Starting phenix.real_space_refine on Fri May 16 15:10:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u2c_41845/05_2025/8u2c_41845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u2c_41845/05_2025/8u2c_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/cci-nas-00/data/ceres_data/8u2c_41845/05_2025/8u2c_41845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u2c_41845/05_2025/8u2c_41845.map" model { file = "/net/cci-nas-00/data/ceres_data/8u2c_41845/05_2025/8u2c_41845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u2c_41845/05_2025/8u2c_41845.cif" } 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. Time to flip 67 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.79, per 1000 atoms: 0.58 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 - 3.00 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 Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.9 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: 1.95 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: 5.36 Time building geometry restraints manager: 4.04 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: 0.00 - 7.08: 20823 7.08 - 14.17: 16 14.17 - 21.25: 1 21.25 - 28.34: 0 28.34 - 35.42: 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 3.040 nonbonded pdb=" OG SER E 49 " pdb=" OE2 GLU E 55 " model vdw 2.548 3.040 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 3.040 nonbonded pdb=" OG SER A 187 " pdb=" OE1 GLU A 190 " model vdw 2.563 3.040 ... (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 Time spend for trying shortcut: 0.01 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: 1.390 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.460 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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:10.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.670 ------------------------------------------------------------------------------- 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 15383 Z= 0.740 Angle : 1.877 35.419 20864 Z= 1.260 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 Details of bonding type rmsd hydrogen bonds : bond 0.18204 ( 721) hydrogen bonds : angle 7.25030 ( 2115) SS BOND : bond 0.01442 ( 11) SS BOND : angle 1.63238 ( 22) covalent geometry : bond 0.01231 (15372) covalent geometry : angle 1.87700 (20842) *********************** 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 to be fit. rotamer outliers: 31 poor density : 470 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6328 (mtp) cc_final: 0.5983 (mmm) REVERT: A 193 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7773 (mtp85) REVERT: A 292 ASP cc_start: 0.7308 (m-30) cc_final: 0.6967 (m-30) REVERT: A 342 TYR cc_start: 0.7617 (t80) cc_final: 0.7281 (t80) REVERT: A 343 LYS cc_start: 0.7031 (mmtt) cc_final: 0.6498 (mtmm) REVERT: A 345 THR cc_start: 0.8355 (m) cc_final: 0.8057 (p) REVERT: A 509 MET cc_start: 0.8967 (ttt) cc_final: 0.8735 (ttm) REVERT: A 510 MET cc_start: 0.8841 (ttm) cc_final: 0.8623 (ttm) REVERT: A 548 MET cc_start: 0.8970 (mtt) cc_final: 0.8688 (mtt) REVERT: B 152 MET cc_start: 0.6348 (mtp) cc_final: 0.5841 (mmm) REVERT: B 163 ARG cc_start: 0.6610 (mtt180) cc_final: 0.6356 (ttp-110) REVERT: B 510 MET cc_start: 0.8760 (ttm) cc_final: 0.8531 (ttm) REVERT: B 548 MET cc_start: 0.8917 (mtt) cc_final: 0.8623 (mtt) REVERT: D 5 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7235 (tp40) REVERT: E 107 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5492 (tpp80) REVERT: F 5 GLN cc_start: 0.7566 (tp-100) cc_final: 0.7189 (tp40) outliers start: 31 outliers final: 13 residues processed: 496 average time/residue: 1.0281 time to fit residues: 570.1739 Evaluate side-chains 349 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 335 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain I residue 156 PRO Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain J residue 173 PHE Chi-restraints excluded: chain L residue 189 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.139738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.112392 restraints weight = 25913.342| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.50 r_work: 0.3440 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15383 Z= 0.152 Angle : 0.725 9.432 20864 Z= 0.379 Chirality : 0.044 0.180 2396 Planarity : 0.005 0.037 2606 Dihedral : 6.730 55.487 2105 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.11 % Favored : 97.68 % Rotamer: Outliers : 4.90 % Allowed : 15.83 % Favored : 79.27 % 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: 0.34 (0.19), residues: 1900 helix: 1.16 (0.20), residues: 688 sheet: 0.34 (0.26), residues: 394 loop : -0.58 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 564 HIS 0.008 0.001 HIS A 155 PHE 0.040 0.002 PHE B 293 TYR 0.022 0.002 TYR F 100 ARG 0.007 0.001 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 721) hydrogen bonds : angle 5.10095 ( 2115) SS BOND : bond 0.00577 ( 11) SS BOND : angle 1.15620 ( 22) covalent geometry : bond 0.00326 (15372) covalent geometry : angle 0.72405 (20842) *********************** 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 429 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 347 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7603 (m) REVERT: A 152 MET cc_start: 0.6648 (mtp) cc_final: 0.6080 (mmm) REVERT: A 163 ARG cc_start: 0.6633 (ttp-110) cc_final: 0.6261 (mtt90) REVERT: A 193 ARG cc_start: 0.8472 (mtt-85) cc_final: 0.8206 (mtt-85) REVERT: B 152 MET cc_start: 0.6640 (mtp) cc_final: 0.6056 (mmm) REVERT: B 342 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7624 (t80) REVERT: C 8 PRO cc_start: 0.7600 (Cg_endo) cc_final: 0.7316 (Cg_exo) REVERT: D 84 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8097 (mtt90) REVERT: E 8 PRO cc_start: 0.7475 (Cg_endo) cc_final: 0.7248 (Cg_exo) REVERT: E 107 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5667 (tpp80) REVERT: I 171 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7414 (t-90) REVERT: I 188 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8439 (m) REVERT: K 202 THR cc_start: 0.8679 (t) cc_final: 0.8431 (t) REVERT: J 171 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.7525 (t-90) REVERT: J 205 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8543 (t) outliers start: 82 outliers final: 24 residues processed: 380 average time/residue: 0.9762 time to fit residues: 418.7208 Evaluate side-chains 332 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain K residue 180 ASN Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain L residue 204 SER Chi-restraints excluded: chain L residue 231 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 68 optimal weight: 0.0770 chunk 60 optimal weight: 0.0270 chunk 149 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 398 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 398 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 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.140887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.113678 restraints weight = 25815.379| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.48 r_work: 0.3461 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15383 Z= 0.123 Angle : 0.650 8.337 20864 Z= 0.332 Chirality : 0.042 0.179 2396 Planarity : 0.004 0.041 2606 Dihedral : 5.454 58.810 2080 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 4.66 % Allowed : 17.50 % Favored : 77.84 % 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: 0.67 (0.20), residues: 1900 helix: 1.55 (0.20), residues: 688 sheet: 0.53 (0.26), residues: 392 loop : -0.50 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.007 0.001 HIS A 155 PHE 0.042 0.001 PHE B 293 TYR 0.022 0.001 TYR A 342 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 721) hydrogen bonds : angle 4.60827 ( 2115) SS BOND : bond 0.00474 ( 11) SS BOND : angle 0.97389 ( 22) covalent geometry : bond 0.00261 (15372) covalent geometry : angle 0.64912 (20842) *********************** 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 394 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 316 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.6709 (mtp) cc_final: 0.6160 (mpt) REVERT: A 193 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.8232 (mtt-85) REVERT: B 152 MET cc_start: 0.6712 (mtp) cc_final: 0.6155 (mpt) REVERT: B 383 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7880 (ttm-80) REVERT: C 24 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8548 (tptt) REVERT: C 70 ASP cc_start: 0.8334 (m-30) cc_final: 0.8132 (m-30) REVERT: C 82 ASP cc_start: 0.7797 (m-30) cc_final: 0.7557 (m-30) REVERT: E 24 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8513 (tptt) REVERT: E 107 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5498 (tpp80) REVERT: F 5 GLN cc_start: 0.8267 (tp40) cc_final: 0.8037 (tp40) REVERT: I 155 GLU cc_start: 0.5397 (tt0) cc_final: 0.5150 (tt0) REVERT: I 171 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7364 (t-90) REVERT: I 188 VAL cc_start: 0.8755 (t) cc_final: 0.8435 (m) REVERT: I 202 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7969 (tp) REVERT: I 204 ASN cc_start: 0.7168 (p0) cc_final: 0.6967 (p0) REVERT: I 215 ASP cc_start: 0.8944 (p0) cc_final: 0.8743 (p0) REVERT: I 216 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6676 (mmtm) REVERT: K 202 THR cc_start: 0.8813 (t) cc_final: 0.7759 (t) REVERT: K 217 GLU cc_start: 0.7374 (pt0) cc_final: 0.6955 (pm20) REVERT: J 171 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7336 (t-90) REVERT: J 188 VAL cc_start: 0.8756 (t) cc_final: 0.8432 (m) REVERT: J 202 ILE cc_start: 0.8062 (tt) cc_final: 0.7850 (tp) REVERT: J 215 ASP cc_start: 0.8922 (p0) cc_final: 0.8721 (p0) outliers start: 78 outliers final: 31 residues processed: 357 average time/residue: 1.0460 time to fit residues: 418.5395 Evaluate side-chains 327 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 383 ARG Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 204 SER Chi-restraints excluded: chain L residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 155 HIS A 582 GLN A 583 HIS B 76 ASN B 155 HIS 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.137474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110267 restraints weight = 25925.119| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.48 r_work: 0.3409 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15383 Z= 0.182 Angle : 0.683 9.088 20864 Z= 0.346 Chirality : 0.044 0.187 2396 Planarity : 0.005 0.053 2606 Dihedral : 5.470 59.212 2080 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 5.44 % Allowed : 18.64 % Favored : 75.93 % 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 (0.19), residues: 1900 helix: 1.58 (0.20), residues: 670 sheet: 0.48 (0.25), residues: 396 loop : -0.58 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 379 HIS 0.007 0.001 HIS B 155 PHE 0.041 0.002 PHE A 293 TYR 0.021 0.002 TYR A 342 ARG 0.007 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 721) hydrogen bonds : angle 4.59428 ( 2115) SS BOND : bond 0.00614 ( 11) SS BOND : angle 1.22921 ( 22) covalent geometry : bond 0.00439 (15372) covalent geometry : angle 0.68233 (20842) *********************** 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 396 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 305 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6613 (mtp) cc_final: 0.6130 (mpp) REVERT: A 193 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8232 (mtt-85) REVERT: A 653 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7891 (mptp) REVERT: B 152 MET cc_start: 0.6607 (mtp) cc_final: 0.6130 (mpp) REVERT: B 383 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7901 (ttm-80) REVERT: E 107 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.5626 (tmm-80) REVERT: I 152 TYR cc_start: 0.8113 (p90) cc_final: 0.7906 (p90) REVERT: I 171 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7483 (t-90) REVERT: I 202 ILE cc_start: 0.8262 (tt) cc_final: 0.8038 (tp) REVERT: I 204 ASN cc_start: 0.7298 (p0) cc_final: 0.7081 (p0) REVERT: I 215 ASP cc_start: 0.9022 (p0) cc_final: 0.8757 (p0) REVERT: I 216 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6975 (mmtm) REVERT: K 217 GLU cc_start: 0.7392 (pt0) cc_final: 0.7018 (pm20) REVERT: J 171 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7478 (t-90) REVERT: J 202 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8028 (tp) REVERT: J 205 VAL cc_start: 0.8665 (p) cc_final: 0.8462 (m) REVERT: J 215 ASP cc_start: 0.8972 (p0) cc_final: 0.8636 (p0) outliers start: 91 outliers final: 50 residues processed: 359 average time/residue: 0.9921 time to fit residues: 400.6100 Evaluate side-chains 345 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 383 ARG Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 204 SER Chi-restraints excluded: chain L residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 155 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 63 optimal weight: 0.0370 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 155 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111842 restraints weight = 25954.289| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.50 r_work: 0.3432 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15383 Z= 0.131 Angle : 0.634 9.565 20864 Z= 0.321 Chirality : 0.042 0.172 2396 Planarity : 0.004 0.052 2606 Dihedral : 5.191 58.712 2080 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer: Outliers : 4.84 % Allowed : 20.31 % Favored : 74.85 % 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: 0.65 (0.19), residues: 1900 helix: 1.67 (0.20), residues: 670 sheet: 0.38 (0.25), residues: 426 loop : -0.55 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 35 HIS 0.007 0.001 HIS B 155 PHE 0.044 0.002 PHE A 293 TYR 0.020 0.001 TYR B 342 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 721) hydrogen bonds : angle 4.41464 ( 2115) SS BOND : bond 0.00470 ( 11) SS BOND : angle 1.01462 ( 22) covalent geometry : bond 0.00302 (15372) covalent geometry : angle 0.63335 (20842) *********************** 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 381 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.6485 (mtp) cc_final: 0.6004 (mpp) REVERT: A 166 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6381 (mm110) REVERT: A 193 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.8198 (mtt-85) REVERT: A 263 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7195 (mmm-85) REVERT: B 152 MET cc_start: 0.6557 (mtp) cc_final: 0.6014 (mpp) REVERT: B 166 GLN cc_start: 0.6932 (tp-100) cc_final: 0.6359 (mm110) REVERT: B 222 ASN cc_start: 0.8456 (t0) cc_final: 0.7844 (t0) REVERT: B 383 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7887 (ttm-80) REVERT: B 653 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7966 (mptp) REVERT: E 78 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6009 (pt) REVERT: E 107 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5419 (tmm-80) REVERT: I 152 TYR cc_start: 0.8071 (p90) cc_final: 0.7790 (p90) REVERT: I 171 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7351 (t-90) REVERT: I 188 VAL cc_start: 0.8697 (t) cc_final: 0.8368 (m) REVERT: I 215 ASP cc_start: 0.9077 (p0) cc_final: 0.8788 (p0) REVERT: I 216 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6984 (mmtm) REVERT: K 130 ARG cc_start: 0.5276 (OUTLIER) cc_final: 0.4830 (tmm160) REVERT: K 217 GLU cc_start: 0.7405 (pt0) cc_final: 0.6949 (pm20) REVERT: J 171 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7443 (t-90) REVERT: L 217 GLU cc_start: 0.7977 (tt0) cc_final: 0.7677 (tp30) outliers start: 81 outliers final: 43 residues processed: 347 average time/residue: 1.0363 time to fit residues: 402.8985 Evaluate side-chains 338 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 383 ARG Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 203 CYS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 204 SER Chi-restraints excluded: chain L residue 231 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS D 5 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.136956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109703 restraints weight = 25995.480| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.49 r_work: 0.3400 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15383 Z= 0.191 Angle : 0.702 10.941 20864 Z= 0.354 Chirality : 0.044 0.180 2396 Planarity : 0.005 0.049 2606 Dihedral : 5.309 57.578 2076 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.05 % Rotamer: Outliers : 5.44 % Allowed : 21.15 % Favored : 73.42 % 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 (0.19), residues: 1900 helix: 1.44 (0.20), residues: 684 sheet: 0.21 (0.25), residues: 412 loop : -0.68 (0.22), residues: 804 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 0.043 0.002 PHE A 293 TYR 0.017 0.002 TYR A 342 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 721) hydrogen bonds : angle 4.47615 ( 2115) SS BOND : bond 0.00666 ( 11) SS BOND : angle 1.34651 ( 22) covalent geometry : bond 0.00461 (15372) covalent geometry : angle 0.70095 (20842) *********************** 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 382 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 291 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.6585 (mtp) cc_final: 0.6126 (mmm) REVERT: A 154 ASN cc_start: 0.6245 (p0) cc_final: 0.5772 (p0) REVERT: A 166 GLN cc_start: 0.6975 (tp-100) cc_final: 0.6367 (mm110) REVERT: A 193 ARG cc_start: 0.8537 (mtt-85) cc_final: 0.8226 (mtt-85) REVERT: A 329 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7895 (mm) REVERT: B 152 MET cc_start: 0.6567 (mtp) cc_final: 0.6080 (mpp) REVERT: B 154 ASN cc_start: 0.6245 (p0) cc_final: 0.5772 (p0) REVERT: B 166 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6378 (mm110) REVERT: B 222 ASN cc_start: 0.8474 (t0) cc_final: 0.7877 (t0) REVERT: B 383 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7908 (ttm-80) REVERT: B 653 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7939 (mptp) REVERT: D 44 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8098 (mmtm) REVERT: E 107 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.5878 (tmm-80) REVERT: F 5 GLN cc_start: 0.8309 (tp40) cc_final: 0.8051 (tp40) REVERT: I 171 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7520 (t-90) REVERT: I 215 ASP cc_start: 0.9042 (p0) cc_final: 0.8675 (p0) REVERT: K 130 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5000 (tmm160) REVERT: K 217 GLU cc_start: 0.7379 (pt0) cc_final: 0.6932 (pm20) REVERT: J 171 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7543 (t-90) REVERT: L 217 GLU cc_start: 0.8008 (tt0) cc_final: 0.7746 (tp30) outliers start: 91 outliers final: 59 residues processed: 345 average time/residue: 1.0037 time to fit residues: 390.2598 Evaluate side-chains 355 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 383 ARG Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 203 CYS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 204 SER Chi-restraints excluded: chain L residue 231 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 116 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 109 optimal weight: 0.3980 chunk 150 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 112 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.140136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112936 restraints weight = 26225.065| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.50 r_work: 0.3455 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15383 Z= 0.120 Angle : 0.642 13.533 20864 Z= 0.322 Chirality : 0.041 0.201 2396 Planarity : 0.004 0.049 2606 Dihedral : 4.916 56.799 2076 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.11 % Rotamer: Outliers : 4.18 % Allowed : 22.70 % Favored : 73.12 % 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: 0.67 (0.19), residues: 1900 helix: 1.75 (0.20), residues: 676 sheet: 0.28 (0.24), residues: 430 loop : -0.56 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 35 HIS 0.007 0.001 HIS B 155 PHE 0.046 0.001 PHE A 293 TYR 0.023 0.001 TYR B 342 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 721) hydrogen bonds : angle 4.25791 ( 2115) SS BOND : bond 0.00418 ( 11) SS BOND : angle 0.98727 ( 22) covalent geometry : bond 0.00273 (15372) covalent geometry : angle 0.64177 (20842) *********************** 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 374 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 304 time to evaluate : 1.878 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.6442 (mtp) cc_final: 0.5938 (mmm) REVERT: A 154 ASN cc_start: 0.6131 (p0) cc_final: 0.5702 (p0) REVERT: A 166 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6504 (tp40) REVERT: A 193 ARG cc_start: 0.8449 (mtt-85) cc_final: 0.8205 (mtt-85) REVERT: B 152 MET cc_start: 0.6524 (mtp) cc_final: 0.5949 (mmm) REVERT: B 154 ASN cc_start: 0.6141 (p0) cc_final: 0.5709 (p0) REVERT: B 166 GLN cc_start: 0.6957 (tp-100) cc_final: 0.6513 (tp40) REVERT: B 222 ASN cc_start: 0.8501 (t0) cc_final: 0.7833 (t0) REVERT: B 653 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7961 (mptp) REVERT: D 44 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8102 (mmtm) REVERT: E 107 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5449 (tmm-80) REVERT: I 152 TYR cc_start: 0.8129 (p90) cc_final: 0.7795 (p90) REVERT: I 157 VAL cc_start: 0.6712 (p) cc_final: 0.6380 (p) REVERT: I 171 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7360 (t-90) REVERT: I 188 VAL cc_start: 0.8733 (t) cc_final: 0.8459 (m) REVERT: I 215 ASP cc_start: 0.9027 (p0) cc_final: 0.8668 (p0) REVERT: K 130 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4543 (tmm160) REVERT: K 217 GLU cc_start: 0.7355 (pt0) cc_final: 0.6868 (pm20) REVERT: J 171 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7425 (t-90) REVERT: J 188 VAL cc_start: 0.8710 (t) cc_final: 0.8448 (m) REVERT: L 217 GLU cc_start: 0.7983 (tt0) cc_final: 0.7660 (tp30) outliers start: 70 outliers final: 44 residues processed: 344 average time/residue: 0.9710 time to fit residues: 376.2876 Evaluate side-chains 335 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 203 CYS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 138 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 283 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.140354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113258 restraints weight = 25800.908| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.48 r_work: 0.3453 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15383 Z= 0.120 Angle : 0.640 12.838 20864 Z= 0.319 Chirality : 0.041 0.189 2396 Planarity : 0.004 0.051 2606 Dihedral : 4.775 55.032 2076 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.84 % Rotamer: Outliers : 3.52 % Allowed : 24.13 % Favored : 72.34 % 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: 0.73 (0.19), residues: 1900 helix: 1.82 (0.20), residues: 678 sheet: 0.30 (0.24), residues: 426 loop : -0.53 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 170 HIS 0.007 0.001 HIS B 155 PHE 0.044 0.002 PHE A 293 TYR 0.020 0.001 TYR A 342 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 721) hydrogen bonds : angle 4.17208 ( 2115) SS BOND : bond 0.00463 ( 11) SS BOND : angle 1.03608 ( 22) covalent geometry : bond 0.00276 (15372) covalent geometry : angle 0.63929 (20842) *********************** 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 357 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 298 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6380 (mtp) cc_final: 0.5967 (mmm) REVERT: A 154 ASN cc_start: 0.6037 (p0) cc_final: 0.5635 (p0) REVERT: A 166 GLN cc_start: 0.6947 (tp-100) cc_final: 0.6509 (tp40) REVERT: A 198 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8413 (mpp) REVERT: A 263 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.7178 (mmm-85) REVERT: A 329 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7818 (mm) REVERT: B 152 MET cc_start: 0.6450 (mtp) cc_final: 0.5971 (mmm) REVERT: B 166 GLN cc_start: 0.6952 (tp-100) cc_final: 0.6507 (tp40) REVERT: B 190 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: B 222 ASN cc_start: 0.8384 (t0) cc_final: 0.7837 (t0) REVERT: B 265 MET cc_start: 0.8841 (mmt) cc_final: 0.8624 (mmm) REVERT: B 653 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7957 (mptp) REVERT: D 44 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8126 (mmtm) REVERT: E 107 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.5568 (tmm-80) REVERT: I 152 TYR cc_start: 0.8103 (p90) cc_final: 0.7768 (p90) REVERT: I 171 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7331 (t-90) REVERT: I 188 VAL cc_start: 0.8634 (t) cc_final: 0.8361 (m) REVERT: I 215 ASP cc_start: 0.9013 (p0) cc_final: 0.8658 (p0) REVERT: K 130 ARG cc_start: 0.5153 (OUTLIER) cc_final: 0.4462 (tmm160) REVERT: K 217 GLU cc_start: 0.7381 (pt0) cc_final: 0.6875 (pm20) REVERT: J 171 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7398 (t-90) REVERT: J 188 VAL cc_start: 0.8608 (t) cc_final: 0.8344 (m) REVERT: L 217 GLU cc_start: 0.7995 (tt0) cc_final: 0.7586 (tp30) outliers start: 59 outliers final: 39 residues processed: 331 average time/residue: 0.9931 time to fit residues: 368.7958 Evaluate side-chains 335 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 203 CYS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 37 optimal weight: 0.0570 chunk 153 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.140113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112968 restraints weight = 25754.885| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.49 r_work: 0.3449 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15383 Z= 0.125 Angle : 0.647 12.139 20864 Z= 0.322 Chirality : 0.041 0.187 2396 Planarity : 0.004 0.051 2606 Dihedral : 4.745 54.081 2076 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.84 % Rotamer: Outliers : 3.29 % Allowed : 24.61 % Favored : 72.10 % 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: 0.78 (0.19), residues: 1900 helix: 1.81 (0.20), residues: 680 sheet: 0.36 (0.24), residues: 426 loop : -0.48 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.007 0.001 HIS B 155 PHE 0.044 0.002 PHE B 293 TYR 0.018 0.001 TYR B 342 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 721) hydrogen bonds : angle 4.16316 ( 2115) SS BOND : bond 0.00498 ( 11) SS BOND : angle 1.15319 ( 22) covalent geometry : bond 0.00295 (15372) covalent geometry : angle 0.64651 (20842) *********************** 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 351 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 296 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6391 (mtp) cc_final: 0.5984 (mmm) REVERT: A 166 GLN cc_start: 0.7108 (tp-100) cc_final: 0.6670 (tp40) REVERT: A 263 ARG cc_start: 0.7470 (mmm-85) cc_final: 0.7226 (mmm-85) REVERT: A 329 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7793 (mm) REVERT: B 152 MET cc_start: 0.6385 (mtp) cc_final: 0.5979 (mmm) REVERT: B 154 ASN cc_start: 0.6118 (p0) cc_final: 0.5649 (p0) REVERT: B 166 GLN cc_start: 0.7061 (tp-100) cc_final: 0.6601 (tp40) REVERT: B 222 ASN cc_start: 0.8403 (t0) cc_final: 0.7849 (t0) REVERT: B 653 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7952 (mptp) REVERT: D 44 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8123 (mmtm) REVERT: E 107 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.5745 (tmm-80) REVERT: I 152 TYR cc_start: 0.8049 (p90) cc_final: 0.7735 (p90) REVERT: I 155 GLU cc_start: 0.5423 (tt0) cc_final: 0.5127 (pt0) REVERT: I 171 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7389 (t-90) REVERT: I 188 VAL cc_start: 0.8625 (t) cc_final: 0.8366 (m) REVERT: K 130 ARG cc_start: 0.5203 (OUTLIER) cc_final: 0.4591 (tmm160) REVERT: K 217 GLU cc_start: 0.7405 (pt0) cc_final: 0.6859 (pm20) REVERT: J 171 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: J 188 VAL cc_start: 0.8601 (t) cc_final: 0.8365 (m) REVERT: L 217 GLU cc_start: 0.7993 (tt0) cc_final: 0.7555 (tp30) outliers start: 55 outliers final: 40 residues processed: 325 average time/residue: 1.0066 time to fit residues: 367.6277 Evaluate side-chains 333 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 203 CYS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 199 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 156 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 B 601 ASN C 89 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.109009 restraints weight = 25840.959| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.50 r_work: 0.3390 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15383 Z= 0.218 Angle : 0.742 11.883 20864 Z= 0.370 Chirality : 0.045 0.237 2396 Planarity : 0.005 0.050 2606 Dihedral : 5.166 53.596 2076 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 3.58 % Allowed : 24.37 % 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: 0.47 (0.19), residues: 1900 helix: 1.42 (0.20), residues: 686 sheet: 0.24 (0.24), residues: 426 loop : -0.57 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 170 HIS 0.008 0.002 HIS B 155 PHE 0.045 0.002 PHE A 293 TYR 0.022 0.002 TYR A 342 ARG 0.006 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 721) hydrogen bonds : angle 4.43940 ( 2115) SS BOND : bond 0.00643 ( 11) SS BOND : angle 1.50793 ( 22) covalent geometry : bond 0.00531 (15372) covalent geometry : angle 0.74109 (20842) ********************** 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 345 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 285 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.6509 (mtp) cc_final: 0.6033 (mpp) REVERT: A 154 ASN cc_start: 0.6283 (p0) cc_final: 0.5805 (p0) REVERT: A 166 GLN cc_start: 0.7066 (tp-100) cc_final: 0.6589 (tp40) REVERT: B 152 MET cc_start: 0.6478 (mtp) cc_final: 0.6002 (mpp) REVERT: B 154 ASN cc_start: 0.6273 (p0) cc_final: 0.5817 (p0) REVERT: B 166 GLN cc_start: 0.6982 (tp-100) cc_final: 0.6505 (tp40) REVERT: B 346 LYS cc_start: 0.7665 (tptt) cc_final: 0.7090 (tmtp) REVERT: B 653 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7987 (mptp) REVERT: D 44 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8143 (mmtm) REVERT: E 107 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.5807 (tmm-80) REVERT: I 155 GLU cc_start: 0.5433 (tt0) cc_final: 0.4742 (tt0) REVERT: I 157 VAL cc_start: 0.6667 (p) cc_final: 0.6382 (p) REVERT: K 130 ARG cc_start: 0.5387 (OUTLIER) cc_final: 0.4859 (tmm160) REVERT: J 171 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7521 (t-90) REVERT: L 217 GLU cc_start: 0.8015 (tt0) cc_final: 0.7606 (tp30) outliers start: 60 outliers final: 41 residues processed: 323 average time/residue: 1.0436 time to fit residues: 378.3763 Evaluate side-chains 328 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain I residue 203 CYS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain K residue 231 PHE Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 203 CYS Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 154 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 107 optimal weight: 0.0170 chunk 19 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 601 ASN C 89 GLN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.139370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112102 restraints weight = 25821.304| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.49 r_work: 0.3435 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15383 Z= 0.125 Angle : 0.668 11.607 20864 Z= 0.332 Chirality : 0.042 0.197 2396 Planarity : 0.004 0.049 2606 Dihedral : 4.831 52.683 2076 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 2.93 % Allowed : 25.09 % Favored : 71.98 % 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: 0.72 (0.19), residues: 1900 helix: 1.72 (0.20), residues: 680 sheet: 0.38 (0.24), residues: 432 loop : -0.51 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 35 HIS 0.008 0.001 HIS B 155 PHE 0.043 0.001 PHE A 293 TYR 0.021 0.001 TYR B 342 ARG 0.005 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 721) hydrogen bonds : angle 4.25656 ( 2115) SS BOND : bond 0.00454 ( 11) SS BOND : angle 1.07152 ( 22) covalent geometry : bond 0.00290 (15372) covalent geometry : angle 0.66789 (20842) =============================================================================== Job complete usr+sys time: 14510.56 seconds wall clock time: 250 minutes 38.48 seconds (15038.48 seconds total)