Starting phenix.real_space_refine on Sat Aug 23 09:26:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8im7_35572/08_2025/8im7_35572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8im7_35572/08_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_35572/08_2025/8im7_35572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8im7_35572/08_2025/8im7_35572.map" model { file = "/net/cci-nas-00/data/ceres_data/8im7_35572/08_2025/8im7_35572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8im7_35572/08_2025/8im7_35572.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.06, per 1000 atoms: 0.19 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: 0.93 Conformation dependent library (CDL) restraints added in 439.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.23 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: 1.31 Time building geometry restraints manager: 1.20 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- 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 : 3.72 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.011 0.001 ARG A 626 TYR 0.042 0.003 TYR A 565 PHE 0.039 0.004 PHE C 132 TRP 0.040 0.004 TRP C 227 HIS 0.021 0.003 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00967 (10858) covalent geometry : angle 1.06014 (14806) SS BOND : bond 0.00554 ( 4) SS BOND : angle 2.93850 ( 8) hydrogen bonds : bond 0.17380 ( 515) hydrogen bonds : angle 6.87977 ( 1485) link_BETA1-3 : bond 0.00096 ( 1) link_BETA1-3 : angle 0.64441 ( 3) link_BETA1-4 : bond 0.00541 ( 7) link_BETA1-4 : angle 2.59228 ( 21) link_BETA1-6 : bond 0.00402 ( 1) link_BETA1-6 : angle 1.48720 ( 3) link_NAG-ASN : bond 0.01210 ( 12) link_NAG-ASN : angle 5.26868 ( 36) *********************** 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 : 0.393 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: 0.0978 time to fit residues: 28.4356 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 : 0.330 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 385 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079551 restraints weight = 22115.744| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.01 r_work: 0.2891 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1968 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= 0.123 Angle : 0.666 10.916 14877 Z= 0.324 Chirality : 0.044 0.270 1772 Planarity : 0.005 0.056 1790 Dihedral : 12.778 113.686 2029 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.72 % Allowed : 8.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.22), residues: 1277 helix: -0.21 (0.19), residues: 676 sheet: -2.13 (0.42), residues: 123 loop : -2.67 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 241 TYR 0.018 0.001 TYR B 446 PHE 0.031 0.002 PHE A 302 TRP 0.020 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00258 (10858) covalent geometry : angle 0.64253 (14806) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.16434 ( 8) hydrogen bonds : bond 0.04541 ( 515) hydrogen bonds : angle 4.53237 ( 1485) link_BETA1-3 : bond 0.00956 ( 1) link_BETA1-3 : angle 1.72724 ( 3) link_BETA1-4 : bond 0.00503 ( 7) link_BETA1-4 : angle 1.43148 ( 21) link_BETA1-6 : bond 0.01586 ( 1) link_BETA1-6 : angle 2.12483 ( 3) link_NAG-ASN : bond 0.00566 ( 12) link_NAG-ASN : angle 3.35424 ( 36) *********************** 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 158 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.9338 (tpp) cc_final: 0.9129 (tpp) REVERT: A 414 ARG cc_start: 0.8903 (ttt90) cc_final: 0.8509 (ttm-80) REVERT: A 612 ASN cc_start: 0.8416 (m-40) cc_final: 0.7976 (t0) REVERT: A 652 ARG cc_start: 0.8814 (mtp85) cc_final: 0.8472 (mtt180) REVERT: A 683 SER cc_start: 0.9088 (t) cc_final: 0.8824 (p) REVERT: A 689 CYS cc_start: 0.8910 (t) cc_final: 0.8701 (t) REVERT: B 134 LEU cc_start: 0.8204 (mp) cc_final: 0.7947 (tp) REVERT: B 184 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 216 LYS cc_start: 0.7956 (tppt) cc_final: 0.7570 (tttt) REVERT: B 244 TRP cc_start: 0.6831 (m-10) cc_final: 0.6194 (m100) REVERT: B 458 ASP cc_start: 0.8735 (m-30) cc_final: 0.8487 (m-30) REVERT: C 116 GLN cc_start: 0.8614 (mt0) cc_final: 0.8204 (mt0) REVERT: C 180 ASP cc_start: 0.8860 (t70) cc_final: 0.8382 (t0) REVERT: D 34 ILE cc_start: 0.7205 (mt) cc_final: 0.6936 (mt) REVERT: D 36 TRP cc_start: 0.7917 (t60) cc_final: 0.7385 (t60) REVERT: D 40 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6967 (mp0) REVERT: D 52 GLN cc_start: 0.7622 (tt0) cc_final: 0.7102 (mm-40) outliers start: 19 outliers final: 11 residues processed: 153 average time/residue: 0.0893 time to fit residues: 19.6449 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 : 0.243 ------------------------------------------------------------------------------- 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 84 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 100 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 GLN B 222 GLN C 136 ASN D 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.076046 restraints weight = 22108.627| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.97 r_work: 0.2819 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10883 Z= 0.234 Angle : 0.714 13.438 14877 Z= 0.341 Chirality : 0.046 0.287 1772 Planarity : 0.004 0.056 1790 Dihedral : 10.951 111.577 2027 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.98 % Allowed : 10.04 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.23), residues: 1277 helix: 0.43 (0.20), residues: 688 sheet: -2.06 (0.43), residues: 128 loop : -2.45 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.020 0.002 TYR B 446 PHE 0.030 0.002 PHE A 302 TRP 0.018 0.002 TRP D 36 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00552 (10858) covalent geometry : angle 0.69388 (14806) SS BOND : bond 0.00562 ( 4) SS BOND : angle 1.22774 ( 8) hydrogen bonds : bond 0.04666 ( 515) hydrogen bonds : angle 4.31333 ( 1485) link_BETA1-3 : bond 0.00874 ( 1) link_BETA1-3 : angle 1.43497 ( 3) link_BETA1-4 : bond 0.00282 ( 7) link_BETA1-4 : angle 1.62133 ( 21) link_BETA1-6 : bond 0.01643 ( 1) link_BETA1-6 : angle 1.89121 ( 3) link_NAG-ASN : bond 0.00572 ( 12) link_NAG-ASN : angle 3.23533 ( 36) *********************** 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 133 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.9360 (tpp) cc_final: 0.9158 (tpp) REVERT: A 612 ASN cc_start: 0.8490 (m-40) cc_final: 0.8008 (t0) REVERT: A 652 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8315 (mtt180) REVERT: B 134 LEU cc_start: 0.8235 (mp) cc_final: 0.7851 (tt) REVERT: B 184 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8508 (mm-30) REVERT: B 244 TRP cc_start: 0.7099 (m-10) cc_final: 0.6391 (m100) REVERT: B 454 GLN cc_start: 0.8786 (tp40) cc_final: 0.8497 (tp40) REVERT: C 116 GLN cc_start: 0.8739 (mt0) cc_final: 0.8127 (mt0) REVERT: C 152 ASP cc_start: 0.9028 (m-30) cc_final: 0.8801 (m-30) REVERT: D 34 ILE cc_start: 0.7330 (mt) cc_final: 0.7076 (mt) REVERT: D 40 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7128 (mp0) REVERT: D 52 GLN cc_start: 0.7665 (tt0) cc_final: 0.7126 (mm-40) outliers start: 33 outliers final: 23 residues processed: 125 average time/residue: 0.0695 time to fit residues: 13.1701 Evaluate side-chains 114 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 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 53 ILE 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 117 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 222 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076050 restraints weight = 22179.955| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.95 r_work: 0.2811 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10883 Z= 0.208 Angle : 0.662 13.873 14877 Z= 0.317 Chirality : 0.045 0.266 1772 Planarity : 0.004 0.053 1790 Dihedral : 10.035 103.500 2027 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.25 % Allowed : 10.58 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.24), residues: 1277 helix: 0.90 (0.20), residues: 686 sheet: -1.87 (0.43), residues: 127 loop : -2.29 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.018 0.001 TYR B 446 PHE 0.028 0.002 PHE A 302 TRP 0.014 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00488 (10858) covalent geometry : angle 0.64389 (14806) SS BOND : bond 0.00748 ( 4) SS BOND : angle 1.13832 ( 8) hydrogen bonds : bond 0.04289 ( 515) hydrogen bonds : angle 4.18262 ( 1485) link_BETA1-3 : bond 0.00741 ( 1) link_BETA1-3 : angle 1.68746 ( 3) link_BETA1-4 : bond 0.00260 ( 7) link_BETA1-4 : angle 1.46445 ( 21) link_BETA1-6 : bond 0.01576 ( 1) link_BETA1-6 : angle 2.61030 ( 3) link_NAG-ASN : bond 0.00485 ( 12) link_NAG-ASN : angle 2.90400 ( 36) *********************** 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 137 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.9385 (tpp) cc_final: 0.9183 (tpp) REVERT: A 548 ASP cc_start: 0.8106 (t0) cc_final: 0.7716 (t0) REVERT: A 612 ASN cc_start: 0.8441 (m-40) cc_final: 0.7935 (t0) REVERT: A 652 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8338 (mtt180) REVERT: B 134 LEU cc_start: 0.8120 (mp) cc_final: 0.7786 (tt) REVERT: B 184 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8523 (mm-30) REVERT: B 244 TRP cc_start: 0.7153 (m-10) cc_final: 0.6395 (m100) REVERT: B 454 GLN cc_start: 0.8766 (tp40) cc_final: 0.8414 (tp-100) REVERT: B 458 ASP cc_start: 0.8554 (m-30) cc_final: 0.8353 (m-30) REVERT: C 28 ASP cc_start: 0.8426 (m-30) cc_final: 0.8110 (t0) REVERT: C 101 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7957 (tt) REVERT: C 116 GLN cc_start: 0.8775 (mt0) cc_final: 0.8174 (mt0) REVERT: C 152 ASP cc_start: 0.9013 (m-30) cc_final: 0.8771 (m-30) REVERT: D 34 ILE cc_start: 0.7261 (mt) cc_final: 0.7000 (mt) REVERT: D 40 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7018 (mp0) REVERT: D 52 GLN cc_start: 0.7593 (tt0) cc_final: 0.7155 (mm-40) outliers start: 36 outliers final: 21 residues processed: 127 average time/residue: 0.0610 time to fit residues: 12.0999 Evaluate side-chains 117 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 605 VAL 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 81 LEU Chi-restraints excluded: chain C residue 101 LEU 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 53 ILE Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.076604 restraints weight = 22158.503| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.95 r_work: 0.2817 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10883 Z= 0.175 Angle : 0.629 13.554 14877 Z= 0.299 Chirality : 0.044 0.258 1772 Planarity : 0.004 0.052 1790 Dihedral : 9.526 95.536 2027 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.53 % Allowed : 11.39 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.24), residues: 1277 helix: 1.16 (0.20), residues: 686 sheet: -1.77 (0.44), residues: 127 loop : -2.19 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.016 0.001 TYR B 446 PHE 0.028 0.001 PHE A 302 TRP 0.011 0.001 TRP C 209 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00411 (10858) covalent geometry : angle 0.61146 (14806) SS BOND : bond 0.00413 ( 4) SS BOND : angle 1.39643 ( 8) hydrogen bonds : bond 0.04037 ( 515) hydrogen bonds : angle 4.08231 ( 1485) link_BETA1-3 : bond 0.00839 ( 1) link_BETA1-3 : angle 2.13268 ( 3) link_BETA1-4 : bond 0.00242 ( 7) link_BETA1-4 : angle 1.44178 ( 21) link_BETA1-6 : bond 0.01702 ( 1) link_BETA1-6 : angle 3.07374 ( 3) link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 2.66258 ( 36) *********************** 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 134 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8119 (t0) cc_final: 0.7721 (t0) REVERT: A 612 ASN cc_start: 0.8478 (m-40) cc_final: 0.7976 (t0) REVERT: A 652 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8308 (mtt180) REVERT: B 134 LEU cc_start: 0.8089 (mp) cc_final: 0.7772 (tt) REVERT: B 184 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 244 TRP cc_start: 0.7153 (m-10) cc_final: 0.6367 (m100) REVERT: B 454 GLN cc_start: 0.8760 (tp40) cc_final: 0.8340 (tp-100) REVERT: C 71 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.7989 (mp) REVERT: C 101 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7970 (tt) REVERT: C 109 ARG cc_start: 0.7447 (ptp-110) cc_final: 0.7165 (ptm-80) REVERT: C 116 GLN cc_start: 0.8748 (mt0) cc_final: 0.8147 (mt0) REVERT: D 34 ILE cc_start: 0.7404 (mt) cc_final: 0.7151 (mt) REVERT: D 40 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6925 (mp0) REVERT: D 52 GLN cc_start: 0.7568 (tt0) cc_final: 0.7152 (mm-40) outliers start: 39 outliers final: 27 residues processed: 126 average time/residue: 0.0678 time to fit residues: 13.4897 Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 605 VAL 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 B residue 419 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 101 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 53 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 77 ILE 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: 2.9990 chunk 120 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.101380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077279 restraints weight = 22125.864| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.94 r_work: 0.2830 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2966 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= 0.146 Angle : 0.605 13.106 14877 Z= 0.285 Chirality : 0.043 0.250 1772 Planarity : 0.004 0.050 1790 Dihedral : 9.072 86.183 2027 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.44 % Allowed : 11.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.24), residues: 1277 helix: 1.38 (0.20), residues: 686 sheet: -1.64 (0.45), residues: 127 loop : -2.06 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.015 0.001 TYR B 446 PHE 0.027 0.001 PHE A 302 TRP 0.010 0.001 TRP A 257 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00341 (10858) covalent geometry : angle 0.58859 (14806) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.11468 ( 8) hydrogen bonds : bond 0.03747 ( 515) hydrogen bonds : angle 3.99610 ( 1485) link_BETA1-3 : bond 0.00896 ( 1) link_BETA1-3 : angle 2.11986 ( 3) link_BETA1-4 : bond 0.00305 ( 7) link_BETA1-4 : angle 1.32462 ( 21) link_BETA1-6 : bond 0.01452 ( 1) link_BETA1-6 : angle 3.31983 ( 3) link_NAG-ASN : bond 0.00364 ( 12) link_NAG-ASN : angle 2.46997 ( 36) *********************** 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 145 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8131 (t0) cc_final: 0.7742 (t0) REVERT: A 612 ASN cc_start: 0.8482 (m-40) cc_final: 0.7996 (t0) REVERT: A 652 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8299 (mtt180) REVERT: B 134 LEU cc_start: 0.8089 (mp) cc_final: 0.7772 (tt) REVERT: B 184 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8404 (mm-30) REVERT: B 244 TRP cc_start: 0.7104 (m-10) cc_final: 0.6283 (m100) REVERT: B 454 GLN cc_start: 0.8754 (tp40) cc_final: 0.8417 (tp-100) REVERT: C 48 LEU cc_start: 0.8724 (mt) cc_final: 0.8306 (tp) REVERT: C 71 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 101 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7966 (tt) REVERT: C 116 GLN cc_start: 0.8736 (mt0) cc_final: 0.8104 (mt0) REVERT: D 34 ILE cc_start: 0.7426 (mt) cc_final: 0.7179 (mt) REVERT: D 40 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6839 (mp0) REVERT: D 52 GLN cc_start: 0.7561 (tt0) cc_final: 0.7161 (mm-40) outliers start: 38 outliers final: 29 residues processed: 136 average time/residue: 0.0799 time to fit residues: 16.6863 Evaluate side-chains 129 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 150 LEU Chi-restraints excluded: chain B residue 211 ILE 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 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 101 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 53 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.100232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.075923 restraints weight = 22136.526| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.95 r_work: 0.2817 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10883 Z= 0.189 Angle : 0.637 14.136 14877 Z= 0.301 Chirality : 0.044 0.250 1772 Planarity : 0.004 0.051 1790 Dihedral : 8.898 78.549 2027 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.53 % Allowed : 13.11 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1277 helix: 1.45 (0.21), residues: 681 sheet: -1.52 (0.47), residues: 115 loop : -2.11 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.015 0.001 TYR B 189 PHE 0.027 0.001 PHE A 302 TRP 0.009 0.001 TRP D 36 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00446 (10858) covalent geometry : angle 0.61989 (14806) SS BOND : bond 0.00480 ( 4) SS BOND : angle 1.81411 ( 8) hydrogen bonds : bond 0.03947 ( 515) hydrogen bonds : angle 4.03720 ( 1485) link_BETA1-3 : bond 0.00813 ( 1) link_BETA1-3 : angle 2.27835 ( 3) link_BETA1-4 : bond 0.00236 ( 7) link_BETA1-4 : angle 1.40411 ( 21) link_BETA1-6 : bond 0.01269 ( 1) link_BETA1-6 : angle 3.58507 ( 3) link_NAG-ASN : bond 0.00377 ( 12) link_NAG-ASN : angle 2.47833 ( 36) *********************** 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 139 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8165 (t0) cc_final: 0.7926 (t0) REVERT: A 612 ASN cc_start: 0.8470 (m-40) cc_final: 0.8007 (t0) REVERT: A 652 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8310 (mtt180) REVERT: B 134 LEU cc_start: 0.8115 (mp) cc_final: 0.7815 (tt) REVERT: B 184 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 222 GLN cc_start: 0.8506 (tt0) cc_final: 0.8172 (pt0) REVERT: B 244 TRP cc_start: 0.7083 (m-10) cc_final: 0.6248 (m100) REVERT: B 247 TRP cc_start: 0.7721 (m100) cc_final: 0.7343 (m100) REVERT: B 454 GLN cc_start: 0.8705 (tp40) cc_final: 0.8338 (tp-100) REVERT: C 48 LEU cc_start: 0.8750 (mt) cc_final: 0.8276 (tp) REVERT: C 71 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8038 (mp) REVERT: C 101 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8008 (tt) REVERT: C 116 GLN cc_start: 0.8766 (mt0) cc_final: 0.8146 (mt0) REVERT: D 34 ILE cc_start: 0.7418 (mt) cc_final: 0.7172 (mt) REVERT: D 40 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6858 (mp0) REVERT: D 52 GLN cc_start: 0.7578 (tt0) cc_final: 0.7174 (mm-40) outliers start: 39 outliers final: 33 residues processed: 132 average time/residue: 0.0740 time to fit residues: 15.2573 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 605 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 211 ILE 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 51 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 101 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 182 CYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 53 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 50 optimal weight: 0.0060 chunk 116 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.102662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.078633 restraints weight = 21742.322| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.93 r_work: 0.2871 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10883 Z= 0.103 Angle : 0.573 11.812 14877 Z= 0.269 Chirality : 0.042 0.237 1772 Planarity : 0.003 0.049 1790 Dihedral : 8.286 73.866 2027 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.98 % Allowed : 13.65 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1277 helix: 1.63 (0.21), residues: 690 sheet: -1.43 (0.46), residues: 127 loop : -1.88 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.014 0.001 TYR A 569 PHE 0.028 0.001 PHE A 302 TRP 0.009 0.001 TRP A 257 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00222 (10858) covalent geometry : angle 0.55788 (14806) SS BOND : bond 0.00232 ( 4) SS BOND : angle 1.27470 ( 8) hydrogen bonds : bond 0.03308 ( 515) hydrogen bonds : angle 3.90399 ( 1485) link_BETA1-3 : bond 0.00972 ( 1) link_BETA1-3 : angle 1.87716 ( 3) link_BETA1-4 : bond 0.00382 ( 7) link_BETA1-4 : angle 1.16067 ( 21) link_BETA1-6 : bond 0.01047 ( 1) link_BETA1-6 : angle 4.19057 ( 3) link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 2.14808 ( 36) *********************** 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 140 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 283 ASP cc_start: 0.9244 (p0) cc_final: 0.9022 (p0) REVERT: A 548 ASP cc_start: 0.8102 (t0) cc_final: 0.7845 (t0) REVERT: A 612 ASN cc_start: 0.8441 (m-40) cc_final: 0.7990 (t0) REVERT: A 652 ARG cc_start: 0.8827 (mtp85) cc_final: 0.8256 (mtt180) REVERT: B 134 LEU cc_start: 0.8216 (mp) cc_final: 0.7902 (tt) REVERT: B 184 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8389 (mm-30) REVERT: B 222 GLN cc_start: 0.8456 (tt0) cc_final: 0.8071 (pt0) REVERT: B 244 TRP cc_start: 0.7084 (m-10) cc_final: 0.6222 (m100) REVERT: C 48 LEU cc_start: 0.8775 (mt) cc_final: 0.8256 (tp) REVERT: C 67 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6950 (tt) REVERT: C 101 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7941 (tt) REVERT: C 116 GLN cc_start: 0.8694 (mt0) cc_final: 0.8055 (mt0) REVERT: D 34 ILE cc_start: 0.7447 (mt) cc_final: 0.7213 (mt) REVERT: D 40 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6840 (mp0) REVERT: D 52 GLN cc_start: 0.7496 (tt0) cc_final: 0.7120 (mm-40) outliers start: 33 outliers final: 25 residues processed: 131 average time/residue: 0.0842 time to fit residues: 17.1878 Evaluate side-chains 123 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 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 198 VAL 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 67 LEU Chi-restraints excluded: chain C residue 101 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 183 GLU Chi-restraints excluded: chain C residue 243 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.077511 restraints weight = 22111.915| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.98 r_work: 0.2858 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3275 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= 0.119 Angle : 0.584 12.537 14877 Z= 0.277 Chirality : 0.042 0.240 1772 Planarity : 0.004 0.049 1790 Dihedral : 7.926 73.315 2025 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.62 % Allowed : 14.47 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1277 helix: 1.71 (0.20), residues: 690 sheet: -1.23 (0.47), residues: 129 loop : -1.82 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 539 TYR 0.020 0.001 TYR B 389 PHE 0.027 0.001 PHE A 302 TRP 0.007 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00272 (10858) covalent geometry : angle 0.56915 (14806) SS BOND : bond 0.00259 ( 4) SS BOND : angle 1.19167 ( 8) hydrogen bonds : bond 0.03427 ( 515) hydrogen bonds : angle 3.89474 ( 1485) link_BETA1-3 : bond 0.00924 ( 1) link_BETA1-3 : angle 2.14964 ( 3) link_BETA1-4 : bond 0.00269 ( 7) link_BETA1-4 : angle 1.25898 ( 21) link_BETA1-6 : bond 0.00704 ( 1) link_BETA1-6 : angle 4.25007 ( 3) link_NAG-ASN : bond 0.00289 ( 12) link_NAG-ASN : angle 2.09427 ( 36) *********************** 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 130 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8171 (t0) cc_final: 0.7908 (t0) REVERT: A 612 ASN cc_start: 0.8440 (m-40) cc_final: 0.7988 (t0) REVERT: A 652 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8562 (mtt180) REVERT: B 134 LEU cc_start: 0.8202 (mp) cc_final: 0.7890 (tt) REVERT: B 184 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8410 (mm-30) REVERT: B 244 TRP cc_start: 0.7062 (m-10) cc_final: 0.6177 (m100) REVERT: B 454 GLN cc_start: 0.8550 (tp40) cc_final: 0.8151 (tp-100) REVERT: C 48 LEU cc_start: 0.8683 (mt) cc_final: 0.8257 (tp) REVERT: C 67 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7058 (tt) REVERT: C 101 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7973 (tt) REVERT: C 116 GLN cc_start: 0.8715 (mt0) cc_final: 0.8092 (mt0) REVERT: D 34 ILE cc_start: 0.7451 (mt) cc_final: 0.7204 (mt) REVERT: D 40 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6851 (mp0) REVERT: D 52 GLN cc_start: 0.7627 (tt0) cc_final: 0.7251 (mm-40) outliers start: 29 outliers final: 25 residues processed: 124 average time/residue: 0.0723 time to fit residues: 14.0109 Evaluate side-chains 125 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 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 198 VAL 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 67 LEU Chi-restraints excluded: chain C residue 101 LEU 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 231 THR 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 20 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 90 optimal weight: 0.0170 chunk 122 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.074973 restraints weight = 22100.870| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.91 r_work: 0.2797 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10883 Z= 0.248 Angle : 0.685 15.770 14877 Z= 0.328 Chirality : 0.046 0.236 1772 Planarity : 0.004 0.050 1790 Dihedral : 7.964 73.520 2025 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.62 % Allowed : 14.38 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.25), residues: 1277 helix: 1.56 (0.20), residues: 688 sheet: -1.23 (0.48), residues: 119 loop : -1.88 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.017 0.002 TYR B 389 PHE 0.026 0.002 PHE A 302 TRP 0.014 0.001 TRP B 247 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00585 (10858) covalent geometry : angle 0.66755 (14806) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.45757 ( 8) hydrogen bonds : bond 0.04286 ( 515) hydrogen bonds : angle 4.08374 ( 1485) link_BETA1-3 : bond 0.00542 ( 1) link_BETA1-3 : angle 2.64519 ( 3) link_BETA1-4 : bond 0.00242 ( 7) link_BETA1-4 : angle 1.55662 ( 21) link_BETA1-6 : bond 0.00466 ( 1) link_BETA1-6 : angle 3.97683 ( 3) link_NAG-ASN : bond 0.00462 ( 12) link_NAG-ASN : angle 2.59438 ( 36) ********************** 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 121 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 548 ASP cc_start: 0.8305 (t0) cc_final: 0.8086 (t0) REVERT: A 612 ASN cc_start: 0.8474 (m-40) cc_final: 0.8034 (t0) REVERT: A 652 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8639 (mtt180) REVERT: B 134 LEU cc_start: 0.8150 (mp) cc_final: 0.7828 (tt) REVERT: B 184 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8516 (mm-30) REVERT: B 222 GLN cc_start: 0.8542 (tt0) cc_final: 0.8211 (pt0) REVERT: B 244 TRP cc_start: 0.7080 (m-10) cc_final: 0.6229 (m100) REVERT: B 454 GLN cc_start: 0.8546 (tp40) cc_final: 0.8177 (tp-100) REVERT: C 101 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8024 (tt) REVERT: C 116 GLN cc_start: 0.8758 (mt0) cc_final: 0.8134 (mt0) REVERT: D 34 ILE cc_start: 0.7405 (mt) cc_final: 0.7150 (mt) REVERT: D 40 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6981 (mp0) REVERT: D 52 GLN cc_start: 0.7659 (tt0) cc_final: 0.7281 (mm-40) outliers start: 29 outliers final: 23 residues processed: 118 average time/residue: 0.0657 time to fit residues: 12.1325 Evaluate side-chains 116 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 114 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 198 VAL 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 101 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 SER 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 214 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 71 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.101629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.076515 restraints weight = 22374.132| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.99 r_work: 0.2836 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10883 Z= 0.123 Angle : 0.595 12.908 14877 Z= 0.285 Chirality : 0.042 0.237 1772 Planarity : 0.004 0.048 1790 Dihedral : 7.572 73.742 2025 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 14.92 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1277 helix: 1.69 (0.20), residues: 692 sheet: -0.91 (0.49), residues: 114 loop : -1.83 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.017 0.001 TYR B 389 PHE 0.027 0.001 PHE A 302 TRP 0.010 0.001 TRP B 247 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00281 (10858) covalent geometry : angle 0.58182 (14806) SS BOND : bond 0.00281 ( 4) SS BOND : angle 1.06400 ( 8) hydrogen bonds : bond 0.03588 ( 515) hydrogen bonds : angle 3.94081 ( 1485) link_BETA1-3 : bond 0.00734 ( 1) link_BETA1-3 : angle 2.03262 ( 3) link_BETA1-4 : bond 0.00360 ( 7) link_BETA1-4 : angle 1.26232 ( 21) link_BETA1-6 : bond 0.00281 ( 1) link_BETA1-6 : angle 3.39549 ( 3) link_NAG-ASN : bond 0.00327 ( 12) link_NAG-ASN : angle 2.11445 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.46 seconds wall clock time: 32 minutes 32.03 seconds (1952.03 seconds total)