVERT: B 152 MET cc_start: 0.7574 (mtp) cc_final: 0.7260 (mtm) REVERT: B 158 ASN cc_start: 0.7261 (m-40) cc_final: 0.7045 (m-40) REVERT: B 243 HIS cc_start: 0.7689 (t70) cc_final: 0.6840 (t70) REVERT: B 244 GLN cc_start: 0.8067 (pt0) cc_final: 0.7587 (pt0) REVERT: B 272 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 479 LEU cc_start: 0.8404 (tp) cc_final: 0.8085 (mt) REVERT: B 489 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 72 LYS cc_start: 0.8107 (mptp) cc_final: 0.7721 (mppt) REVERT: A 152 MET cc_start: 0.7417 (mtp) cc_final: 0.7072 (mtm) REVERT: A 243 HIS cc_start: 0.7539 (t70) cc_final: 0.7021 (t70) REVERT: A 393 GLN cc_start: 0.7337 (mp10) cc_final: 0.7041 (mp10) REVERT: A 489 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8103 (t80) REVERT: A 540 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8147 (mm) REVERT: C 15 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7261 (mp) outliers start: 63 outliers final: 33 residues processed: 197 average time/residue: 1.1589 time to fit residues: 252.7636 Evaluate side-chains 183 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 65 THR 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 77 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 153 optimal weight: 0.4980 chunk 54 optimal weight: 0.0670 chunk 141 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 chunk 85 optimal weight: 0.7980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105172 restraints weight = 15915.881| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.85 r_work: 0.3118 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13045 Z= 0.099 Angle : 0.552 7.736 17760 Z= 0.275 Chirality : 0.040 0.182 2052 Planarity : 0.004 0.049 2144 Dihedral : 10.126 128.046 2530 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.04 % Allowed : 15.41 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1558 helix: 1.64 (0.20), residues: 672 sheet: -0.33 (0.32), residues: 258 loop : -1.30 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 35 HIS 0.003 0.001 HIS A 40 PHE 0.015 0.001 PHE F 79 TYR 0.011 0.001 TYR F 95 ARG 0.007 0.000 ARG A 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 2) link_NAG-ASN : angle 2.99496 ( 6) link_BETA1-4 : bond 0.00228 ( 2) link_BETA1-4 : angle 2.55787 ( 6) hydrogen bonds : bond 0.03518 ( 628) hydrogen bonds : angle 4.21251 ( 1908) SS BOND : bond 0.00341 ( 7) SS BOND : angle 0.67584 ( 14) covalent geometry : bond 0.00207 (13034) covalent geometry : angle 0.54730 (17734) *********************** 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 199 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.369 Fit side-chains REVERT: D 111 GLN cc_start: 0.7903 (pm20) cc_final: 0.7682 (pm20) REVERT: F 3 GLN cc_start: 0.7894 (tp40) cc_final: 0.7478 (mm-40) REVERT: B 89 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8082 (tm) REVERT: B 152 MET cc_start: 0.7549 (mtp) cc_final: 0.7153 (mtm) REVERT: B 158 ASN cc_start: 0.7255 (m-40) cc_final: 0.7026 (m-40) REVERT: B 243 HIS cc_start: 0.7656 (t70) cc_final: 0.6846 (t70) REVERT: B 244 GLN cc_start: 0.7979 (pt0) cc_final: 0.7512 (pt0) REVERT: B 272 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 296 ASP cc_start: 0.6489 (m-30) cc_final: 0.6243 (m-30) REVERT: B 479 LEU cc_start: 0.8274 (tp) cc_final: 0.7979 (mp) REVERT: B 489 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 72 LYS cc_start: 0.7997 (mptp) cc_final: 0.7646 (mppt) REVERT: A 152 MET cc_start: 0.7373 (mtp) cc_final: 0.7080 (mtm) REVERT: A 153 THR cc_start: 0.6786 (m) cc_final: 0.6279 (p) REVERT: A 154 ASN cc_start: 0.6539 (OUTLIER) cc_final: 0.5839 (t0) REVERT: A 160 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6974 (tpt-90) REVERT: A 243 HIS cc_start: 0.7549 (t70) cc_final: 0.7123 (t70) REVERT: A 393 GLN cc_start: 0.7354 (mp10) cc_final: 0.7036 (mp10) REVERT: A 489 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8127 (t80) REVERT: C 24 LYS cc_start: 0.8474 (tttt) cc_final: 0.8271 (tttp) REVERT: C 70 ASP cc_start: 0.8200 (m-30) cc_final: 0.7908 (m-30) outliers start: 41 outliers final: 14 residues processed: 188 average time/residue: 1.2088 time to fit residues: 248.8884 Evaluate side-chains 168 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 139 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101815 restraints weight = 16016.221| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.90 r_work: 0.3065 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13045 Z= 0.147 Angle : 0.613 7.569 17760 Z= 0.305 Chirality : 0.042 0.186 2052 Planarity : 0.004 0.041 2144 Dihedral : 10.047 124.143 2530 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.70 % Allowed : 15.04 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1558 helix: 1.71 (0.20), residues: 674 sheet: -0.28 (0.31), residues: 278 loop : -1.38 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 35 HIS 0.004 0.001 HIS B 243 PHE 0.019 0.002 PHE F 79 TYR 0.013 0.002 TYR B 336 ARG 0.006 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 2) link_NAG-ASN : angle 3.06670 ( 6) link_BETA1-4 : bond 0.00164 ( 2) link_BETA1-4 : angle 2.54325 ( 6) hydrogen bonds : bond 0.04141 ( 628) hydrogen bonds : angle 4.29957 ( 1908) SS BOND : bond 0.00673 ( 7) SS BOND : angle 1.21538 ( 14) covalent geometry : bond 0.00339 (13034) covalent geometry : angle 0.60812 (17734) *********************** 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 204 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 1.462 Fit side-chains REVERT: D 111 GLN cc_start: 0.7987 (pm20) cc_final: 0.7760 (pm20) REVERT: F 3 GLN cc_start: 0.7948 (tp40) cc_final: 0.7492 (mm-40) REVERT: B 152 MET cc_start: 0.7577 (mtp) cc_final: 0.7153 (mtm) REVERT: B 158 ASN cc_start: 0.7340 (m-40) cc_final: 0.7090 (m-40) REVERT: B 243 HIS cc_start: 0.7563 (t70) cc_final: 0.6817 (t70) REVERT: B 244 GLN cc_start: 0.7999 (pt0) cc_final: 0.7578 (pt0) REVERT: B 272 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: B 479 LEU cc_start: 0.8361 (tp) cc_final: 0.8064 (mp) REVERT: B 489 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8139 (t80) REVERT: A 72 LYS cc_start: 0.8065 (mptp) cc_final: 0.7707 (mppt) REVERT: A 152 MET cc_start: 0.7379 (mtp) cc_final: 0.7068 (mtm) REVERT: A 154 ASN cc_start: 0.6489 (OUTLIER) cc_final: 0.5843 (t0) REVERT: A 243 HIS cc_start: 0.7557 (t70) cc_final: 0.7185 (t70) REVERT: A 393 GLN cc_start: 0.7346 (mp10) cc_final: 0.7023 (mp10) REVERT: A 489 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8177 (t80) REVERT: A 504 ASP cc_start: 0.8428 (p0) cc_final: 0.8110 (p0) REVERT: A 540 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8189 (mm) REVERT: C 15 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7305 (mp) REVERT: C 24 LYS cc_start: 0.8509 (tttt) cc_final: 0.8292 (tptp) outliers start: 50 outliers final: 30 residues processed: 187 average time/residue: 1.3234 time to fit residues: 274.3325 Evaluate side-chains 184 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 65 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 33 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099329 restraints weight = 16205.003| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.85 r_work: 0.3021 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13045 Z= 0.280 Angle : 0.764 9.009 17760 Z= 0.382 Chirality : 0.049 0.234 2052 Planarity : 0.005 0.041 2144 Dihedral : 10.565 124.999 2530 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.44 % Allowed : 15.41 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1558 helix: 1.34 (0.20), residues: 674 sheet: -0.46 (0.30), residues: 278 loop : -1.58 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 35 HIS 0.006 0.002 HIS B 243 PHE 0.023 0.003 PHE F 79 TYR 0.017 0.003 TYR B 336 ARG 0.007 0.001 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 2) link_NAG-ASN : angle 3.97621 ( 6) link_BETA1-4 : bond 0.00180 ( 2) link_BETA1-4 : angle 2.64022 ( 6) hydrogen bonds : bond 0.05321 ( 628) hydrogen bonds : angle 4.64490 ( 1908) SS BOND : bond 0.01019 ( 7) SS BOND : angle 1.72471 ( 14) covalent geometry : bond 0.00670 (13034) covalent geometry : angle 0.75830 (17734) *********************** 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 210 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 1.533 Fit side-chains REVERT: D 111 GLN cc_start: 0.8042 (pm20) cc_final: 0.7800 (pm20) REVERT: E 47 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8512 (tp) REVERT: F 3 GLN cc_start: 0.8012 (tp40) cc_final: 0.7524 (mm-40) REVERT: B 152 MET cc_start: 0.7587 (mtp) cc_final: 0.7186 (mtm) REVERT: B 243 HIS cc_start: 0.7598 (t70) cc_final: 0.6875 (t70) REVERT: B 244 GLN cc_start: 0.8023 (pt0) cc_final: 0.7593 (pt0) REVERT: B 272 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 479 LEU cc_start: 0.8454 (tp) cc_final: 0.8141 (mt) REVERT: B 489 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8102 (t80) REVERT: A 72 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7804 (mppt) REVERT: A 152 MET cc_start: 0.7476 (mtp) cc_final: 0.7096 (mtm) REVERT: A 154 ASN cc_start: 0.6507 (OUTLIER) cc_final: 0.5878 (t0) REVERT: A 243 HIS cc_start: 0.7537 (t70) cc_final: 0.7223 (t70) REVERT: A 393 GLN cc_start: 0.7352 (mp10) cc_final: 0.7035 (mp10) REVERT: A 479 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 489 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8095 (t80) REVERT: A 540 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8226 (mm) REVERT: C 11 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6270 (t80) REVERT: C 15 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7229 (mp) REVERT: C 24 LYS cc_start: 0.8555 (tttt) cc_final: 0.8313 (tttp) REVERT: C 103 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7961 (mtpp) outliers start: 60 outliers final: 34 residues processed: 191 average time/residue: 1.1526 time to fit residues: 244.5674 Evaluate side-chains 188 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 144 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100580 restraints weight = 15990.054| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.86 r_work: 0.3045 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13045 Z= 0.184 Angle : 0.660 7.737 17760 Z= 0.331 Chirality : 0.044 0.186 2052 Planarity : 0.004 0.042 2144 Dihedral : 10.196 121.265 2530 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.93 % Allowed : 16.74 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1558 helix: 1.50 (0.20), residues: 676 sheet: -0.38 (0.31), residues: 278 loop : -1.49 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 35 HIS 0.004 0.001 HIS B 243 PHE 0.021 0.002 PHE D 79 TYR 0.013 0.002 TYR A 336 ARG 0.008 0.001 ARG F 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 3.41158 ( 6) link_BETA1-4 : bond 0.00116 ( 2) link_BETA1-4 : angle 2.47528 ( 6) hydrogen bonds : bond 0.04535 ( 628) hydrogen bonds : angle 4.47638 ( 1908) SS BOND : bond 0.00766 ( 7) SS BOND : angle 1.37874 ( 14) covalent geometry : bond 0.00433 (13034) covalent geometry : angle 0.65520 (17734) *********************** 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 204 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.616 Fit side-chains REVERT: D 3 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7655 (mm-40) REVERT: D 111 GLN cc_start: 0.7990 (pm20) cc_final: 0.7754 (pm20) REVERT: F 3 GLN cc_start: 0.7978 (tp40) cc_final: 0.7507 (mm-40) REVERT: B 152 MET cc_start: 0.7560 (mtp) cc_final: 0.7174 (mtm) REVERT: B 243 HIS cc_start: 0.7593 (t70) cc_final: 0.6905 (t70) REVERT: B 244 GLN cc_start: 0.7961 (pt0) cc_final: 0.7557 (pt0) REVERT: B 272 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: B 479 LEU cc_start: 0.8401 (tp) cc_final: 0.8061 (mt) REVERT: B 489 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8061 (t80) REVERT: A 72 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7752 (mppt) REVERT: A 152 MET cc_start: 0.7429 (mtp) cc_final: 0.7037 (mtm) REVERT: A 154 ASN cc_start: 0.6421 (OUTLIER) cc_final: 0.5807 (t0) REVERT: A 243 HIS cc_start: 0.7528 (t70) cc_final: 0.7221 (t70) REVERT: A 393 GLN cc_start: 0.7355 (mp10) cc_final: 0.7011 (mp10) REVERT: A 489 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8087 (t80) REVERT: C 11 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6276 (t80) REVERT: C 15 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7253 (mp) REVERT: C 103 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7938 (mtpp) outliers start: 53 outliers final: 32 residues processed: 187 average time/residue: 1.3181 time to fit residues: 271.4412 Evaluate side-chains 189 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 65 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101131 restraints weight = 16022.268| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.87 r_work: 0.3053 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13045 Z= 0.162 Angle : 0.638 7.888 17760 Z= 0.320 Chirality : 0.043 0.176 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.930 115.268 2530 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.56 % Allowed : 17.19 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1558 helix: 1.66 (0.20), residues: 674 sheet: -0.28 (0.31), residues: 276 loop : -1.45 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 35 HIS 0.004 0.001 HIS B 243 PHE 0.020 0.002 PHE F 79 TYR 0.012 0.002 TYR A 336 ARG 0.010 0.001 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 2) link_NAG-ASN : angle 3.21919 ( 6) link_BETA1-4 : bond 0.00262 ( 2) link_BETA1-4 : angle 2.41310 ( 6) hydrogen bonds : bond 0.04311 ( 628) hydrogen bonds : angle 4.39370 ( 1908) SS BOND : bond 0.00718 ( 7) SS BOND : angle 1.27002 ( 14) covalent geometry : bond 0.00378 (13034) covalent geometry : angle 0.63321 (17734) *********************** 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 198 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 2.872 Fit side-chains REVERT: D 111 GLN cc_start: 0.7987 (pm20) cc_final: 0.7762 (pm20) REVERT: E 94 THR cc_start: 0.7362 (t) cc_final: 0.6908 (p) REVERT: F 3 GLN cc_start: 0.7971 (tp40) cc_final: 0.7491 (mm-40) REVERT: B 152 MET cc_start: 0.7597 (mtp) cc_final: 0.7188 (mtm) REVERT: B 243 HIS cc_start: 0.7502 (t70) cc_final: 0.6916 (t-90) REVERT: B 244 GLN cc_start: 0.7928 (pt0) cc_final: 0.7663 (pt0) REVERT: B 272 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: B 479 LEU cc_start: 0.8400 (tp) cc_final: 0.8095 (mp) REVERT: B 489 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8086 (t80) REVERT: A 72 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (mppt) REVERT: A 152 MET cc_start: 0.7463 (mtp) cc_final: 0.7060 (mtm) REVERT: A 154 ASN cc_start: 0.6494 (OUTLIER) cc_final: 0.5874 (t0) REVERT: A 243 HIS cc_start: 0.7502 (t70) cc_final: 0.7215 (t70) REVERT: A 393 GLN cc_start: 0.7356 (mp10) cc_final: 0.7014 (mp10) REVERT: A 489 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8120 (t80) REVERT: A 540 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 11 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6450 (t80) REVERT: C 15 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7247 (mp) REVERT: C 103 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7917 (mtpp) outliers start: 48 outliers final: 31 residues processed: 182 average time/residue: 1.3518 time to fit residues: 276.3227 Evaluate side-chains 187 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 65 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103569 restraints weight = 15989.222| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.87 r_work: 0.3101 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13045 Z= 0.110 Angle : 0.571 8.332 17760 Z= 0.286 Chirality : 0.041 0.196 2052 Planarity : 0.004 0.045 2144 Dihedral : 9.367 103.587 2530 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.37 % Allowed : 18.59 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1558 helix: 1.94 (0.20), residues: 674 sheet: -0.10 (0.32), residues: 268 loop : -1.25 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.018 0.001 PHE F 79 TYR 0.010 0.001 TYR F 51 ARG 0.007 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 2) link_NAG-ASN : angle 2.79311 ( 6) link_BETA1-4 : bond 0.00168 ( 2) link_BETA1-4 : angle 2.32534 ( 6) hydrogen bonds : bond 0.03620 ( 628) hydrogen bonds : angle 4.18034 ( 1908) SS BOND : bond 0.00463 ( 7) SS BOND : angle 0.86244 ( 14) covalent geometry : bond 0.00245 (13034) covalent geometry : angle 0.56737 (17734) *********************** 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 188 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 2.347 Fit side-chains REVERT: D 111 GLN cc_start: 0.7935 (pm20) cc_final: 0.7728 (pm20) REVERT: E 94 THR cc_start: 0.7324 (t) cc_final: 0.6849 (p) REVERT: F 3 GLN cc_start: 0.7905 (tp40) cc_final: 0.7431 (mm-40) REVERT: B 152 MET cc_start: 0.7578 (mtp) cc_final: 0.7134 (mtm) REVERT: B 243 HIS cc_start: 0.7372 (t70) cc_final: 0.7068 (t-90) REVERT: B 272 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 296 ASP cc_start: 0.6475 (m-30) cc_final: 0.6258 (m-30) REVERT: B 479 LEU cc_start: 0.8319 (tp) cc_final: 0.8053 (mp) REVERT: B 489 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8106 (t80) REVERT: A 72 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7685 (mppt) REVERT: A 125 VAL cc_start: 0.8745 (t) cc_final: 0.8535 (m) REVERT: A 152 MET cc_start: 0.7452 (mtp) cc_final: 0.7063 (mtm) REVERT: A 154 ASN cc_start: 0.6497 (OUTLIER) cc_final: 0.5838 (t0) REVERT: A 243 HIS cc_start: 0.7491 (t70) cc_final: 0.7196 (t70) REVERT: A 393 GLN cc_start: 0.7350 (mp10) cc_final: 0.7031 (mp10) REVERT: A 489 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8120 (t80) REVERT: A 598 THR cc_start: 0.7411 (m) cc_final: 0.7021 (p) REVERT: C 24 LYS cc_start: 0.8438 (tttp) cc_final: 0.8175 (tptp) REVERT: C 70 ASP cc_start: 0.8129 (m-30) cc_final: 0.7849 (m-30) REVERT: C 103 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7862 (mtpp) outliers start: 32 outliers final: 22 residues processed: 178 average time/residue: 1.1346 time to fit residues: 223.9969 Evaluate side-chains 177 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 29 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 600 ASN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100051 restraints weight = 15955.658| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.86 r_work: 0.3035 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13045 Z= 0.230 Angle : 0.707 9.076 17760 Z= 0.355 Chirality : 0.046 0.211 2052 Planarity : 0.005 0.043 2144 Dihedral : 9.737 96.714 2530 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.59 % Allowed : 18.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1558 helix: 1.59 (0.20), residues: 674 sheet: -0.20 (0.31), residues: 276 loop : -1.43 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.005 0.001 HIS B 243 PHE 0.022 0.002 PHE F 79 TYR 0.015 0.002 TYR B 336 ARG 0.008 0.001 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 3.53805 ( 6) link_BETA1-4 : bond 0.00095 ( 2) link_BETA1-4 : angle 2.41418 ( 6) hydrogen bonds : bond 0.04874 ( 628) hydrogen bonds : angle 4.48335 ( 1908) SS BOND : bond 0.00917 ( 7) SS BOND : angle 1.53269 ( 14) covalent geometry : bond 0.00548 (13034) covalent geometry : angle 0.70215 (17734) ********************** 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 181 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.523 Fit side-chains REVERT: F 3 GLN cc_start: 0.7968 (tp40) cc_final: 0.7486 (mm-40) REVERT: B 152 MET cc_start: 0.7601 (mtp) cc_final: 0.7176 (mtm) REVERT: B 243 HIS cc_start: 0.7542 (t70) cc_final: 0.7002 (t-90) REVERT: B 244 GLN cc_start: 0.7949 (pt0) cc_final: 0.7662 (pt0) REVERT: B 272 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 489 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 72 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7776 (mppt) REVERT: A 152 MET cc_start: 0.7450 (mtp) cc_final: 0.7032 (mtm) REVERT: A 154 ASN cc_start: 0.6430 (OUTLIER) cc_final: 0.5803 (t0) REVERT: A 231 MET cc_start: 0.8102 (mtm) cc_final: 0.7746 (mtm) REVERT: A 243 HIS cc_start: 0.7506 (t70) cc_final: 0.7239 (t70) REVERT: A 393 GLN cc_start: 0.7352 (mp10) cc_final: 0.7025 (mp10) REVERT: A 489 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8095 (t80) REVERT: C 15 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7257 (mp) REVERT: C 103 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7996 (mtpp) outliers start: 35 outliers final: 25 residues processed: 170 average time/residue: 1.0628 time to fit residues: 200.7425 Evaluate side-chains 175 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 9 optimal weight: 0.9980 chunk 118 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103175 restraints weight = 15962.110| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.88 r_work: 0.3092 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13045 Z= 0.120 Angle : 0.593 8.524 17760 Z= 0.298 Chirality : 0.041 0.173 2052 Planarity : 0.004 0.044 2144 Dihedral : 9.249 87.853 2530 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.30 % Allowed : 18.81 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1558 helix: 1.83 (0.20), residues: 674 sheet: 0.02 (0.33), residues: 256 loop : -1.26 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.020 0.001 PHE F 79 TYR 0.011 0.001 TYR A 336 ARG 0.007 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 2) link_NAG-ASN : angle 2.88249 ( 6) link_BETA1-4 : bond 0.00165 ( 2) link_BETA1-4 : angle 2.28938 ( 6) hydrogen bonds : bond 0.03834 ( 628) hydrogen bonds : angle 4.24898 ( 1908) SS BOND : bond 0.00538 ( 7) SS BOND : angle 0.93439 ( 14) covalent geometry : bond 0.00269 (13034) covalent geometry : angle 0.58853 (17734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12430.23 seconds wall clock time: 221 minutes 57.69 seconds (13317.69 seconds total)