Starting phenix.real_space_refine on Sun Nov 17 03:02:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7b_18210/11_2024/8q7b_18210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7b_18210/11_2024/8q7b_18210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7b_18210/11_2024/8q7b_18210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7b_18210/11_2024/8q7b_18210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7b_18210/11_2024/8q7b_18210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7b_18210/11_2024/8q7b_18210.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8306 2.51 5 N 2042 2.21 5 O 2354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12770 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'BWQ': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'BWQ': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.14, per 1000 atoms: 0.79 Number of scatterers: 12770 At special positions: 0 Unit cell: (99.66, 96.36, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2354 8.00 N 2042 7.00 C 8306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN B 596 " " NAG H 1 " - " ASN A 596 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 18 sheets defined 46.3% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 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: 5.53 Time building geometry restraints manager: 4.16 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: 0.00 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: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.880 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.220 ------------------------------------------------------------------------------- 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 13034 Z= 0.466 Angle : 0.934 9.938 17734 Z= 0.460 Chirality : 0.059 0.359 2052 Planarity : 0.005 0.044 2144 Dihedral : 13.885 147.244 5312 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 1.48 % Allowed : 6.89 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.18), residues: 1558 helix: -1.00 (0.18), residues: 652 sheet: -1.23 (0.28), residues: 288 loop : -2.31 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 35 HIS 0.005 0.002 HIS A 583 PHE 0.024 0.003 PHE D 54 TYR 0.023 0.003 TYR A 369 ARG 0.004 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 1.857 Fit side-chains REVERT: F 3 GLN cc_start: 0.7373 (tp-100) cc_final: 0.7080 (tm-30) REVERT: F 6 GLU cc_start: 0.8027 (mp0) cc_final: 0.7767 (mp0) REVERT: B 138 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6907 (mt-10) REVERT: B 152 MET cc_start: 0.7672 (mtp) cc_final: 0.7435 (mtm) REVERT: B 158 ASN cc_start: 0.7360 (m-40) cc_final: 0.7023 (m-40) REVERT: B 198 MET cc_start: 0.8398 (mtp) cc_final: 0.8162 (mtp) REVERT: B 236 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6688 (ttm110) REVERT: B 243 HIS cc_start: 0.7518 (t70) cc_final: 0.6817 (t70) REVERT: B 244 GLN cc_start: 0.7951 (pt0) cc_final: 0.7546 (pt0) REVERT: B 489 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.7929 (t80) REVERT: B 515 MET cc_start: 0.8500 (mmm) cc_final: 0.8251 (mmm) REVERT: A 152 MET cc_start: 0.7538 (mtp) cc_final: 0.7196 (mtm) REVERT: A 158 ASN cc_start: 0.7285 (m-40) cc_final: 0.7032 (m-40) REVERT: A 198 MET cc_start: 0.8403 (mtp) cc_final: 0.8143 (mtp) REVERT: A 214 THR cc_start: 0.8048 (m) cc_final: 0.7677 (m) REVERT: A 243 HIS cc_start: 0.7410 (t70) cc_final: 0.6757 (t70) REVERT: A 244 GLN cc_start: 0.7917 (pt0) cc_final: 0.7612 (pt0) REVERT: A 489 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.7945 (t80) outliers start: 20 outliers final: 9 residues processed: 249 average time/residue: 1.3739 time to fit residues: 372.5799 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 : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 GLN D 16 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 77 ASN E 6 GLN E 79 GLN F 3 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 77 ASN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 109 ASN B 418 ASN B 425 ASN B 457 HIS B 531 GLN B 582 GLN B 583 HIS B 589 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 418 ASN A 425 ASN A 457 HIS A 531 GLN A 583 HIS A 589 GLN C 6 GLN C 79 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13034 Z= 0.197 Angle : 0.639 7.521 17734 Z= 0.317 Chirality : 0.043 0.176 2052 Planarity : 0.004 0.049 2144 Dihedral : 11.277 135.335 2549 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.33 % Allowed : 12.22 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1558 helix: 0.76 (0.20), residues: 670 sheet: -0.73 (0.30), residues: 278 loop : -1.72 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35 HIS 0.003 0.001 HIS B 630 PHE 0.019 0.002 PHE F 79 TYR 0.013 0.002 TYR B 336 ARG 0.006 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.570 Fit side-chains REVERT: F 3 GLN cc_start: 0.7334 (tp40) cc_final: 0.7028 (mm-40) REVERT: B 71 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6391 (mtp) REVERT: B 152 MET cc_start: 0.7558 (mtp) cc_final: 0.7353 (mtm) REVERT: B 158 ASN cc_start: 0.7329 (m-40) cc_final: 0.6991 (m-40) REVERT: B 198 MET cc_start: 0.8174 (mtp) cc_final: 0.7918 (mtp) REVERT: B 243 HIS cc_start: 0.7471 (t70) cc_final: 0.6624 (t70) REVERT: B 244 GLN cc_start: 0.7894 (pt0) cc_final: 0.7418 (pt0) REVERT: B 398 GLN cc_start: 0.7824 (mm110) cc_final: 0.7595 (mm110) REVERT: B 479 LEU cc_start: 0.8459 (tp) cc_final: 0.8157 (mp) REVERT: B 481 MET cc_start: 0.7561 (tpt) cc_final: 0.7293 (tpt) REVERT: B 489 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 515 MET cc_start: 0.8530 (mmm) cc_final: 0.8024 (mmm) REVERT: A 152 MET cc_start: 0.7383 (mtp) cc_final: 0.7042 (mtm) REVERT: A 158 ASN cc_start: 0.7271 (m-40) cc_final: 0.7046 (m-40) REVERT: A 236 ARG cc_start: 0.7383 (ttp-170) cc_final: 0.7105 (ttm110) REVERT: A 243 HIS cc_start: 0.7355 (t70) cc_final: 0.6680 (t70) REVERT: A 244 GLN cc_start: 0.7868 (pt0) cc_final: 0.7460 (pt0) REVERT: A 477 ASP cc_start: 0.7661 (m-30) cc_final: 0.7456 (m-30) REVERT: A 481 MET cc_start: 0.7671 (tpt) cc_final: 0.7420 (tpt) REVERT: A 489 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8030 (t80) REVERT: C 15 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7257 (mp) outliers start: 45 outliers final: 11 residues processed: 203 average time/residue: 1.2881 time to fit residues: 286.9282 Evaluate side-chains 161 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13034 Z= 0.319 Angle : 0.700 8.024 17734 Z= 0.350 Chirality : 0.046 0.199 2052 Planarity : 0.005 0.052 2144 Dihedral : 10.758 129.640 2534 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.52 % Allowed : 13.78 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1558 helix: 1.11 (0.20), residues: 672 sheet: -0.62 (0.30), residues: 278 loop : -1.59 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 35 HIS 0.004 0.001 HIS B 630 PHE 0.021 0.002 PHE F 79 TYR 0.016 0.002 TYR B 605 ARG 0.010 0.001 ARG A 147 *********************** 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 216 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 1.419 Fit side-chains REVERT: D 16 GLN cc_start: 0.6602 (tt0) cc_final: 0.6398 (tt0) REVERT: D 111 GLN cc_start: 0.7664 (pm20) cc_final: 0.7450 (pm20) REVERT: F 3 GLN cc_start: 0.7399 (tp40) cc_final: 0.7107 (mm-40) REVERT: B 152 MET cc_start: 0.7589 (mtp) cc_final: 0.7296 (mtm) REVERT: B 158 ASN cc_start: 0.7284 (m-40) cc_final: 0.7023 (m-40) REVERT: B 243 HIS cc_start: 0.7516 (t70) cc_final: 0.6680 (t70) REVERT: B 244 GLN cc_start: 0.7889 (pt0) cc_final: 0.7408 (pt0) REVERT: B 272 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: B 481 MET cc_start: 0.7618 (tpt) cc_final: 0.7296 (tpt) REVERT: B 489 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.7988 (t80) REVERT: A 72 LYS cc_start: 0.7912 (mptp) cc_final: 0.7576 (mppt) REVERT: A 152 MET cc_start: 0.7354 (mtp) cc_final: 0.7020 (mtm) REVERT: A 154 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6302 (t0) REVERT: A 243 HIS cc_start: 0.7422 (t70) cc_final: 0.6967 (t70) REVERT: A 489 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 504 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7554 (p0) REVERT: A 540 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8127 (mm) REVERT: C 15 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7214 (mp) outliers start: 61 outliers final: 30 residues processed: 197 average time/residue: 1.1599 time to fit residues: 251.7866 Evaluate side-chains 181 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 86 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 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 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 154 ASN 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 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 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13034 Z= 0.175 Angle : 0.576 7.496 17734 Z= 0.289 Chirality : 0.042 0.185 2052 Planarity : 0.004 0.050 2144 Dihedral : 10.230 128.229 2532 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.78 % Allowed : 14.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1558 helix: 1.63 (0.20), residues: 672 sheet: -0.37 (0.30), residues: 278 loop : -1.42 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.019 0.002 PHE F 79 TYR 0.012 0.001 TYR F 95 ARG 0.007 0.000 ARG A 147 *********************** 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 205 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 1.489 Fit side-chains REVERT: D 111 GLN cc_start: 0.7651 (pm20) cc_final: 0.7438 (pm20) REVERT: F 3 GLN cc_start: 0.7295 (tp40) cc_final: 0.7008 (mm-40) REVERT: B 152 MET cc_start: 0.7536 (mtp) cc_final: 0.7147 (mtm) REVERT: B 158 ASN cc_start: 0.7287 (m-40) cc_final: 0.7024 (m-40) REVERT: B 243 HIS cc_start: 0.7467 (t70) cc_final: 0.6650 (t70) REVERT: B 244 GLN cc_start: 0.7807 (pt0) cc_final: 0.7328 (pt0) REVERT: B 272 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: B 479 LEU cc_start: 0.8419 (tp) cc_final: 0.8115 (mp) REVERT: B 489 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.7981 (t80) REVERT: A 72 LYS cc_start: 0.7818 (mptp) cc_final: 0.7519 (mppt) REVERT: A 152 MET cc_start: 0.7325 (mtp) cc_final: 0.7074 (mtm) REVERT: A 243 HIS cc_start: 0.7408 (t70) cc_final: 0.7040 (t70) REVERT: A 247 TYR cc_start: 0.7010 (t80) cc_final: 0.6782 (t80) REVERT: A 489 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 504 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7465 (p0) outliers start: 51 outliers final: 24 residues processed: 190 average time/residue: 1.2353 time to fit residues: 257.5994 Evaluate side-chains 176 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 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 532 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 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 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.0040 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.1198 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13034 Z= 0.328 Angle : 0.681 7.973 17734 Z= 0.341 Chirality : 0.045 0.203 2052 Planarity : 0.005 0.049 2144 Dihedral : 10.385 126.408 2532 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.07 % Allowed : 15.19 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1558 helix: 1.48 (0.20), residues: 676 sheet: -0.39 (0.31), residues: 278 loop : -1.47 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 35 HIS 0.005 0.001 HIS B 243 PHE 0.021 0.002 PHE F 79 TYR 0.015 0.002 TYR B 336 ARG 0.007 0.001 ARG C 61 *********************** 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 201 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 1.507 Fit side-chains REVERT: D 111 GLN cc_start: 0.7693 (pm20) cc_final: 0.7468 (pm20) REVERT: F 3 GLN cc_start: 0.7404 (tp40) cc_final: 0.7080 (mm-40) REVERT: B 152 MET cc_start: 0.7556 (mtp) cc_final: 0.7134 (mtm) REVERT: B 158 ASN cc_start: 0.7382 (m-40) cc_final: 0.7154 (m-40) REVERT: B 243 HIS cc_start: 0.7379 (t70) cc_final: 0.6624 (t70) REVERT: B 244 GLN cc_start: 0.7809 (pt0) cc_final: 0.7363 (pt0) REVERT: B 272 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: B 296 ASP cc_start: 0.6491 (m-30) cc_final: 0.6239 (m-30) REVERT: B 489 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8006 (t80) REVERT: A 72 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7612 (mppt) REVERT: A 152 MET cc_start: 0.7359 (mtp) cc_final: 0.7054 (mtm) REVERT: A 243 HIS cc_start: 0.7388 (t70) cc_final: 0.7025 (t70) REVERT: A 247 TYR cc_start: 0.7126 (t80) cc_final: 0.6872 (t80) REVERT: A 489 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8050 (t80) REVERT: A 504 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7582 (p0) REVERT: A 540 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8172 (mm) REVERT: C 15 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7231 (mp) REVERT: C 103 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7939 (ttmm) outliers start: 55 outliers final: 34 residues processed: 181 average time/residue: 1.2165 time to fit residues: 242.8359 Evaluate side-chains 185 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 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 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 72 LYS 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 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 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 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 50 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13034 Z= 0.186 Angle : 0.589 7.846 17734 Z= 0.296 Chirality : 0.041 0.178 2052 Planarity : 0.004 0.047 2144 Dihedral : 9.953 122.551 2532 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.63 % Allowed : 16.00 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1558 helix: 1.78 (0.20), residues: 674 sheet: -0.25 (0.31), residues: 278 loop : -1.39 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.019 0.001 PHE F 79 TYR 0.012 0.001 TYR F 95 ARG 0.008 0.001 ARG B 147 *********************** 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 202 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.394 Fit side-chains REVERT: D 111 GLN cc_start: 0.7645 (pm20) cc_final: 0.7436 (pm20) REVERT: F 3 GLN cc_start: 0.7334 (tp40) cc_final: 0.7032 (mm-40) REVERT: B 152 MET cc_start: 0.7548 (mtp) cc_final: 0.7125 (mtm) REVERT: B 158 ASN cc_start: 0.7395 (m-40) cc_final: 0.7180 (m-40) REVERT: B 243 HIS cc_start: 0.7359 (t70) cc_final: 0.6647 (t70) REVERT: B 244 GLN cc_start: 0.7743 (pt0) cc_final: 0.7295 (pt0) REVERT: B 272 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: B 296 ASP cc_start: 0.6563 (m-30) cc_final: 0.6345 (m-30) REVERT: B 489 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8001 (t80) REVERT: A 72 LYS cc_start: 0.7826 (mptp) cc_final: 0.7554 (mppt) REVERT: A 152 MET cc_start: 0.7337 (mtp) cc_final: 0.7013 (mtm) REVERT: A 243 HIS cc_start: 0.7387 (t70) cc_final: 0.7066 (t70) REVERT: A 247 TYR cc_start: 0.7100 (t80) cc_final: 0.6856 (t80) REVERT: A 489 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 504 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7518 (p0) REVERT: C 15 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7280 (mp) REVERT: C 103 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7914 (ttmm) outliers start: 49 outliers final: 30 residues processed: 185 average time/residue: 1.2408 time to fit residues: 251.6572 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 : 1.576 ------------------------------------------------------------------------------- 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 22 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 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 C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 103 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13034 Z= 0.193 Angle : 0.590 8.011 17734 Z= 0.296 Chirality : 0.042 0.173 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.724 117.372 2532 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.78 % Allowed : 16.07 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1558 helix: 1.88 (0.20), residues: 674 sheet: -0.16 (0.31), residues: 278 loop : -1.33 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.019 0.002 PHE F 79 TYR 0.012 0.002 TYR F 95 ARG 0.005 0.000 ARG B 147 *********************** 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 202 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 1.320 Fit side-chains REVERT: D 111 GLN cc_start: 0.7650 (pm20) cc_final: 0.7443 (pm20) REVERT: F 3 GLN cc_start: 0.7333 (tp40) cc_final: 0.7022 (mm-40) REVERT: B 152 MET cc_start: 0.7546 (mtp) cc_final: 0.7121 (mtm) REVERT: B 158 ASN cc_start: 0.7356 (m-40) cc_final: 0.7111 (m-40) REVERT: B 243 HIS cc_start: 0.7334 (t70) cc_final: 0.6630 (t70) REVERT: B 244 GLN cc_start: 0.7738 (pt0) cc_final: 0.7290 (pt0) REVERT: B 272 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: B 489 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 72 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7541 (mppt) REVERT: A 152 MET cc_start: 0.7352 (mtp) cc_final: 0.7028 (mtm) REVERT: A 243 HIS cc_start: 0.7373 (t70) cc_final: 0.7077 (t70) REVERT: A 247 TYR cc_start: 0.7110 (t80) cc_final: 0.6899 (t80) REVERT: A 489 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8102 (t80) REVERT: A 504 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7502 (p0) REVERT: A 540 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8149 (mm) REVERT: C 11 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6293 (t80) REVERT: C 15 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7285 (mp) REVERT: C 103 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7917 (ttmm) outliers start: 51 outliers final: 31 residues processed: 183 average time/residue: 1.1785 time to fit residues: 238.7226 Evaluate side-chains 186 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 74 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 GLN 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 72 LYS 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 11 PHE 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 59 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13034 Z= 0.199 Angle : 0.594 8.173 17734 Z= 0.298 Chirality : 0.042 0.177 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.535 110.314 2530 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.41 % Allowed : 16.67 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1558 helix: 1.89 (0.20), residues: 674 sheet: -0.12 (0.31), residues: 278 loop : -1.28 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.019 0.002 PHE F 79 TYR 0.011 0.002 TYR B 336 ARG 0.004 0.000 ARG A 147 *********************** 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 194 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 1.476 Fit side-chains REVERT: D 111 GLN cc_start: 0.7667 (pm20) cc_final: 0.7463 (pm20) REVERT: F 3 GLN cc_start: 0.7343 (tp40) cc_final: 0.7026 (tm-30) REVERT: B 152 MET cc_start: 0.7531 (mtp) cc_final: 0.7099 (mtm) REVERT: B 158 ASN cc_start: 0.7303 (m-40) cc_final: 0.7047 (m-40) REVERT: B 243 HIS cc_start: 0.7330 (t70) cc_final: 0.6623 (t70) REVERT: B 244 GLN cc_start: 0.7788 (pt0) cc_final: 0.7350 (pt0) REVERT: B 272 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 489 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8038 (t80) REVERT: A 72 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7548 (mppt) REVERT: A 125 VAL cc_start: 0.8636 (t) cc_final: 0.8431 (m) REVERT: A 152 MET cc_start: 0.7339 (mtp) cc_final: 0.6967 (mtm) REVERT: A 243 HIS cc_start: 0.7362 (t70) cc_final: 0.7075 (t70) REVERT: A 489 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8103 (t80) REVERT: A 504 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7503 (p0) REVERT: C 11 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6244 (t80) REVERT: C 15 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7273 (mp) REVERT: C 103 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (ttmm) outliers start: 46 outliers final: 32 residues processed: 180 average time/residue: 1.1142 time to fit residues: 223.8167 Evaluate side-chains 184 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 166 GLN 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 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 201 ILE 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 534 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 65 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 142 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 531 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13034 Z= 0.192 Angle : 0.589 8.536 17734 Z= 0.296 Chirality : 0.042 0.173 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.360 101.242 2530 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.26 % Allowed : 16.89 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1558 helix: 1.92 (0.20), residues: 674 sheet: -0.05 (0.31), residues: 278 loop : -1.25 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.019 0.002 PHE F 79 TYR 0.011 0.002 TYR B 336 ARG 0.004 0.000 ARG C 61 *********************** 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 191 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.469 Fit side-chains REVERT: F 3 GLN cc_start: 0.7341 (tp40) cc_final: 0.7026 (tm-30) REVERT: B 152 MET cc_start: 0.7501 (mtp) cc_final: 0.7070 (mtm) REVERT: B 158 ASN cc_start: 0.7233 (m-40) cc_final: 0.6982 (m-40) REVERT: B 243 HIS cc_start: 0.7363 (t70) cc_final: 0.6641 (t70) REVERT: B 244 GLN cc_start: 0.7767 (pt0) cc_final: 0.7324 (pt0) REVERT: B 272 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 489 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 72 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7556 (mppt) REVERT: A 152 MET cc_start: 0.7355 (mtp) cc_final: 0.6968 (mtm) REVERT: A 243 HIS cc_start: 0.7395 (t70) cc_final: 0.7127 (t70) REVERT: A 489 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 504 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7521 (p0) REVERT: A 540 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8126 (mm) REVERT: C 15 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7273 (mp) REVERT: C 70 ASP cc_start: 0.7617 (m-30) cc_final: 0.7408 (m-30) REVERT: C 103 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7940 (ttmm) outliers start: 44 outliers final: 32 residues processed: 178 average time/residue: 1.1094 time to fit residues: 219.0333 Evaluate side-chains 183 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 166 GLN 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 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 ARG 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 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 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 153 optimal weight: 0.1980 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 68 ASN B 531 GLN B 600 ASN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13034 Z= 0.207 Angle : 0.603 8.739 17734 Z= 0.303 Chirality : 0.042 0.185 2052 Planarity : 0.004 0.043 2144 Dihedral : 9.258 92.726 2530 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.11 % Allowed : 17.41 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1558 helix: 1.90 (0.20), residues: 674 sheet: -0.04 (0.31), residues: 278 loop : -1.23 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 35 HIS 0.003 0.001 HIS B 243 PHE 0.019 0.002 PHE F 79 TYR 0.012 0.002 TYR B 336 ARG 0.004 0.000 ARG C 61 ********************** 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 189 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.417 Fit side-chains REVERT: F 3 GLN cc_start: 0.7363 (tp40) cc_final: 0.7043 (tm-30) REVERT: B 152 MET cc_start: 0.7505 (mtp) cc_final: 0.7077 (mtm) REVERT: B 158 ASN cc_start: 0.7231 (m-40) cc_final: 0.6979 (m-40) REVERT: B 243 HIS cc_start: 0.7388 (t70) cc_final: 0.6683 (t70) REVERT: B 244 GLN cc_start: 0.7774 (pt0) cc_final: 0.7351 (pt0) REVERT: B 272 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: B 479 LEU cc_start: 0.8517 (tp) cc_final: 0.8187 (mt) REVERT: B 489 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8056 (t80) REVERT: A 72 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7555 (mppt) REVERT: A 152 MET cc_start: 0.7354 (mtp) cc_final: 0.6959 (mtm) REVERT: A 243 HIS cc_start: 0.7388 (t70) cc_final: 0.7114 (t70) REVERT: A 489 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 504 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7544 (p0) REVERT: A 540 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8094 (mm) REVERT: C 15 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7271 (mp) REVERT: C 70 ASP cc_start: 0.7594 (m-30) cc_final: 0.7391 (m-30) REVERT: C 103 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7948 (ttmm) outliers start: 42 outliers final: 32 residues processed: 177 average time/residue: 1.1253 time to fit residues: 220.8242 Evaluate side-chains 186 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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 563 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 504 ASP 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 20 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 166 GLN 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 = 0.3704 r_free = 0.3704 target = 0.139305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.097671 restraints weight = 15623.163| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.90 r_work: 0.2989 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13034 Z= 0.456 Angle : 0.776 9.238 17734 Z= 0.391 Chirality : 0.050 0.241 2052 Planarity : 0.005 0.049 2144 Dihedral : 9.871 88.603 2530 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.04 % Allowed : 17.70 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1558 helix: 1.37 (0.20), residues: 674 sheet: -0.28 (0.31), residues: 278 loop : -1.46 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 35 HIS 0.005 0.002 HIS B 243 PHE 0.024 0.003 PHE D 79 TYR 0.018 0.003 TYR B 336 ARG 0.006 0.001 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5063.06 seconds wall clock time: 91 minutes 47.31 seconds (5507.31 seconds total)