Starting phenix.real_space_refine on Tue Jul 29 07:38:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8im7_35572/07_2025/8im7_35572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8im7_35572/07_2025/8im7_35572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8im7_35572/07_2025/8im7_35572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8im7_35572/07_2025/8im7_35572.map" model { file = "/net/cci-nas-00/data/ceres_data/8im7_35572/07_2025/8im7_35572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8im7_35572/07_2025/8im7_35572.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 6941 2.51 5 N 1669 2.21 5 O 1937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10587 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2247 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 2 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.66, per 1000 atoms: 0.63 Number of scatterers: 10587 At special positions: 0 Unit cell: (109.79, 95.5173, 131.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 2 15.00 O 1937 8.00 N 1669 7.00 C 6941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 57.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.180A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.006A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.921A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.515A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.257A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.599A pdb=" N GLN A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.748A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.538A pdb=" N SER A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.983A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.870A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.721A pdb=" N ILE A 537 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.810A pdb=" N LEU A 546 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.572A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.724A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.697A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.588A pdb=" N LEU A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 104 Proline residue: B 88 - end of helix removed outlier: 4.047A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 155 removed outlier: 3.537A pdb=" N MET B 139 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 4.581A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 219 through 240 removed outlier: 3.599A pdb=" N TYR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.616A pdb=" N ALA B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.569A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.873A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 3.872A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.239A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.948A pdb=" N PHE C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 61 removed outlier: 4.233A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 96 removed outlier: 3.801A pdb=" N GLN C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 3.513A pdb=" N ALA C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 113 through 135 removed outlier: 3.606A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 184 removed outlier: 3.692A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 203 removed outlier: 3.601A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.750A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.900A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.541A pdb=" N GLY D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 81 removed outlier: 3.770A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.575A pdb=" N TYR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.822A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 212 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.552A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.504A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 3.540A pdb=" N VAL B 193 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 515 hydrogen bonds defined for protein. 1485 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: 3.38 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1749 1.32 - 1.45: 3002 1.45 - 1.57: 6043 1.57 - 1.69: 6 1.69 - 1.82: 58 Bond restraints: 10858 Sorted by residual: bond pdb=" N LEU B 435 " pdb=" CA LEU B 435 " ideal model delta sigma weight residual 1.462 1.491 -0.029 7.70e-03 1.69e+04 1.44e+01 bond pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.15e-02 7.56e+03 1.31e+01 bond pdb=" N VAL B 379 " pdb=" CA VAL B 379 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" C5 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.417 1.479 -0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.94e+00 ... (remaining 10853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 14170 2.40 - 4.80: 569 4.80 - 7.19: 51 7.19 - 9.59: 14 9.59 - 11.99: 2 Bond angle restraints: 14806 Sorted by residual: angle pdb=" N LYS B 80 " pdb=" CA LYS B 80 " pdb=" C LYS B 80 " ideal model delta sigma weight residual 113.97 108.11 5.86 1.28e+00 6.10e-01 2.10e+01 angle pdb=" N ASN C 207 " pdb=" CA ASN C 207 " pdb=" C ASN C 207 " ideal model delta sigma weight residual 109.81 119.23 -9.42 2.21e+00 2.05e-01 1.82e+01 angle pdb=" C VAL A 408 " pdb=" CA VAL A 408 " pdb=" CB VAL A 408 " ideal model delta sigma weight residual 110.13 113.76 -3.63 9.70e-01 1.06e+00 1.40e+01 angle pdb=" C ASN A 264 " pdb=" N THR A 265 " pdb=" CA THR A 265 " ideal model delta sigma weight residual 121.54 128.66 -7.12 1.91e+00 2.74e-01 1.39e+01 angle pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N PRO A 93 " ideal model delta sigma weight residual 117.93 121.90 -3.97 1.20e+00 6.94e-01 1.09e+01 ... (remaining 14801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 6404 22.35 - 44.71: 218 44.71 - 67.06: 51 67.06 - 89.41: 26 89.41 - 111.76: 18 Dihedral angle restraints: 6717 sinusoidal: 2954 harmonic: 3763 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -170.69 84.69 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CA SER A 559 " pdb=" C SER A 559 " pdb=" N PRO A 560 " pdb=" CA PRO A 560 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 6714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1611 0.104 - 0.207: 147 0.207 - 0.311: 9 0.311 - 0.414: 4 0.414 - 0.518: 1 Chirality restraints: 1772 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C17 CLR C 302 " pdb=" C13 CLR C 302 " pdb=" C16 CLR C 302 " pdb=" C20 CLR C 302 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1769 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.044 5.00e-02 4.00e+02 6.53e-02 6.81e+00 pdb=" N PRO A 560 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 565 " -0.019 2.00e-02 2.50e+03 1.76e-02 6.19e+00 pdb=" CG TYR A 565 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 565 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 565 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 565 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 565 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 565 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 565 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.015 2.00e-02 2.50e+03 1.52e-02 5.76e+00 pdb=" CG TRP C 227 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.002 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2338 2.78 - 3.31: 9478 3.31 - 3.84: 17189 3.84 - 4.37: 19498 4.37 - 4.90: 34384 Nonbonded interactions: 82887 Sorted by model distance: nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.245 3.040 nonbonded pdb=" O SER A 234 " pdb=" OG SER A 238 " model vdw 2.295 3.040 nonbonded pdb=" O PHE B 86 " pdb=" OG1 THR B 90 " model vdw 2.299 3.040 nonbonded pdb=" CD2 LEU B 381 " pdb=" CE2 PHE B 386 " model vdw 2.311 3.760 nonbonded pdb=" O LEU B 174 " pdb=" OG SER B 178 " model vdw 2.316 3.040 ... (remaining 82882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.540 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.010 0.081 10883 Z= 0.437 Angle : 1.096 14.087 14877 Z= 0.572 Chirality : 0.064 0.518 1772 Planarity : 0.007 0.065 1790 Dihedral : 14.519 111.763 4279 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.90 % Allowed : 1.90 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.18), residues: 1277 helix: -2.21 (0.15), residues: 674 sheet: -2.30 (0.43), residues: 128 loop : -3.36 (0.22), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 227 HIS 0.021 0.003 HIS C 197 PHE 0.039 0.004 PHE C 132 TYR 0.042 0.003 TYR A 565 ARG 0.011 0.001 ARG A 626 Details of bonding type rmsd link_NAG-ASN : bond 0.01210 ( 12) link_NAG-ASN : angle 5.26868 ( 36) link_BETA1-4 : bond 0.00541 ( 7) link_BETA1-4 : angle 2.59228 ( 21) hydrogen bonds : bond 0.17380 ( 515) hydrogen bonds : angle 6.87977 ( 1485) link_BETA1-6 : bond 0.00402 ( 1) link_BETA1-6 : angle 1.48720 ( 3) SS BOND : bond 0.00554 ( 4) SS BOND : angle 2.93850 ( 8) link_BETA1-3 : bond 0.00096 ( 1) link_BETA1-3 : angle 0.64441 ( 3) covalent geometry : bond 0.00967 (10858) covalent geometry : angle 1.06014 (14806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8975 (mmt) cc_final: 0.8712 (mmm) REVERT: A 414 ARG cc_start: 0.8621 (ttt90) cc_final: 0.8404 (ttm-80) REVERT: A 612 ASN cc_start: 0.8241 (m-40) cc_final: 0.7836 (t0) REVERT: A 649 THR cc_start: 0.9522 (p) cc_final: 0.9282 (p) REVERT: A 652 ARG cc_start: 0.8564 (mtp85) cc_final: 0.7968 (mtt180) REVERT: A 689 CYS cc_start: 0.8555 (t) cc_final: 0.8269 (t) REVERT: B 134 LEU cc_start: 0.8197 (mp) cc_final: 0.7963 (tp) REVERT: B 146 MET cc_start: 0.7454 (mmt) cc_final: 0.7218 (mmt) REVERT: B 244 TRP cc_start: 0.6966 (m-10) cc_final: 0.6355 (m100) REVERT: C 116 GLN cc_start: 0.8283 (mt0) cc_final: 0.7999 (mt0) REVERT: C 180 ASP cc_start: 0.8995 (t70) cc_final: 0.8554 (t0) REVERT: C 183 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7957 (mm-30) REVERT: D 34 ILE cc_start: 0.7041 (mt) cc_final: 0.6786 (mt) REVERT: D 52 GLN cc_start: 0.7668 (tt0) cc_final: 0.7213 (mm-40) REVERT: D 93 SER cc_start: 0.9623 (t) cc_final: 0.9317 (p) outliers start: 10 outliers final: 4 residues processed: 214 average time/residue: 0.2604 time to fit residues: 75.5780 Evaluate side-chains 112 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 149 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 313 GLN A 355 GLN A 454 GLN A 531 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS B 112 GLN B 222 GLN B 405 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079517 restraints weight = 21714.252| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.00 r_work: 0.2888 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10883 Z= 0.125 Angle : 0.669 11.303 14877 Z= 0.326 Chirality : 0.044 0.270 1772 Planarity : 0.005 0.056 1790 Dihedral : 12.929 113.078 2029 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.81 % Allowed : 8.23 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1277 helix: -0.20 (0.19), residues: 677 sheet: -1.97 (0.43), residues: 125 loop : -2.68 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.018 0.001 TYR B 446 ARG 0.007 0.001 ARG C 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 12) link_NAG-ASN : angle 3.39617 ( 36) link_BETA1-4 : bond 0.00419 ( 7) link_BETA1-4 : angle 1.48402 ( 21) hydrogen bonds : bond 0.04502 ( 515) hydrogen bonds : angle 4.52697 ( 1485) link_BETA1-6 : bond 0.01740 ( 1) link_BETA1-6 : angle 2.23653 ( 3) SS BOND : bond 0.00455 ( 4) SS BOND : angle 1.12961 ( 8) link_BETA1-3 : bond 0.00837 ( 1) link_BETA1-3 : angle 1.56071 ( 3) covalent geometry : bond 0.00263 (10858) covalent geometry : angle 0.64519 (14806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.9321 (tpp) cc_final: 0.9109 (tpp) REVERT: A 414 ARG cc_start: 0.8880 (ttt90) cc_final: 0.8468 (ttm-80) REVERT: A 612 ASN cc_start: 0.8449 (m-40) cc_final: 0.8006 (t0) REVERT: A 652 ARG cc_start: 0.8786 (mtp85) cc_final: 0.8423 (mtt180) REVERT: A 683 SER cc_start: 0.9087 (t) cc_final: 0.8823 (p) REVERT: A 689 CYS cc_start: 0.8872 (t) cc_final: 0.8657 (t) REVERT: B 134 LEU cc_start: 0.8202 (mp) cc_final: 0.7947 (tp) REVERT: B 184 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8396 (mm-30) REVERT: B 216 LYS cc_start: 0.7944 (tppt) cc_final: 0.7575 (tttt) REVERT: B 244 TRP cc_start: 0.6843 (m-10) cc_final: 0.6203 (m100) REVERT: B 458 ASP cc_start: 0.8707 (m-30) cc_final: 0.8456 (m-30) REVERT: C 116 GLN cc_start: 0.8618 (mt0) cc_final: 0.8175 (mt0) REVERT: C 180 ASP cc_start: 0.8844 (t70) cc_final: 0.8386 (t0) REVERT: D 34 ILE cc_start: 0.7194 (mt) cc_final: 0.6929 (mt) REVERT: D 36 TRP cc_start: 0.7926 (t60) cc_final: 0.7219 (t60) REVERT: D 40 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6944 (mp0) REVERT: D 52 GLN cc_start: 0.7623 (tt0) cc_final: 0.7119 (mm-40) outliers start: 20 outliers final: 11 residues processed: 154 average time/residue: 0.2303 time to fit residues: 51.1133 Evaluate side-chains 118 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 55 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 606 GLN B 222 GLN C 136 ASN D 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.075035 restraints weight = 22276.748| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.95 r_work: 0.2799 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10883 Z= 0.263 Angle : 0.734 13.418 14877 Z= 0.352 Chirality : 0.047 0.283 1772 Planarity : 0.004 0.056 1790 Dihedral : 11.049 111.737 2027 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.16 % Allowed : 9.95 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1277 helix: 0.36 (0.20), residues: 691 sheet: -1.98 (0.43), residues: 125 loop : -2.51 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 36 HIS 0.008 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.019 0.002 TYR B 446 ARG 0.004 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 12) link_NAG-ASN : angle 3.33080 ( 36) link_BETA1-4 : bond 0.00189 ( 7) link_BETA1-4 : angle 1.66609 ( 21) hydrogen bonds : bond 0.04812 ( 515) hydrogen bonds : angle 4.36307 ( 1485) link_BETA1-6 : bond 0.01682 ( 1) link_BETA1-6 : angle 1.91727 ( 3) SS BOND : bond 0.00584 ( 4) SS BOND : angle 1.28566 ( 8) link_BETA1-3 : bond 0.00802 ( 1) link_BETA1-3 : angle 1.39655 ( 3) covalent geometry : bond 0.00624 (10858) covalent geometry : angle 0.71330 (14806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 612 ASN cc_start: 0.8496 (m-40) cc_final: 0.7999 (t0) REVERT: A 652 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8384 (mtt180) REVERT: B 134 LEU cc_start: 0.8230 (mp) cc_final: 0.7854 (tt) REVERT: B 184 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8490 (mm-30) REVERT: B 244 TRP cc_start: 0.7120 (m-10) cc_final: 0.6403 (m100) REVERT: B 454 GLN cc_start: 0.8810 (tp40) cc_final: 0.8571 (tp40) REVERT: C 116 GLN cc_start: 0.8780 (mt0) cc_final: 0.8186 (mt0) REVERT: C 152 ASP cc_start: 0.9020 (m-30) cc_final: 0.8816 (m-30) REVERT: D 34 ILE cc_start: 0.7335 (mt) cc_final: 0.7083 (mt) REVERT: D 40 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7097 (mp0) REVERT: D 52 GLN cc_start: 0.7665 (tt0) cc_final: 0.7216 (mm-40) outliers start: 35 outliers final: 25 residues processed: 124 average time/residue: 0.2022 time to fit residues: 37.5552 Evaluate side-chains 118 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN B 222 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.080011 restraints weight = 21681.955| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.95 r_work: 0.2878 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10883 Z= 0.102 Angle : 0.590 11.284 14877 Z= 0.279 Chirality : 0.042 0.254 1772 Planarity : 0.004 0.051 1790 Dihedral : 9.953 104.927 2027 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.26 % Allowed : 11.21 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1277 helix: 0.96 (0.20), residues: 685 sheet: -1.92 (0.44), residues: 123 loop : -2.18 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.004 0.001 HIS C 197 PHE 0.028 0.001 PHE A 302 TYR 0.017 0.001 TYR B 446 ARG 0.004 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 12) link_NAG-ASN : angle 2.65142 ( 36) link_BETA1-4 : bond 0.00450 ( 7) link_BETA1-4 : angle 1.24701 ( 21) hydrogen bonds : bond 0.03631 ( 515) hydrogen bonds : angle 4.05722 ( 1485) link_BETA1-6 : bond 0.01586 ( 1) link_BETA1-6 : angle 2.51322 ( 3) SS BOND : bond 0.00412 ( 4) SS BOND : angle 0.86423 ( 8) link_BETA1-3 : bond 0.00942 ( 1) link_BETA1-3 : angle 1.42866 ( 3) covalent geometry : bond 0.00212 (10858) covalent geometry : angle 0.57296 (14806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8152 (mt) REVERT: A 333 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 612 ASN cc_start: 0.8485 (m-40) cc_final: 0.7976 (t0) REVERT: A 652 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8320 (mtt180) REVERT: B 134 LEU cc_start: 0.8216 (mp) cc_final: 0.7843 (tt) REVERT: B 184 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8410 (mm-30) REVERT: B 216 LYS cc_start: 0.7916 (tppt) cc_final: 0.7612 (tttt) REVERT: B 244 TRP cc_start: 0.7023 (m-10) cc_final: 0.6317 (m100) REVERT: B 454 GLN cc_start: 0.8746 (tp40) cc_final: 0.8376 (tp-100) REVERT: B 458 ASP cc_start: 0.8526 (m-30) cc_final: 0.8301 (m-30) REVERT: C 48 LEU cc_start: 0.8658 (mt) cc_final: 0.8297 (tp) REVERT: C 116 GLN cc_start: 0.8623 (mt0) cc_final: 0.8086 (mt0) REVERT: D 34 ILE cc_start: 0.7255 (mt) cc_final: 0.7009 (mt) REVERT: D 36 TRP cc_start: 0.7836 (t60) cc_final: 0.7303 (t60) REVERT: D 40 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6993 (mp0) REVERT: D 52 GLN cc_start: 0.7580 (tt0) cc_final: 0.7211 (mm-40) outliers start: 25 outliers final: 14 residues processed: 124 average time/residue: 0.1807 time to fit residues: 34.3231 Evaluate side-chains 111 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 39 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.076349 restraints weight = 21987.144| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.95 r_work: 0.2823 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10883 Z= 0.184 Angle : 0.634 12.806 14877 Z= 0.301 Chirality : 0.044 0.264 1772 Planarity : 0.004 0.053 1790 Dihedral : 9.620 99.453 2027 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.89 % Allowed : 11.66 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1277 helix: 1.15 (0.20), residues: 686 sheet: -1.80 (0.45), residues: 125 loop : -2.12 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 209 HIS 0.005 0.001 HIS C 58 PHE 0.028 0.002 PHE A 302 TYR 0.015 0.001 TYR B 446 ARG 0.002 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 12) link_NAG-ASN : angle 2.67995 ( 36) link_BETA1-4 : bond 0.00231 ( 7) link_BETA1-4 : angle 1.44443 ( 21) hydrogen bonds : bond 0.03962 ( 515) hydrogen bonds : angle 4.05930 ( 1485) link_BETA1-6 : bond 0.01571 ( 1) link_BETA1-6 : angle 2.75430 ( 3) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.63874 ( 8) link_BETA1-3 : bond 0.00791 ( 1) link_BETA1-3 : angle 1.86963 ( 3) covalent geometry : bond 0.00435 (10858) covalent geometry : angle 0.61589 (14806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8096 (t0) cc_final: 0.7753 (t0) REVERT: A 612 ASN cc_start: 0.8466 (m-40) cc_final: 0.7952 (t0) REVERT: A 652 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8314 (mtt180) REVERT: B 134 LEU cc_start: 0.8173 (mp) cc_final: 0.7813 (tt) REVERT: B 244 TRP cc_start: 0.7135 (m-10) cc_final: 0.6381 (m100) REVERT: B 454 GLN cc_start: 0.8795 (tp40) cc_final: 0.8401 (tp-100) REVERT: C 116 GLN cc_start: 0.8687 (mt0) cc_final: 0.8037 (mt0) REVERT: C 192 LEU cc_start: 0.8912 (tp) cc_final: 0.8527 (tt) REVERT: D 34 ILE cc_start: 0.7392 (mt) cc_final: 0.7132 (mt) REVERT: D 40 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6980 (mp0) REVERT: D 52 GLN cc_start: 0.7601 (tt0) cc_final: 0.7226 (mm-40) outliers start: 32 outliers final: 23 residues processed: 119 average time/residue: 0.2098 time to fit residues: 38.6939 Evaluate side-chains 117 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 16 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 8.9990 chunk 100 optimal weight: 0.0770 chunk 88 optimal weight: 4.9990 overall best weight: 3.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.098924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.074712 restraints weight = 22080.727| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.92 r_work: 0.2803 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10883 Z= 0.237 Angle : 0.679 14.583 14877 Z= 0.323 Chirality : 0.045 0.269 1772 Planarity : 0.004 0.052 1790 Dihedral : 9.426 91.935 2027 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.35 % Allowed : 12.03 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1277 helix: 1.23 (0.20), residues: 681 sheet: -1.67 (0.47), residues: 116 loop : -2.15 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 209 HIS 0.006 0.001 HIS C 58 PHE 0.027 0.002 PHE A 302 TYR 0.019 0.002 TYR B 189 ARG 0.003 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 12) link_NAG-ASN : angle 2.78209 ( 36) link_BETA1-4 : bond 0.00231 ( 7) link_BETA1-4 : angle 1.51146 ( 21) hydrogen bonds : bond 0.04342 ( 515) hydrogen bonds : angle 4.13876 ( 1485) link_BETA1-6 : bond 0.01567 ( 1) link_BETA1-6 : angle 3.15046 ( 3) SS BOND : bond 0.00450 ( 4) SS BOND : angle 1.49344 ( 8) link_BETA1-3 : bond 0.00748 ( 1) link_BETA1-3 : angle 2.30711 ( 3) covalent geometry : bond 0.00562 (10858) covalent geometry : angle 0.66146 (14806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8181 (t0) cc_final: 0.7934 (t0) REVERT: A 612 ASN cc_start: 0.8469 (m-40) cc_final: 0.8002 (t0) REVERT: A 652 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8339 (mtt180) REVERT: B 134 LEU cc_start: 0.8095 (mp) cc_final: 0.7775 (tt) REVERT: B 154 TYR cc_start: 0.7108 (t80) cc_final: 0.6866 (t80) REVERT: B 244 TRP cc_start: 0.7160 (m-10) cc_final: 0.6375 (m100) REVERT: B 247 TRP cc_start: 0.7841 (m100) cc_final: 0.7492 (m100) REVERT: B 454 GLN cc_start: 0.8755 (tp40) cc_final: 0.8410 (tp-100) REVERT: C 116 GLN cc_start: 0.8754 (mt0) cc_final: 0.8141 (mt0) REVERT: D 34 ILE cc_start: 0.7422 (mt) cc_final: 0.7170 (mt) REVERT: D 40 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6951 (mp0) REVERT: D 52 GLN cc_start: 0.7640 (tt0) cc_final: 0.7243 (mm-40) outliers start: 37 outliers final: 30 residues processed: 123 average time/residue: 0.2444 time to fit residues: 46.7546 Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077224 restraints weight = 22076.396| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.95 r_work: 0.2839 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10883 Z= 0.124 Angle : 0.595 12.988 14877 Z= 0.280 Chirality : 0.043 0.241 1772 Planarity : 0.004 0.049 1790 Dihedral : 8.903 82.200 2027 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.44 % Allowed : 12.93 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1277 helix: 1.43 (0.20), residues: 691 sheet: -1.63 (0.45), residues: 128 loop : -1.89 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 257 HIS 0.004 0.001 HIS C 58 PHE 0.027 0.001 PHE A 302 TYR 0.014 0.001 TYR B 446 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 12) link_NAG-ASN : angle 2.33964 ( 36) link_BETA1-4 : bond 0.00313 ( 7) link_BETA1-4 : angle 1.26556 ( 21) hydrogen bonds : bond 0.03632 ( 515) hydrogen bonds : angle 3.98637 ( 1485) link_BETA1-6 : bond 0.01391 ( 1) link_BETA1-6 : angle 3.49641 ( 3) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.94386 ( 8) link_BETA1-3 : bond 0.00906 ( 1) link_BETA1-3 : angle 2.08853 ( 3) covalent geometry : bond 0.00281 (10858) covalent geometry : angle 0.58034 (14806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8145 (t0) cc_final: 0.7872 (t0) REVERT: A 612 ASN cc_start: 0.8460 (m-40) cc_final: 0.7996 (t0) REVERT: A 652 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8261 (mtt180) REVERT: B 134 LEU cc_start: 0.8070 (mp) cc_final: 0.7762 (tt) REVERT: B 244 TRP cc_start: 0.7084 (m-10) cc_final: 0.6297 (m100) REVERT: B 454 GLN cc_start: 0.8697 (tp40) cc_final: 0.8296 (tp-100) REVERT: C 48 LEU cc_start: 0.8717 (mt) cc_final: 0.8295 (tp) REVERT: C 71 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.7990 (mp) REVERT: C 116 GLN cc_start: 0.8704 (mt0) cc_final: 0.8069 (mt0) REVERT: D 34 ILE cc_start: 0.7414 (mt) cc_final: 0.7170 (mt) REVERT: D 40 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6861 (mp0) REVERT: D 52 GLN cc_start: 0.7622 (tt0) cc_final: 0.7241 (mm-40) outliers start: 27 outliers final: 21 residues processed: 123 average time/residue: 0.2168 time to fit residues: 41.5314 Evaluate side-chains 118 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 69 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 9 optimal weight: 0.0980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080987 restraints weight = 21838.026| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.94 r_work: 0.2892 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10883 Z= 0.096 Angle : 0.573 10.951 14877 Z= 0.268 Chirality : 0.042 0.255 1772 Planarity : 0.004 0.049 1790 Dihedral : 8.180 73.526 2025 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.17 % Allowed : 14.29 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1277 helix: 1.62 (0.21), residues: 690 sheet: -1.20 (0.49), residues: 116 loop : -1.84 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 257 HIS 0.004 0.001 HIS C 58 PHE 0.029 0.001 PHE A 302 TYR 0.023 0.001 TYR B 389 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 12) link_NAG-ASN : angle 2.08112 ( 36) link_BETA1-4 : bond 0.00399 ( 7) link_BETA1-4 : angle 1.12596 ( 21) hydrogen bonds : bond 0.03093 ( 515) hydrogen bonds : angle 3.91727 ( 1485) link_BETA1-6 : bond 0.01104 ( 1) link_BETA1-6 : angle 4.06081 ( 3) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.57042 ( 8) link_BETA1-3 : bond 0.00959 ( 1) link_BETA1-3 : angle 1.73752 ( 3) covalent geometry : bond 0.00198 (10858) covalent geometry : angle 0.55884 (14806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.9034 (mmm) cc_final: 0.8523 (mtp) REVERT: A 548 ASP cc_start: 0.8085 (t0) cc_final: 0.7693 (t0) REVERT: A 612 ASN cc_start: 0.8422 (m-40) cc_final: 0.7956 (t0) REVERT: A 652 ARG cc_start: 0.8792 (mtp85) cc_final: 0.8216 (mtt180) REVERT: B 134 LEU cc_start: 0.8265 (mp) cc_final: 0.7892 (tt) REVERT: B 222 GLN cc_start: 0.8498 (tt0) cc_final: 0.8184 (pt0) REVERT: B 244 TRP cc_start: 0.7056 (m-10) cc_final: 0.6261 (m100) REVERT: B 385 ASP cc_start: 0.8504 (m-30) cc_final: 0.8043 (t70) REVERT: B 454 GLN cc_start: 0.8618 (tp40) cc_final: 0.8416 (tp40) REVERT: C 48 LEU cc_start: 0.8736 (mt) cc_final: 0.8293 (tp) REVERT: C 116 GLN cc_start: 0.8596 (mt0) cc_final: 0.7922 (mt0) REVERT: D 34 ILE cc_start: 0.7437 (mt) cc_final: 0.7195 (mt) REVERT: D 40 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6808 (mp0) REVERT: D 52 GLN cc_start: 0.7573 (tt0) cc_final: 0.7229 (mm-40) outliers start: 24 outliers final: 21 residues processed: 135 average time/residue: 0.1980 time to fit residues: 41.1359 Evaluate side-chains 126 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078248 restraints weight = 22248.760| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.92 r_work: 0.2845 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10883 Z= 0.155 Angle : 0.612 13.028 14877 Z= 0.286 Chirality : 0.043 0.238 1772 Planarity : 0.004 0.049 1790 Dihedral : 7.979 72.922 2025 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.99 % Allowed : 14.74 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1277 helix: 1.68 (0.20), residues: 691 sheet: -1.26 (0.48), residues: 122 loop : -1.82 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 PHE 0.027 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 12) link_NAG-ASN : angle 2.16292 ( 36) link_BETA1-4 : bond 0.00219 ( 7) link_BETA1-4 : angle 1.30801 ( 21) hydrogen bonds : bond 0.03511 ( 515) hydrogen bonds : angle 3.91039 ( 1485) link_BETA1-6 : bond 0.00829 ( 1) link_BETA1-6 : angle 4.21917 ( 3) SS BOND : bond 0.00420 ( 4) SS BOND : angle 1.85112 ( 8) link_BETA1-3 : bond 0.00835 ( 1) link_BETA1-3 : angle 2.23112 ( 3) covalent geometry : bond 0.00361 (10858) covalent geometry : angle 0.59644 (14806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8206 (t0) cc_final: 0.7943 (t0) REVERT: A 612 ASN cc_start: 0.8445 (m-40) cc_final: 0.7962 (t0) REVERT: A 652 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8254 (mtt180) REVERT: B 134 LEU cc_start: 0.8205 (mp) cc_final: 0.7894 (tt) REVERT: B 222 GLN cc_start: 0.8542 (tt0) cc_final: 0.8235 (pt0) REVERT: B 244 TRP cc_start: 0.7105 (m-10) cc_final: 0.6217 (m100) REVERT: B 454 GLN cc_start: 0.8666 (tp40) cc_final: 0.8446 (tp40) REVERT: C 48 LEU cc_start: 0.8695 (mt) cc_final: 0.8278 (tp) REVERT: C 71 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7950 (mp) REVERT: C 116 GLN cc_start: 0.8707 (mt0) cc_final: 0.8035 (mt0) REVERT: D 34 ILE cc_start: 0.7432 (mt) cc_final: 0.7186 (mt) REVERT: D 40 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6841 (mp0) REVERT: D 52 GLN cc_start: 0.7601 (tt0) cc_final: 0.7241 (mm-40) outliers start: 22 outliers final: 18 residues processed: 117 average time/residue: 0.1820 time to fit residues: 33.0045 Evaluate side-chains 116 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079329 restraints weight = 21846.822| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.92 r_work: 0.2868 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10883 Z= 0.112 Angle : 0.582 12.174 14877 Z= 0.273 Chirality : 0.042 0.233 1772 Planarity : 0.003 0.047 1790 Dihedral : 7.676 72.957 2025 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.72 % Allowed : 15.01 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1277 helix: 1.77 (0.20), residues: 691 sheet: -1.17 (0.48), residues: 122 loop : -1.72 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 247 HIS 0.004 0.001 HIS C 58 PHE 0.028 0.001 PHE A 302 TYR 0.014 0.001 TYR B 446 ARG 0.002 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 12) link_NAG-ASN : angle 2.08541 ( 36) link_BETA1-4 : bond 0.00326 ( 7) link_BETA1-4 : angle 1.20504 ( 21) hydrogen bonds : bond 0.03310 ( 515) hydrogen bonds : angle 3.87648 ( 1485) link_BETA1-6 : bond 0.00350 ( 1) link_BETA1-6 : angle 3.99427 ( 3) SS BOND : bond 0.00301 ( 4) SS BOND : angle 1.52509 ( 8) link_BETA1-3 : bond 0.00890 ( 1) link_BETA1-3 : angle 2.02293 ( 3) covalent geometry : bond 0.00251 (10858) covalent geometry : angle 0.56810 (14806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8193 (t0) cc_final: 0.7920 (t0) REVERT: A 612 ASN cc_start: 0.8432 (m-40) cc_final: 0.7989 (t0) REVERT: A 652 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8179 (mtt180) REVERT: B 134 LEU cc_start: 0.8178 (mp) cc_final: 0.7869 (tt) REVERT: B 244 TRP cc_start: 0.7109 (m-10) cc_final: 0.6289 (m100) REVERT: C 48 LEU cc_start: 0.8680 (mt) cc_final: 0.8273 (tp) REVERT: C 67 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7105 (tt) REVERT: C 116 GLN cc_start: 0.8706 (mt0) cc_final: 0.8080 (mt0) REVERT: D 34 ILE cc_start: 0.7546 (mt) cc_final: 0.7295 (mt) REVERT: D 40 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6836 (mp0) REVERT: D 52 GLN cc_start: 0.7577 (tt0) cc_final: 0.7238 (mm-40) outliers start: 19 outliers final: 17 residues processed: 118 average time/residue: 0.1805 time to fit residues: 33.5517 Evaluate side-chains 118 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.076694 restraints weight = 21938.056| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.92 r_work: 0.2822 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10883 Z= 0.191 Angle : 0.639 14.574 14877 Z= 0.303 Chirality : 0.044 0.235 1772 Planarity : 0.004 0.049 1790 Dihedral : 7.634 72.766 2025 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.08 % Allowed : 15.19 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1277 helix: 1.70 (0.20), residues: 692 sheet: -1.28 (0.48), residues: 122 loop : -1.76 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 247 HIS 0.005 0.001 HIS C 58 PHE 0.026 0.002 PHE A 302 TYR 0.015 0.001 TYR B 389 ARG 0.002 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 12) link_NAG-ASN : angle 2.30470 ( 36) link_BETA1-4 : bond 0.00211 ( 7) link_BETA1-4 : angle 1.42387 ( 21) hydrogen bonds : bond 0.03866 ( 515) hydrogen bonds : angle 3.96969 ( 1485) link_BETA1-6 : bond 0.00393 ( 1) link_BETA1-6 : angle 3.60173 ( 3) SS BOND : bond 0.00410 ( 4) SS BOND : angle 1.71002 ( 8) link_BETA1-3 : bond 0.00813 ( 1) link_BETA1-3 : angle 2.51467 ( 3) covalent geometry : bond 0.00448 (10858) covalent geometry : angle 0.62381 (14806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.80 seconds wall clock time: 86 minutes 18.42 seconds (5178.42 seconds total)