Starting phenix.real_space_refine on Sat Aug 23 14:28:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7b_18210/08_2025/8q7b_18210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7b_18210/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q7b_18210/08_2025/8q7b_18210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7b_18210/08_2025/8q7b_18210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q7b_18210/08_2025/8q7b_18210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7b_18210/08_2025/8q7b_18210.map" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.55, per 1000 atoms: 0.20 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: 0.94 Conformation dependent library (CDL) restraints added in 486.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.79 Time building geometry restraints manager: 1.30 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: 0.02 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.660 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG A 575 TYR 0.023 0.003 TYR A 369 PHE 0.024 0.003 PHE D 54 TRP 0.020 0.003 TRP D 35 HIS 0.005 0.002 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00723 (13034) covalent geometry : angle 0.93442 (17734) SS BOND : bond 0.00895 ( 7) SS BOND : angle 1.55870 ( 14) hydrogen bonds : bond 0.15786 ( 628) hydrogen bonds : angle 6.34841 ( 1908) link_BETA1-4 : bond 0.00203 ( 2) link_BETA1-4 : angle 4.11970 ( 6) link_NAG-ASN : bond 0.01256 ( 2) link_NAG-ASN : angle 10.70547 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.400 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: 0.5393 time to fit residues: 145.6582 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 : 0.438 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.143758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103599 restraints weight = 16031.344| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.89 r_work: 0.3090 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13045 Z= 0.130 Angle : 0.648 8.674 17760 Z= 0.317 Chirality : 0.043 0.176 2052 Planarity : 0.004 0.047 2144 Dihedral : 11.325 136.260 2549 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.19 % Allowed : 12.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1558 helix: 0.75 (0.20), residues: 670 sheet: -0.72 (0.30), residues: 278 loop : -1.73 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 163 TYR 0.014 0.001 TYR A 336 PHE 0.019 0.002 PHE A 182 TRP 0.017 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00286 (13034) covalent geometry : angle 0.63365 (17734) SS BOND : bond 0.00449 ( 7) SS BOND : angle 0.72391 ( 14) hydrogen bonds : bond 0.04367 ( 628) hydrogen bonds : angle 4.60095 ( 1908) link_BETA1-4 : bond 0.00178 ( 2) link_BETA1-4 : angle 2.55731 ( 6) link_NAG-ASN : bond 0.01108 ( 2) link_NAG-ASN : angle 7.04198 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.314 Fit side-chains REVERT: D 5 GLN cc_start: 0.8318 (tp40) cc_final: 0.8088 (tp-100) REVERT: F 3 GLN cc_start: 0.7923 (tp40) cc_final: 0.7498 (mm-40) REVERT: B 71 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.6860 (mtp) REVERT: B 107 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7719 (tp) REVERT: B 152 MET cc_start: 0.7569 (mtp) cc_final: 0.7318 (mtm) REVERT: B 158 ASN cc_start: 0.7346 (m-40) cc_final: 0.7013 (m-40) REVERT: B 198 MET cc_start: 0.8496 (mtp) cc_final: 0.8276 (mtp) REVERT: B 243 HIS cc_start: 0.7669 (t70) cc_final: 0.6796 (t70) REVERT: B 244 GLN cc_start: 0.8119 (pt0) cc_final: 0.7660 (pt0) REVERT: B 398 GLN cc_start: 0.8032 (mm110) cc_final: 0.7803 (mm110) REVERT: B 479 LEU cc_start: 0.8407 (tp) cc_final: 0.8095 (mp) REVERT: B 489 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8081 (t80) REVERT: A 71 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7764 (mtp) REVERT: A 152 MET cc_start: 0.7463 (mtp) cc_final: 0.7092 (mtm) REVERT: A 153 THR cc_start: 0.6849 (m) cc_final: 0.6394 (p) REVERT: A 158 ASN cc_start: 0.7268 (m-40) cc_final: 0.7059 (m-40) REVERT: A 207 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 236 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7300 (ttm110) REVERT: A 243 HIS cc_start: 0.7497 (t70) cc_final: 0.6758 (t70) REVERT: A 244 GLN cc_start: 0.7961 (pt0) cc_final: 0.7544 (pt0) REVERT: A 393 GLN cc_start: 0.7249 (mp10) cc_final: 0.6754 (mm-40) REVERT: A 477 ASP cc_start: 0.8085 (m-30) cc_final: 0.7875 (m-30) REVERT: A 489 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8119 (t80) REVERT: C 15 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7257 (mp) outliers start: 43 outliers final: 11 residues processed: 201 average time/residue: 0.4878 time to fit residues: 107.0421 Evaluate side-chains 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 107 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 71 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 LEU 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 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 154 ASN A 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100428 restraints weight = 16058.666| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.87 r_work: 0.3040 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13045 Z= 0.219 Angle : 0.715 8.050 17760 Z= 0.356 Chirality : 0.046 0.203 2052 Planarity : 0.005 0.052 2144 Dihedral : 10.771 129.637 2534 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.74 % Allowed : 13.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1558 helix: 1.03 (0.20), residues: 676 sheet: -0.58 (0.31), residues: 278 loop : -1.58 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 147 TYR 0.017 0.002 TYR B 605 PHE 0.021 0.002 PHE F 79 TRP 0.020 0.002 TRP D 35 HIS 0.004 0.001 HIS B 630 Details of bonding type rmsd covalent geometry : bond 0.00519 (13034) covalent geometry : angle 0.70828 (17734) SS BOND : bond 0.00810 ( 7) SS BOND : angle 1.50244 ( 14) hydrogen bonds : bond 0.05013 ( 628) hydrogen bonds : angle 4.63464 ( 1908) link_BETA1-4 : bond 0.00127 ( 2) link_BETA1-4 : angle 2.92974 ( 6) link_NAG-ASN : bond 0.00302 ( 2) link_NAG-ASN : angle 3.93294 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.338 Fit side-chains REVERT: D 3 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7692 (mm-40) REVERT: D 111 GLN cc_start: 0.8035 (pm20) cc_final: 0.7769 (pm20) REVERT: F 3 GLN cc_start: 0.7993 (tp40) cc_final: 0.7561 (mm-40) REVERT: B 152 MET cc_start: 0.7598 (mtp) cc_final: 0.7265 (mtm) REVERT: B 158 ASN cc_start: 0.7289 (m-40) cc_final: 0.7053 (m-40) REVERT: B 243 HIS cc_start: 0.7696 (t70) cc_final: 0.6858 (t70) REVERT: B 244 GLN cc_start: 0.8101 (pt0) cc_final: 0.7636 (pt0) REVERT: B 272 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 479 LEU cc_start: 0.8411 (tp) cc_final: 0.8081 (mt) REVERT: B 489 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 152 MET cc_start: 0.7470 (mtp) cc_final: 0.7110 (mtm) REVERT: A 243 HIS cc_start: 0.7562 (t70) cc_final: 0.7059 (t70) REVERT: A 393 GLN cc_start: 0.7323 (mp10) cc_final: 0.7050 (mp10) REVERT: A 489 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8119 (t80) REVERT: A 540 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8177 (mm) REVERT: C 15 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7241 (mp) outliers start: 64 outliers final: 33 residues processed: 201 average time/residue: 0.4457 time to fit residues: 99.0614 Evaluate side-chains 182 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 58 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 ILE 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 20 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 153 THR 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 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 7 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN 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 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101486 restraints weight = 16010.772| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.86 r_work: 0.3061 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13045 Z= 0.156 Angle : 0.632 7.398 17760 Z= 0.315 Chirality : 0.043 0.205 2052 Planarity : 0.004 0.049 2144 Dihedral : 10.455 128.810 2532 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.15 % Allowed : 14.52 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1558 helix: 1.43 (0.20), residues: 674 sheet: -0.47 (0.30), residues: 278 loop : -1.51 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 147 TYR 0.013 0.002 TYR B 336 PHE 0.019 0.002 PHE F 79 TRP 0.020 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00362 (13034) covalent geometry : angle 0.62636 (17734) SS BOND : bond 0.00665 ( 7) SS BOND : angle 1.21878 ( 14) hydrogen bonds : bond 0.04316 ( 628) hydrogen bonds : angle 4.43493 ( 1908) link_BETA1-4 : bond 0.00114 ( 2) link_BETA1-4 : angle 2.69186 ( 6) link_NAG-ASN : bond 0.00232 ( 2) link_NAG-ASN : angle 3.26988 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.391 Fit side-chains REVERT: D 111 GLN cc_start: 0.8051 (pm20) cc_final: 0.7796 (pm20) REVERT: F 3 GLN cc_start: 0.7966 (tp40) cc_final: 0.7539 (mm-40) REVERT: B 152 MET cc_start: 0.7555 (mtp) cc_final: 0.7151 (mtm) REVERT: B 158 ASN cc_start: 0.7286 (m-40) cc_final: 0.7072 (m-40) REVERT: B 243 HIS cc_start: 0.7691 (t70) cc_final: 0.6851 (t70) REVERT: B 244 GLN cc_start: 0.8033 (pt0) cc_final: 0.7566 (pt0) REVERT: B 272 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: B 296 ASP cc_start: 0.6486 (m-30) cc_final: 0.6234 (m-30) REVERT: B 479 LEU cc_start: 0.8374 (tp) cc_final: 0.8073 (mp) REVERT: B 489 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8087 (t80) REVERT: A 72 LYS cc_start: 0.8062 (mptp) cc_final: 0.7712 (mppt) REVERT: A 152 MET cc_start: 0.7398 (mtp) cc_final: 0.7083 (mtm) REVERT: A 243 HIS cc_start: 0.7540 (t70) cc_final: 0.7077 (t70) REVERT: A 247 TYR cc_start: 0.6979 (t80) cc_final: 0.6775 (t80) REVERT: A 393 GLN cc_start: 0.7357 (mp10) cc_final: 0.7038 (mp10) REVERT: A 489 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8130 (t80) REVERT: A 504 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8087 (p0) REVERT: C 15 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7265 (mp) REVERT: C 24 LYS cc_start: 0.8542 (tttt) cc_final: 0.8317 (tptp) outliers start: 56 outliers final: 28 residues processed: 190 average time/residue: 0.4926 time to fit residues: 102.5170 Evaluate side-chains 180 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 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 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 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 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 261 SER 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 504 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 531 GLN A 600 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102792 restraints weight = 16026.487| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.86 r_work: 0.3080 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2304 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= 0.127 Angle : 0.592 8.070 17760 Z= 0.295 Chirality : 0.042 0.195 2052 Planarity : 0.004 0.042 2144 Dihedral : 10.126 125.713 2532 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.56 % Allowed : 15.78 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.21), residues: 1558 helix: 1.71 (0.20), residues: 674 sheet: -0.30 (0.30), residues: 278 loop : -1.42 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 65 TYR 0.011 0.001 TYR B 336 PHE 0.019 0.002 PHE F 79 TRP 0.018 0.002 TRP D 35 HIS 0.005 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00288 (13034) covalent geometry : angle 0.58691 (17734) SS BOND : bond 0.00542 ( 7) SS BOND : angle 1.01421 ( 14) hydrogen bonds : bond 0.03938 ( 628) hydrogen bonds : angle 4.28755 ( 1908) link_BETA1-4 : bond 0.00278 ( 2) link_BETA1-4 : angle 2.55639 ( 6) link_NAG-ASN : bond 0.00231 ( 2) link_NAG-ASN : angle 2.95750 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.391 Fit side-chains REVERT: D 111 GLN cc_start: 0.8020 (pm20) cc_final: 0.7781 (pm20) REVERT: F 3 GLN cc_start: 0.7921 (tp40) cc_final: 0.7473 (mm-40) REVERT: B 152 MET cc_start: 0.7576 (mtp) cc_final: 0.7147 (mtm) REVERT: B 158 ASN cc_start: 0.7304 (m-40) cc_final: 0.7096 (m-40) REVERT: B 243 HIS cc_start: 0.7516 (t70) cc_final: 0.6782 (t70) REVERT: B 244 GLN cc_start: 0.7991 (pt0) cc_final: 0.7563 (pt0) REVERT: B 272 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: B 479 LEU cc_start: 0.8367 (tp) cc_final: 0.8078 (mp) REVERT: B 489 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 72 LYS cc_start: 0.8052 (mptp) cc_final: 0.7695 (mppt) REVERT: A 152 MET cc_start: 0.7405 (mtp) cc_final: 0.7072 (mtm) REVERT: A 243 HIS cc_start: 0.7558 (t70) cc_final: 0.7187 (t70) REVERT: A 247 TYR cc_start: 0.6975 (t80) cc_final: 0.6771 (t80) REVERT: A 393 GLN cc_start: 0.7373 (mp10) cc_final: 0.7048 (mp10) REVERT: A 489 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8151 (t80) REVERT: A 504 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8041 (p0) REVERT: C 24 LYS cc_start: 0.8503 (tttt) cc_final: 0.8290 (tptp) REVERT: C 103 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8042 (ttmm) outliers start: 48 outliers final: 31 residues processed: 190 average time/residue: 0.4625 time to fit residues: 96.2660 Evaluate side-chains 181 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 19 VAL Chi-restraints excluded: chain E residue 20 THR 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 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 272 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL 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 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 504 ASP 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 33 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 103 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 153 optimal weight: 0.0980 chunk 106 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102577 restraints weight = 15885.468| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.87 r_work: 0.3067 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13045 Z= 0.141 Angle : 0.609 7.642 17760 Z= 0.304 Chirality : 0.042 0.184 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.945 121.933 2532 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.15 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1558 helix: 1.82 (0.20), residues: 674 sheet: -0.23 (0.31), residues: 278 loop : -1.38 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 147 TYR 0.012 0.002 TYR B 336 PHE 0.019 0.002 PHE F 79 TRP 0.018 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00325 (13034) covalent geometry : angle 0.60401 (17734) SS BOND : bond 0.00633 ( 7) SS BOND : angle 1.15358 ( 14) hydrogen bonds : bond 0.04053 ( 628) hydrogen bonds : angle 4.29927 ( 1908) link_BETA1-4 : bond 0.00105 ( 2) link_BETA1-4 : angle 2.48210 ( 6) link_NAG-ASN : bond 0.00228 ( 2) link_NAG-ASN : angle 2.98287 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.388 Fit side-chains REVERT: D 111 GLN cc_start: 0.8060 (pm20) cc_final: 0.7827 (pm20) REVERT: F 3 GLN cc_start: 0.7953 (tp40) cc_final: 0.7502 (mm-40) REVERT: B 152 MET cc_start: 0.7564 (mtp) cc_final: 0.7121 (mtm) REVERT: B 243 HIS cc_start: 0.7536 (t70) cc_final: 0.6817 (t70) REVERT: B 244 GLN cc_start: 0.7981 (pt0) cc_final: 0.7548 (pt0) REVERT: B 272 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 479 LEU cc_start: 0.8382 (tp) cc_final: 0.8093 (mp) REVERT: B 489 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8141 (t80) REVERT: A 72 LYS cc_start: 0.8054 (mptp) cc_final: 0.7714 (mppt) REVERT: A 152 MET cc_start: 0.7395 (mtp) cc_final: 0.7047 (mtm) REVERT: A 243 HIS cc_start: 0.7531 (t70) cc_final: 0.7209 (t70) REVERT: A 393 GLN cc_start: 0.7378 (mp10) cc_final: 0.7057 (mp10) REVERT: A 489 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8169 (t80) REVERT: A 504 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8066 (p0) REVERT: A 540 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (mm) REVERT: C 15 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7298 (mp) REVERT: C 103 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8062 (ttmm) outliers start: 56 outliers final: 33 residues processed: 185 average time/residue: 0.4317 time to fit residues: 88.1631 Evaluate side-chains 187 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 76 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 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 89 LEU Chi-restraints excluded: chain A residue 130 VAL 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 504 ASP 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 Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 103 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 7.9990 chunk 141 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103037 restraints weight = 15991.932| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.88 r_work: 0.3095 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13045 Z= 0.118 Angle : 0.577 8.029 17760 Z= 0.288 Chirality : 0.041 0.176 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.637 117.123 2532 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.56 % Allowed : 16.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.22), residues: 1558 helix: 1.95 (0.20), residues: 674 sheet: -0.06 (0.32), residues: 258 loop : -1.25 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 147 TYR 0.011 0.001 TYR F 95 PHE 0.018 0.001 PHE F 79 TRP 0.018 0.001 TRP D 35 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00264 (13034) covalent geometry : angle 0.57237 (17734) SS BOND : bond 0.00534 ( 7) SS BOND : angle 0.97865 ( 14) hydrogen bonds : bond 0.03762 ( 628) hydrogen bonds : angle 4.20068 ( 1908) link_BETA1-4 : bond 0.00245 ( 2) link_BETA1-4 : angle 2.35421 ( 6) link_NAG-ASN : bond 0.00232 ( 2) link_NAG-ASN : angle 2.79669 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.592 Fit side-chains REVERT: D 111 GLN cc_start: 0.7988 (pm20) cc_final: 0.7746 (pm20) REVERT: E 61 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7337 (mtm-85) REVERT: F 3 GLN cc_start: 0.7913 (tp40) cc_final: 0.7436 (mm-40) REVERT: B 152 MET cc_start: 0.7560 (mtp) cc_final: 0.7119 (mtm) REVERT: B 243 HIS cc_start: 0.7430 (t70) cc_final: 0.6726 (t70) REVERT: B 244 GLN cc_start: 0.7955 (pt0) cc_final: 0.7521 (pt0) REVERT: B 272 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 479 LEU cc_start: 0.8306 (tp) cc_final: 0.8032 (mp) REVERT: B 489 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8119 (t80) REVERT: A 72 LYS cc_start: 0.8008 (mptp) cc_final: 0.7647 (mppt) REVERT: A 125 VAL cc_start: 0.8691 (t) cc_final: 0.8472 (m) REVERT: A 152 MET cc_start: 0.7384 (mtp) cc_final: 0.7019 (mtm) REVERT: A 243 HIS cc_start: 0.7496 (t70) cc_final: 0.7173 (t70) REVERT: A 393 GLN cc_start: 0.7373 (mp10) cc_final: 0.7041 (mp10) REVERT: A 489 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8146 (t80) REVERT: A 504 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7977 (p0) REVERT: C 15 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7291 (mp) REVERT: C 103 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8042 (ttmm) outliers start: 48 outliers final: 31 residues processed: 186 average time/residue: 0.4244 time to fit residues: 87.8153 Evaluate side-chains 184 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 76 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 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 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 504 ASP 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 33 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 103 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 141 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102829 restraints weight = 15756.864| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.84 r_work: 0.3081 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13045 Z= 0.130 Angle : 0.592 8.351 17760 Z= 0.296 Chirality : 0.042 0.182 2052 Planarity : 0.004 0.042 2144 Dihedral : 9.475 109.925 2530 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.48 % Allowed : 16.74 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1558 helix: 1.95 (0.20), residues: 674 sheet: -0.06 (0.31), residues: 278 loop : -1.26 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 147 TYR 0.011 0.002 TYR B 336 PHE 0.019 0.002 PHE F 79 TRP 0.017 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00297 (13034) covalent geometry : angle 0.58760 (17734) SS BOND : bond 0.00619 ( 7) SS BOND : angle 1.11566 ( 14) hydrogen bonds : bond 0.03916 ( 628) hydrogen bonds : angle 4.22463 ( 1908) link_BETA1-4 : bond 0.00195 ( 2) link_BETA1-4 : angle 2.32494 ( 6) link_NAG-ASN : bond 0.00221 ( 2) link_NAG-ASN : angle 2.91145 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.376 Fit side-chains REVERT: D 111 GLN cc_start: 0.8039 (pm20) cc_final: 0.7829 (pm20) REVERT: E 94 THR cc_start: 0.7273 (t) cc_final: 0.6816 (p) REVERT: F 3 GLN cc_start: 0.7939 (tp40) cc_final: 0.7475 (mm-40) REVERT: B 152 MET cc_start: 0.7537 (mtp) cc_final: 0.7088 (mtm) REVERT: B 243 HIS cc_start: 0.7479 (t70) cc_final: 0.6716 (t70) REVERT: B 244 GLN cc_start: 0.7970 (pt0) cc_final: 0.7513 (pt0) REVERT: B 272 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 479 LEU cc_start: 0.8366 (tp) cc_final: 0.8084 (mp) REVERT: B 489 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 72 LYS cc_start: 0.8018 (mptp) cc_final: 0.7695 (mppt) REVERT: A 125 VAL cc_start: 0.8722 (t) cc_final: 0.8513 (m) REVERT: A 152 MET cc_start: 0.7422 (mtp) cc_final: 0.7037 (mtm) REVERT: A 243 HIS cc_start: 0.7529 (t70) cc_final: 0.7241 (t70) REVERT: A 393 GLN cc_start: 0.7374 (mp10) cc_final: 0.7044 (mp10) REVERT: A 489 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8184 (t80) REVERT: A 540 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8170 (mm) REVERT: C 15 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7292 (mp) REVERT: C 103 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8055 (ttmm) outliers start: 47 outliers final: 30 residues processed: 184 average time/residue: 0.4379 time to fit residues: 89.4793 Evaluate side-chains 182 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 89 LEU Chi-restraints excluded: chain A residue 130 VAL 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 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 Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 103 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3765 r_free = 0.3765 target = 0.143673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103374 restraints weight = 15939.154| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.87 r_work: 0.3102 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13045 Z= 0.116 Angle : 0.575 8.452 17760 Z= 0.287 Chirality : 0.041 0.171 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.230 99.623 2530 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.96 % Allowed : 17.41 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.22), residues: 1558 helix: 2.01 (0.20), residues: 674 sheet: 0.10 (0.33), residues: 258 loop : -1.14 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 147 TYR 0.010 0.001 TYR A 336 PHE 0.018 0.001 PHE F 79 TRP 0.018 0.001 TRP D 35 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00262 (13034) covalent geometry : angle 0.57084 (17734) SS BOND : bond 0.00554 ( 7) SS BOND : angle 0.99467 ( 14) hydrogen bonds : bond 0.03722 ( 628) hydrogen bonds : angle 4.16424 ( 1908) link_BETA1-4 : bond 0.00231 ( 2) link_BETA1-4 : angle 2.25821 ( 6) link_NAG-ASN : bond 0.00196 ( 2) link_NAG-ASN : angle 2.76939 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.551 Fit side-chains REVERT: D 111 GLN cc_start: 0.7995 (pm20) cc_final: 0.7749 (pm20) REVERT: E 15 LEU cc_start: 0.7709 (mp) cc_final: 0.7200 (tp) REVERT: E 47 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8279 (tp) REVERT: E 94 THR cc_start: 0.7265 (t) cc_final: 0.6779 (p) REVERT: F 3 GLN cc_start: 0.7930 (tp40) cc_final: 0.7454 (mm-40) REVERT: B 152 MET cc_start: 0.7485 (mtp) cc_final: 0.7028 (mtm) REVERT: B 243 HIS cc_start: 0.7466 (t70) cc_final: 0.6729 (t70) REVERT: B 244 GLN cc_start: 0.7936 (pt0) cc_final: 0.7485 (pt0) REVERT: B 272 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 479 LEU cc_start: 0.8301 (tp) cc_final: 0.8023 (mp) REVERT: B 489 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8123 (t80) REVERT: A 72 LYS cc_start: 0.7982 (mptp) cc_final: 0.7637 (mppt) REVERT: A 125 VAL cc_start: 0.8700 (t) cc_final: 0.8490 (m) REVERT: A 152 MET cc_start: 0.7397 (mtp) cc_final: 0.6999 (mtm) REVERT: A 243 HIS cc_start: 0.7500 (t70) cc_final: 0.7221 (t70) REVERT: A 393 GLN cc_start: 0.7310 (mp10) cc_final: 0.6984 (mp10) REVERT: A 489 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8157 (t80) REVERT: C 15 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7288 (mp) REVERT: C 70 ASP cc_start: 0.8155 (m-30) cc_final: 0.7879 (m-30) REVERT: C 103 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8048 (ttmm) outliers start: 40 outliers final: 30 residues processed: 179 average time/residue: 0.5299 time to fit residues: 105.2397 Evaluate side-chains 183 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 20 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 532 SER Chi-restraints excluded: chain B residue 534 VAL 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 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 15 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 59 optimal weight: 0.0000 chunk 142 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.144261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103974 restraints weight = 15971.918| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.88 r_work: 0.3106 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13045 Z= 0.108 Angle : 0.560 8.442 17760 Z= 0.281 Chirality : 0.040 0.165 2052 Planarity : 0.004 0.043 2144 Dihedral : 8.957 88.606 2530 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.30 % Allowed : 18.15 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.22), residues: 1558 helix: 2.09 (0.20), residues: 674 sheet: 0.18 (0.33), residues: 258 loop : -1.09 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 147 TYR 0.010 0.001 TYR F 51 PHE 0.017 0.001 PHE F 79 TRP 0.018 0.001 TRP D 35 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00240 (13034) covalent geometry : angle 0.55583 (17734) SS BOND : bond 0.00515 ( 7) SS BOND : angle 0.89639 ( 14) hydrogen bonds : bond 0.03577 ( 628) hydrogen bonds : angle 4.11386 ( 1908) link_BETA1-4 : bond 0.00231 ( 2) link_BETA1-4 : angle 2.21501 ( 6) link_NAG-ASN : bond 0.00209 ( 2) link_NAG-ASN : angle 2.73190 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.556 Fit side-chains REVERT: D 111 GLN cc_start: 0.8013 (pm20) cc_final: 0.7785 (pm20) REVERT: E 15 LEU cc_start: 0.7728 (mp) cc_final: 0.7252 (tp) REVERT: E 47 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8249 (tp) REVERT: E 94 THR cc_start: 0.7246 (t) cc_final: 0.6774 (p) REVERT: F 3 GLN cc_start: 0.7907 (tp40) cc_final: 0.7447 (mm-40) REVERT: B 152 MET cc_start: 0.7497 (mtp) cc_final: 0.7016 (mtm) REVERT: B 243 HIS cc_start: 0.7477 (t70) cc_final: 0.6752 (t70) REVERT: B 244 GLN cc_start: 0.7951 (pt0) cc_final: 0.7512 (pt0) REVERT: B 272 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: B 479 LEU cc_start: 0.8313 (tp) cc_final: 0.8040 (mp) REVERT: B 489 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 72 LYS cc_start: 0.7984 (mptp) cc_final: 0.7653 (mppt) REVERT: A 152 MET cc_start: 0.7409 (mtp) cc_final: 0.6996 (mtm) REVERT: A 243 HIS cc_start: 0.7515 (t70) cc_final: 0.7228 (t70) REVERT: A 393 GLN cc_start: 0.7290 (mp10) cc_final: 0.6962 (mp10) REVERT: A 489 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8190 (t80) REVERT: C 103 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8066 (ttmm) outliers start: 31 outliers final: 20 residues processed: 171 average time/residue: 0.5388 time to fit residues: 101.8660 Evaluate side-chains 171 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 22 SER 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 17 SER Chi-restraints excluded: chain F residue 20 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 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.0060 chunk 122 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3736 r_free = 0.3736 target = 0.141338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100821 restraints weight = 15949.388| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.86 r_work: 0.3062 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13045 Z= 0.196 Angle : 0.676 9.056 17760 Z= 0.339 Chirality : 0.045 0.194 2052 Planarity : 0.004 0.041 2144 Dihedral : 9.346 87.577 2528 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.81 % Allowed : 17.78 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1558 helix: 1.81 (0.20), residues: 672 sheet: -0.08 (0.31), residues: 278 loop : -1.26 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 147 TYR 0.014 0.002 TYR B 336 PHE 0.020 0.002 PHE F 79 TRP 0.016 0.002 TRP D 35 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00466 (13034) covalent geometry : angle 0.67110 (17734) SS BOND : bond 0.00923 ( 7) SS BOND : angle 1.54652 ( 14) hydrogen bonds : bond 0.04613 ( 628) hydrogen bonds : angle 4.40479 ( 1908) link_BETA1-4 : bond 0.00103 ( 2) link_BETA1-4 : angle 2.28489 ( 6) link_NAG-ASN : bond 0.00119 ( 2) link_NAG-ASN : angle 3.38523 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5104.37 seconds wall clock time: 87 minutes 33.85 seconds (5253.85 seconds total)