Starting phenix.real_space_refine on Sun Dec 10 17:00:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2c_41845/12_2023/8u2c_41845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2c_41845/12_2023/8u2c_41845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2c_41845/12_2023/8u2c_41845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2c_41845/12_2023/8u2c_41845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2c_41845/12_2023/8u2c_41845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2c_41845/12_2023/8u2c_41845.pdb" } resolution = 2.5 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 ------------------------------------------------------------------------------- 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= 0.075 sd= 1.000 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 76 5.16 5 C 9670 2.51 5 N 2480 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 575": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "K ARG 130": "NH1" <-> "NH2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L ARG 164": "NH1" <-> "NH2" Residue "L PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15042 Number of models: 1 Model: "" Number of chains: 10 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: "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: "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: "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: "I" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 650 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 79} Chain breaks: 2 Chain: "K" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 88} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 650 Classifications: {'peptide': 89} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 79} Chain breaks: 2 Chain: "L" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 88} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.17, per 1000 atoms: 0.54 Number of scatterers: 15042 At special positions: 0 Unit cell: (101.85, 160.65, 161.7, 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 76 16.00 O 2816 8.00 N 2480 7.00 C 9670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 203 " distance=2.04 Simple disulfide: pdb=" SG CYS K 156 " - pdb=" SG CYS K 216 " distance=2.05 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.04 Simple disulfide: pdb=" SG CYS L 156 " - pdb=" SG CYS L 216 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 3.1 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 39.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.524A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.598A pdb=" N ASN A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.585A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.614A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.810A pdb=" N ALA A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.840A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.186A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.592A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.929A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.544A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 395 through 413 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: 4.066A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 479 through 498 Proline residue: A 485 - end of helix removed outlier: 4.978A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.045A 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: 4.343A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.592A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.227A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 587 removed outlier: 3.848A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.551A 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 622 through 650 removed outlier: 3.647A pdb=" N LEU A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.571A pdb=" N ASN B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.568A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.614A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.823A pdb=" N ALA B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.830A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 271 through 281 removed outlier: 4.599A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.931A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.591A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 Processing helix chain 'B' and resid 395 through 413 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: 4.107A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 450' Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 485 - end of helix removed outlier: 4.982A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.044A 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: 4.353A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.593A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.229A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 587 removed outlier: 3.849A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.546A 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 622 through 650 removed outlier: 3.648A pdb=" N LEU B 626 " --> pdb=" O SER B 622 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.776A pdb=" N VAL C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.753A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.025A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'K' and resid 145 through 149 removed outlier: 3.521A pdb=" N LYS K 148 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'L' and resid 145 through 149 removed outlier: 3.525A pdb=" N LYS L 148 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 71 removed outlier: 6.712A pdb=" N SER A 65 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N CYS A 43 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.343A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 255 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 71 removed outlier: 6.694A pdb=" N SER B 65 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N CYS B 43 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.357A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 255 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.695A pdb=" N SER C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.695A pdb=" N SER C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY C 84 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.261A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.261A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.480A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.480A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.677A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.016A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 128 through 131 removed outlier: 3.951A pdb=" N GLY I 146 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP I 151 " --> pdb=" O TYR I 183 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR I 183 " --> pdb=" O ASP I 151 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N SER I 184 " --> pdb=" O ALA I 175 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA I 175 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER I 186 " --> pdb=" O PHE I 173 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 159 through 161 Processing sheet with id=AC2, first strand: chain 'K' and resid 136 through 140 removed outlier: 4.801A pdb=" N TYR K 195 " --> pdb=" O ASN K 160 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN K 182 " --> pdb=" O THR K 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AC4, first strand: chain 'J' and resid 128 through 131 removed outlier: 3.948A pdb=" N GLY J 146 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP J 151 " --> pdb=" O TYR J 183 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER J 184 " --> pdb=" O ALA J 175 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA J 175 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER J 186 " --> pdb=" O PHE J 173 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 159 through 161 Processing sheet with id=AC6, first strand: chain 'L' and resid 136 through 140 removed outlier: 4.907A pdb=" N TYR L 195 " --> pdb=" O ASN L 160 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER L 196 " --> pdb=" O THR L 186 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 168 through 170 removed outlier: 4.017A pdb=" N VAL L 227 " --> pdb=" O VAL L 218 " (cutoff:3.500A) 758 hydrogen bonds defined for protein. 2115 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: 5.07 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3628 1.33 - 1.46: 3142 1.46 - 1.58: 8488 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 15372 Sorted by residual: bond pdb=" CA ASP B 203 " pdb=" CB ASP B 203 " ideal model delta sigma weight residual 1.522 1.546 -0.024 7.00e-03 2.04e+04 1.19e+01 bond pdb=" N ASP A 203 " pdb=" CA ASP A 203 " ideal model delta sigma weight residual 1.458 1.483 -0.025 7.40e-03 1.83e+04 1.18e+01 bond pdb=" N ASP B 203 " pdb=" CA ASP B 203 " ideal model delta sigma weight residual 1.458 1.483 -0.025 7.40e-03 1.83e+04 1.17e+01 bond pdb=" CA ASP A 203 " pdb=" CB ASP A 203 " ideal model delta sigma weight residual 1.522 1.546 -0.024 7.00e-03 2.04e+04 1.14e+01 bond pdb=" CZ ARG E 61 " pdb=" NH2 ARG E 61 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 ... (remaining 15367 not shown) Histogram of bond angle deviations from ideal: 90.55 - 102.80: 77 102.80 - 115.05: 9250 115.05 - 127.29: 11376 127.29 - 139.54: 137 139.54 - 151.79: 2 Bond angle restraints: 20842 Sorted by residual: angle pdb=" CA LEU B 595 " pdb=" C LEU B 595 " pdb=" N ASN B 596 " ideal model delta sigma weight residual 116.37 151.79 -35.42 1.28e+00 6.10e-01 7.66e+02 angle pdb=" O LEU B 595 " pdb=" C LEU B 595 " pdb=" N ASN B 596 " ideal model delta sigma weight residual 123.13 90.55 32.58 1.26e+00 6.30e-01 6.69e+02 angle pdb=" C LEU B 595 " pdb=" N ASN B 596 " pdb=" CA ASN B 596 " ideal model delta sigma weight residual 120.71 139.63 -18.92 1.42e+00 4.96e-01 1.78e+02 angle pdb=" N LYS J 150 " pdb=" CA LYS J 150 " pdb=" C LYS J 150 " ideal model delta sigma weight residual 111.14 119.46 -8.32 1.08e+00 8.57e-01 5.93e+01 angle pdb=" CA PHE J 173 " pdb=" CB PHE J 173 " pdb=" CG PHE J 173 " ideal model delta sigma weight residual 113.80 121.27 -7.47 1.00e+00 1.00e+00 5.59e+01 ... (remaining 20837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8336 17.90 - 35.80: 617 35.80 - 53.70: 97 53.70 - 71.60: 33 71.60 - 89.50: 22 Dihedral angle restraints: 9105 sinusoidal: 3507 harmonic: 5598 Sorted by residual: dihedral pdb=" C LYS J 208 " pdb=" N LYS J 208 " pdb=" CA LYS J 208 " pdb=" CB LYS J 208 " ideal model delta harmonic sigma weight residual -122.60 -137.80 15.20 0 2.50e+00 1.60e-01 3.70e+01 dihedral pdb=" CA VAL I 149 " pdb=" C VAL I 149 " pdb=" N LYS I 150 " pdb=" CA LYS I 150 " ideal model delta harmonic sigma weight residual -180.00 -150.52 -29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLU J 155 " pdb=" C GLU J 155 " pdb=" N PRO J 156 " pdb=" CA PRO J 156 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1673 0.098 - 0.197: 627 0.197 - 0.295: 79 0.295 - 0.394: 13 0.394 - 0.492: 4 Chirality restraints: 2396 Sorted by residual: chirality pdb=" CA LYS J 208 " pdb=" N LYS J 208 " pdb=" C LYS J 208 " pdb=" CB LYS J 208 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA ASP F 90 " pdb=" N ASP F 90 " pdb=" C ASP F 90 " pdb=" CB ASP F 90 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CA ASP D 90 " pdb=" N ASP D 90 " pdb=" C ASP D 90 " pdb=" CB ASP D 90 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 2393 not shown) Planarity restraints: 2606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 96 " 0.137 2.00e-02 2.50e+03 8.08e-02 1.63e+02 pdb=" CG TRP E 96 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP E 96 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP E 96 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP E 96 " -0.074 2.00e-02 2.50e+03 pdb=" CE2 TRP E 96 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 96 " -0.110 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 96 " 0.104 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 96 " -0.063 2.00e-02 2.50e+03 pdb=" CH2 TRP E 96 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 96 " -0.130 2.00e-02 2.50e+03 7.80e-02 1.52e+02 pdb=" CG TRP C 96 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP C 96 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP C 96 " 0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP C 96 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP C 96 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 96 " 0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 96 " -0.099 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 96 " 0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP C 96 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 282 " 0.155 2.00e-02 2.50e+03 8.15e-02 1.33e+02 pdb=" CG TYR B 282 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 282 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR B 282 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR B 282 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR B 282 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 282 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 282 " 0.114 2.00e-02 2.50e+03 ... (remaining 2603 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 7399 3.01 - 3.49: 14896 3.49 - 3.96: 23826 3.96 - 4.43: 26734 4.43 - 4.90: 45260 Nonbonded interactions: 118115 Sorted by model distance: nonbonded pdb=" O LYS J 150 " pdb=" OG SER J 184 " model vdw 2.543 2.440 nonbonded pdb=" OG SER E 49 " pdb=" OE2 GLU E 55 " model vdw 2.548 2.440 nonbonded pdb=" O LEU B 595 " pdb=" CA ASN B 596 " model vdw 2.548 2.776 nonbonded pdb=" OG SER L 204 " pdb=" OD1 ASP L 207 " model vdw 2.559 2.440 nonbonded pdb=" OG SER A 187 " pdb=" OE1 GLU A 190 " model vdw 2.563 2.440 ... (remaining 118110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.350 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 42.430 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.012 0.044 15372 Z= 0.797 Angle : 1.877 35.419 20842 Z= 1.261 Chirality : 0.097 0.492 2396 Planarity : 0.015 0.141 2606 Dihedral : 13.834 89.496 5480 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.11 % Favored : 95.63 % Rotamer: Outliers : 1.85 % Allowed : 6.63 % Favored : 91.52 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 4.76 % 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: -1.26 (0.17), residues: 1900 helix: -0.91 (0.17), residues: 674 sheet: 0.33 (0.26), residues: 362 loop : -1.20 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.137 0.022 TRP E 96 HIS 0.014 0.004 HIS L 220 PHE 0.078 0.012 PHE I 153 TYR 0.155 0.024 TYR B 282 ARG 0.009 0.001 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 470 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 496 average time/residue: 1.0802 time to fit residues: 598.5519 Evaluate side-chains 345 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 332 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 2 average time/residue: 0.2818 time to fit residues: 2.9432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 170 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN A 155 HIS A 425 ASN A 437 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 425 ASN B 437 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 169 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15372 Z= 0.209 Angle : 0.720 11.116 20842 Z= 0.373 Chirality : 0.044 0.181 2396 Planarity : 0.005 0.037 2606 Dihedral : 5.892 27.333 2070 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.05 % Favored : 97.74 % Rotamer: Outliers : 5.32 % Allowed : 15.89 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.35 (0.19), residues: 1900 helix: 1.19 (0.20), residues: 688 sheet: 0.34 (0.26), residues: 398 loop : -0.59 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 564 HIS 0.008 0.001 HIS B 155 PHE 0.042 0.002 PHE B 293 TYR 0.022 0.002 TYR F 100 ARG 0.006 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 346 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 29 residues processed: 383 average time/residue: 1.0060 time to fit residues: 434.2593 Evaluate side-chains 333 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 304 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 14 residues processed: 16 average time/residue: 0.1889 time to fit residues: 7.2140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 0.0060 overall best weight: 1.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 398 GLN A 582 GLN A 583 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 398 GLN B 582 GLN B 583 HIS B 601 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15372 Z= 0.309 Angle : 0.716 10.590 20842 Z= 0.363 Chirality : 0.045 0.174 2396 Planarity : 0.005 0.055 2606 Dihedral : 5.531 29.296 2070 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.79 % Rotamer: Outliers : 5.68 % Allowed : 16.37 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.40 (0.20), residues: 1900 helix: 1.39 (0.20), residues: 672 sheet: 0.36 (0.25), residues: 406 loop : -0.69 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 379 HIS 0.007 0.002 HIS B 155 PHE 0.041 0.002 PHE B 293 TYR 0.018 0.002 TYR A 342 ARG 0.005 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 309 time to evaluate : 1.879 Fit side-chains revert: symmetry clash outliers start: 95 outliers final: 54 residues processed: 362 average time/residue: 1.0646 time to fit residues: 433.1405 Evaluate side-chains 347 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 293 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 34 residues processed: 22 average time/residue: 0.2799 time to fit residues: 11.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS B 76 ASN B 155 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS ** K 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 15372 Z= 0.362 Angle : 0.739 8.544 20842 Z= 0.373 Chirality : 0.045 0.196 2396 Planarity : 0.005 0.047 2606 Dihedral : 5.514 30.076 2070 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.89 % Favored : 96.00 % Rotamer: Outliers : 6.81 % Allowed : 17.98 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.14 (0.19), residues: 1900 helix: 1.23 (0.20), residues: 684 sheet: 0.07 (0.25), residues: 422 loop : -0.85 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 379 HIS 0.008 0.002 HIS I 171 PHE 0.043 0.002 PHE A 293 TYR 0.021 0.002 TYR A 342 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 302 time to evaluate : 1.756 Fit side-chains outliers start: 114 outliers final: 61 residues processed: 374 average time/residue: 1.0254 time to fit residues: 431.8892 Evaluate side-chains 343 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 282 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 47 residues processed: 17 average time/residue: 0.2011 time to fit residues: 7.7247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 283 HIS A 398 GLN B 155 HIS B 283 HIS B 601 ASN C 89 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN L 169 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15372 Z= 0.442 Angle : 0.776 10.813 20842 Z= 0.392 Chirality : 0.047 0.221 2396 Planarity : 0.005 0.052 2606 Dihedral : 5.649 30.307 2070 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 7.71 % Allowed : 19.06 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.07 (0.19), residues: 1900 helix: 1.06 (0.20), residues: 686 sheet: -0.04 (0.24), residues: 422 loop : -0.99 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 170 HIS 0.008 0.002 HIS A 155 PHE 0.044 0.002 PHE A 293 TYR 0.022 0.003 TYR A 342 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 287 time to evaluate : 1.675 Fit side-chains revert: symmetry clash outliers start: 129 outliers final: 75 residues processed: 370 average time/residue: 1.0378 time to fit residues: 432.0642 Evaluate side-chains 356 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 281 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 53 residues processed: 22 average time/residue: 0.4569 time to fit residues: 15.2189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN B 116 ASN B 601 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15372 Z= 0.209 Angle : 0.669 10.989 20842 Z= 0.335 Chirality : 0.042 0.212 2396 Planarity : 0.004 0.047 2606 Dihedral : 5.037 28.294 2070 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.74 % Rotamer: Outliers : 5.68 % Allowed : 21.62 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.33 (0.20), residues: 1900 helix: 1.49 (0.20), residues: 686 sheet: 0.16 (0.24), residues: 416 loop : -0.83 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 35 HIS 0.013 0.001 HIS A 155 PHE 0.046 0.002 PHE A 293 TYR 0.021 0.001 TYR B 342 ARG 0.006 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 286 time to evaluate : 1.710 Fit side-chains outliers start: 95 outliers final: 61 residues processed: 360 average time/residue: 0.9532 time to fit residues: 388.5539 Evaluate side-chains 334 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 273 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 50 residues processed: 11 average time/residue: 0.4850 time to fit residues: 9.0310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 132 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15372 Z= 0.202 Angle : 0.659 10.356 20842 Z= 0.327 Chirality : 0.042 0.211 2396 Planarity : 0.004 0.047 2606 Dihedral : 4.765 26.449 2070 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.58 % Rotamer: Outliers : 5.02 % Allowed : 22.94 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.42 (0.20), residues: 1900 helix: 1.55 (0.20), residues: 684 sheet: 0.12 (0.24), residues: 426 loop : -0.71 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 35 HIS 0.005 0.001 HIS B 155 PHE 0.046 0.002 PHE A 293 TYR 0.020 0.001 TYR A 342 ARG 0.007 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 289 time to evaluate : 1.846 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 61 residues processed: 350 average time/residue: 1.0176 time to fit residues: 403.7726 Evaluate side-chains 343 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 282 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 45 residues processed: 16 average time/residue: 0.4652 time to fit residues: 11.7636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15372 Z= 0.363 Angle : 0.729 10.775 20842 Z= 0.364 Chirality : 0.045 0.204 2396 Planarity : 0.005 0.049 2606 Dihedral : 5.093 27.254 2070 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 4.90 % Allowed : 24.31 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.16 (0.19), residues: 1900 helix: 1.33 (0.20), residues: 684 sheet: 0.06 (0.24), residues: 436 loop : -0.92 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 379 HIS 0.007 0.002 HIS B 155 PHE 0.044 0.002 PHE A 293 TYR 0.019 0.002 TYR B 342 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 285 time to evaluate : 1.762 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 57 residues processed: 343 average time/residue: 1.0246 time to fit residues: 395.8168 Evaluate side-chains 340 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 283 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 44 residues processed: 13 average time/residue: 0.3487 time to fit residues: 8.4359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS C 31 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15372 Z= 0.211 Angle : 0.675 11.522 20842 Z= 0.332 Chirality : 0.042 0.205 2396 Planarity : 0.004 0.047 2606 Dihedral : 4.738 25.830 2070 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.52 % Allowed : 25.45 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.46 (0.19), residues: 1900 helix: 1.64 (0.20), residues: 678 sheet: 0.13 (0.24), residues: 426 loop : -0.73 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 35 HIS 0.008 0.001 HIS B 155 PHE 0.046 0.002 PHE A 293 TYR 0.015 0.001 TYR B 342 ARG 0.007 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 280 time to evaluate : 1.776 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 50 residues processed: 332 average time/residue: 1.0277 time to fit residues: 384.1806 Evaluate side-chains 325 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 275 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 4 average time/residue: 0.6002 time to fit residues: 5.2330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 187 optimal weight: 0.0970 chunk 172 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS C 31 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15372 Z= 0.188 Angle : 0.657 10.969 20842 Z= 0.324 Chirality : 0.041 0.179 2396 Planarity : 0.004 0.046 2606 Dihedral : 4.523 24.511 2070 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.11 % Rotamer: Outliers : 3.17 % Allowed : 26.22 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.20), residues: 1900 helix: 1.75 (0.21), residues: 678 sheet: 0.18 (0.24), residues: 428 loop : -0.60 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 35 HIS 0.009 0.001 HIS A 155 PHE 0.045 0.001 PHE A 293 TYR 0.021 0.001 TYR B 342 ARG 0.006 0.000 ARG C 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 286 time to evaluate : 1.787 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 47 residues processed: 335 average time/residue: 0.9922 time to fit residues: 377.0119 Evaluate side-chains 320 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 273 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 44 residues processed: 3 average time/residue: 0.3198 time to fit residues: 3.8029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.0970 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS C 31 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.138844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111676 restraints weight = 25887.667| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.48 r_work: 0.3430 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15372 Z= 0.210 Angle : 0.664 10.941 20842 Z= 0.326 Chirality : 0.042 0.191 2396 Planarity : 0.004 0.047 2606 Dihedral : 4.522 24.058 2070 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.89 % Favored : 96.00 % Rotamer: Outliers : 3.05 % Allowed : 26.76 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.60 (0.20), residues: 1900 helix: 1.71 (0.20), residues: 682 sheet: 0.17 (0.24), residues: 430 loop : -0.58 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.008 0.001 HIS A 155 PHE 0.045 0.002 PHE A 293 TYR 0.013 0.001 TYR I 152 ARG 0.008 0.000 ARG E 18 =============================================================================== Job complete usr+sys time: 6950.62 seconds wall clock time: 123 minutes 34.44 seconds (7414.44 seconds total)