Starting phenix.real_space_refine on Sat May 24 16:02:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3k_39746/05_2025/8z3k_39746_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3k_39746/05_2025/8z3k_39746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3k_39746/05_2025/8z3k_39746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3k_39746/05_2025/8z3k_39746.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3k_39746/05_2025/8z3k_39746_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3k_39746/05_2025/8z3k_39746_trim.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 18 5.49 5 S 117 5.16 5 C 15976 2.51 5 N 4752 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25451 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4741 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 40, 'TRANS': 572} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "C" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4810 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 40, 'TRANS': 572} Chain breaks: 1 Chain: "D" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4759 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 40, 'TRANS': 573} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3014 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 27, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2979 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 27, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "H" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "I" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.84, per 1000 atoms: 0.66 Number of scatterers: 25451 At special positions: 0 Unit cell: (98.792, 150.984, 213.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 117 16.00 P 18 15.00 O 4586 8.00 N 4752 7.00 C 15976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 471 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 264 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 266 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 266 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 264 " 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5990 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 17 sheets defined 51.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 42 through 52 removed outlier: 3.697A pdb=" N HIS A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.800A pdb=" N HIS A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.500A pdb=" N MET A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 153 removed outlier: 3.695A pdb=" N TRP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 217 Processing helix chain 'A' and resid 218 through 221 removed outlier: 4.047A pdb=" N LEU A 221 " --> pdb=" O TRP A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.549A pdb=" N LEU A 277 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 317 through 321 removed outlier: 5.336A pdb=" N ALA A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.726A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 365 through 384 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.846A pdb=" N LEU A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 428 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 458 through 465 removed outlier: 4.015A pdb=" N HIS A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 553 through 561 Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.734A pdb=" N ALA A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 608 removed outlier: 3.561A pdb=" N LEU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'B' and resid 16 through 23 removed outlier: 3.519A pdb=" N GLU B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.511A pdb=" N HIS B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 198 through 217 removed outlier: 3.548A pdb=" N THR B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 219 No H-bonds generated for 'chain 'B' and resid 218 through 219' Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.939A pdb=" N LEU B 277 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.633A pdb=" N LYS B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 365 through 384 Processing helix chain 'B' and resid 409 through 428 removed outlier: 3.889A pdb=" N ALA B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.908A pdb=" N ILE B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 553 through 561 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 589 removed outlier: 3.781A pdb=" N ALA B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 608 removed outlier: 3.674A pdb=" N LEU B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.743A pdb=" N HIS C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.906A pdb=" N ARG C 152 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.647A pdb=" N TRP C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.542A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 318 removed outlier: 3.936A pdb=" N GLY C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 327 removed outlier: 3.717A pdb=" N ARG C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 346 Processing helix chain 'C' and resid 365 through 384 Processing helix chain 'C' and resid 409 through 428 removed outlier: 3.703A pdb=" N ALA C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 removed outlier: 4.222A pdb=" N ARG C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.515A pdb=" N PHE C 454 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU C 456 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 464 removed outlier: 4.365A pdb=" N VAL C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 removed outlier: 3.554A pdb=" N ILE C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 501 removed outlier: 4.189A pdb=" N GLY C 500 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 501 " --> pdb=" O SER C 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 501' Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 553 through 560 Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.507A pdb=" N SER C 574 " --> pdb=" O ASN C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 593 through 608 removed outlier: 3.525A pdb=" N LEU C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 624 removed outlier: 3.676A pdb=" N SER C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 42 through 53 Processing helix chain 'D' and resid 71 through 89 removed outlier: 3.517A pdb=" N SER D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.518A pdb=" N TRP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 198 through 221 removed outlier: 3.562A pdb=" N GLY D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.723A pdb=" N ASN D 321 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 327 removed outlier: 4.092A pdb=" N ARG D 327 " --> pdb=" O ALA D 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 327' Processing helix chain 'D' and resid 328 through 347 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.535A pdb=" N ALA D 361 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.558A pdb=" N GLY D 390 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU D 391 " --> pdb=" O PRO D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 391' Processing helix chain 'D' and resid 410 through 428 removed outlier: 3.750A pdb=" N ARG D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 3.613A pdb=" N THR D 459 " --> pdb=" O ARG D 455 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 553 through 561 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 577 through 589 Processing helix chain 'D' and resid 595 through 608 Processing helix chain 'D' and resid 611 through 625 removed outlier: 3.747A pdb=" N SER D 624 " --> pdb=" O ARG D 620 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 625 " --> pdb=" O ARG D 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.519A pdb=" N LEU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP E 239 " --> pdb=" O GLY E 235 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 258 removed outlier: 4.070A pdb=" N ASP E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 274 through 282 removed outlier: 3.541A pdb=" N VAL E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 328 through 347 removed outlier: 3.678A pdb=" N LEU E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR E 340 " --> pdb=" O CYS E 336 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 Processing helix chain 'E' and resid 365 through 384 Processing helix chain 'E' and resid 409 through 428 removed outlier: 3.578A pdb=" N ALA E 413 " --> pdb=" O ASP E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 465 removed outlier: 6.154A pdb=" N GLU E 456 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU E 457 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 488 Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 519 through 527 Processing helix chain 'E' and resid 553 through 561 Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 577 through 589 removed outlier: 3.698A pdb=" N ARG E 587 " --> pdb=" O LEU E 583 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS E 589 " --> pdb=" O ALA E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 608 Processing helix chain 'E' and resid 611 through 623 removed outlier: 3.623A pdb=" N THR E 617 " --> pdb=" O THR E 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.661A pdb=" N THR F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 232' Processing helix chain 'F' and resid 233 through 241 removed outlier: 3.599A pdb=" N TRP F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 257 removed outlier: 3.534A pdb=" N GLY F 257 " --> pdb=" O ARG F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 282 Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 328 through 345 removed outlier: 3.800A pdb=" N ASP F 345 " --> pdb=" O ARG F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 383 removed outlier: 3.923A pdb=" N GLY F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 426 removed outlier: 3.997A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 426 " --> pdb=" O VAL F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 454 Processing helix chain 'F' and resid 454 through 463 removed outlier: 3.905A pdb=" N PHE F 458 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 460 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG F 463 " --> pdb=" O THR F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 487 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 513 Processing helix chain 'F' and resid 519 through 527 Processing helix chain 'F' and resid 553 through 561 Processing helix chain 'F' and resid 570 through 575 Processing helix chain 'F' and resid 577 through 589 removed outlier: 3.528A pdb=" N ALA F 586 " --> pdb=" O LEU F 582 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 587 " --> pdb=" O LEU F 583 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 608 removed outlier: 3.988A pdb=" N ALA F 604 " --> pdb=" O LEU F 600 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU F 605 " --> pdb=" O GLN F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 623 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 7.112A pdb=" N ALA A 5 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS A 33 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU A 7 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 35 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 9 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE A 60 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 190 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A 192 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A 185 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 266 removed outlier: 4.599A pdb=" N ILE A 261 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU A 352 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 263 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG A 354 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS A 265 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 395 " --> pdb=" O CYS A 349 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N VAL A 396 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N GLY A 438 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 398 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP A 440 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 400 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 437 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR A 469 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL A 439 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N HIS A 471 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 492 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 493 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161 removed outlier: 6.551A pdb=" N VAL B 98 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 10 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU B 7 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU B 35 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 9 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 32 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR B 61 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 34 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 60 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 193 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU B 186 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG B 192 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 182 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 261 through 266 removed outlier: 4.580A pdb=" N ILE B 261 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU B 352 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU B 263 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B 354 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B 265 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL B 437 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU B 398 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL B 439 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 400 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 468 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N GLY B 494 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 470 " --> pdb=" O GLY B 494 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 493 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 403 through 404 removed outlier: 3.654A pdb=" N ARG B 404 " --> pdb=" O ALA B 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 7 through 10 removed outlier: 5.969A pdb=" N LEU C 7 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 35 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 9 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 32 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR C 61 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 34 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 60 " --> pdb=" O ARG C 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'C' and resid 260 through 266 removed outlier: 4.636A pdb=" N ILE C 261 " --> pdb=" O TYR C 350 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU C 352 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU C 263 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 354 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS C 265 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 395 " --> pdb=" O CYS C 349 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL C 437 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU C 398 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 439 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU C 400 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU C 441 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 402 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLY C 443 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 404 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 467 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY C 443 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 468 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLY C 494 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 470 " --> pdb=" O GLY C 494 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU C 493 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 6 through 9 removed outlier: 6.335A pdb=" N HIS D 6 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N CYS D 99 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE D 8 " --> pdb=" O CYS D 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 34 through 35 removed outlier: 6.466A pdb=" N VAL D 34 " --> pdb=" O THR D 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 124 through 128 Processing sheet with id=AB4, first strand: chain 'D' and resid 265 through 266 removed outlier: 6.374A pdb=" N CYS D 265 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA D 351 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE D 399 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 353 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL D 437 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU D 398 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL D 439 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU D 400 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 437 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR D 469 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL D 439 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL D 468 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY D 494 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL D 470 " --> pdb=" O GLY D 494 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 516 " --> pdb=" O THR D 565 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 265 through 266 removed outlier: 6.710A pdb=" N CYS E 265 " --> pdb=" O ARG E 354 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA E 351 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE E 399 " --> pdb=" O ALA E 351 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 353 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL E 437 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU E 398 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL E 439 " --> pdb=" O LEU E 398 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU E 400 " --> pdb=" O VAL E 439 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 492 through 493 removed outlier: 7.092A pdb=" N LEU E 493 " --> pdb=" O GLU E 517 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AB8, first strand: chain 'F' and resid 354 through 355 removed outlier: 4.815A pdb=" N LEU F 398 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL F 439 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU F 400 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR F 469 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL F 439 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG F 492 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL F 516 " --> pdb=" O THR F 565 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 3084 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: 9.85 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8816 1.34 - 1.46: 4848 1.46 - 1.58: 12226 1.58 - 1.69: 32 1.69 - 1.81: 150 Bond restraints: 26072 Sorted by residual: bond pdb=" C4 ATP C 702 " pdb=" C5 ATP C 702 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.64e+01 bond pdb=" C5 ATP C 702 " pdb=" C6 ATP C 702 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.23e+01 bond pdb=" C5 ATP C 702 " pdb=" N7 ATP C 702 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.25e+01 bond pdb=" C8 ATP C 702 " pdb=" N7 ATP C 702 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.17e+01 bond pdb=" C4 ATP C 702 " pdb=" N9 ATP C 702 " ideal model delta sigma weight residual 1.374 1.328 0.046 1.00e-02 1.00e+04 2.10e+01 ... (remaining 26067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 35473 4.54 - 9.09: 74 9.09 - 13.63: 5 13.63 - 18.18: 1 18.18 - 22.72: 1 Bond angle restraints: 35554 Sorted by residual: angle pdb=" PB ATP C 702 " pdb=" O3B ATP C 702 " pdb=" PG ATP C 702 " ideal model delta sigma weight residual 139.87 117.15 22.72 1.00e+00 1.00e+00 5.16e+02 angle pdb=" PA ATP C 702 " pdb=" O3A ATP C 702 " pdb=" PB ATP C 702 " ideal model delta sigma weight residual 136.83 122.46 14.37 1.00e+00 1.00e+00 2.07e+02 angle pdb=" C5 ATP C 702 " pdb=" C4 ATP C 702 " pdb=" N3 ATP C 702 " ideal model delta sigma weight residual 126.80 118.65 8.15 1.00e+00 1.00e+00 6.64e+01 angle pdb=" N3 ATP C 702 " pdb=" C4 ATP C 702 " pdb=" N9 ATP C 702 " ideal model delta sigma weight residual 127.04 135.09 -8.05 1.15e+00 7.59e-01 4.91e+01 angle pdb=" N1 ATP C 702 " pdb=" C2 ATP C 702 " pdb=" N3 ATP C 702 " ideal model delta sigma weight residual 128.69 123.16 5.53 1.00e+00 1.00e+00 3.05e+01 ... (remaining 35549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 14149 16.90 - 33.80: 1186 33.80 - 50.69: 266 50.69 - 67.59: 36 67.59 - 84.49: 27 Dihedral angle restraints: 15664 sinusoidal: 6389 harmonic: 9275 Sorted by residual: dihedral pdb=" CA ALA C 387 " pdb=" C ALA C 387 " pdb=" N PRO C 388 " pdb=" CA PRO C 388 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ALA B 387 " pdb=" C ALA B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA PRO A 142 " pdb=" C PRO A 142 " pdb=" N SER A 143 " pdb=" CA SER A 143 " ideal model delta harmonic sigma weight residual 180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 15661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3395 0.059 - 0.119: 507 0.119 - 0.178: 31 0.178 - 0.237: 6 0.237 - 0.296: 3 Chirality restraints: 3942 Sorted by residual: chirality pdb=" C2' ATP B 702 " pdb=" C1' ATP B 702 " pdb=" C3' ATP B 702 " pdb=" O2' ATP B 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' ATP B 702 " pdb=" C2' ATP B 702 " pdb=" C4' ATP B 702 " pdb=" O3' ATP B 702 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C4' ATP B 702 " pdb=" C3' ATP B 702 " pdb=" C5' ATP B 702 " pdb=" O4' ATP B 702 " both_signs ideal model delta sigma weight residual False -2.49 -2.75 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 3939 not shown) Planarity restraints: 4660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 387 " 0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO C 388 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 387 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO B 388 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 387 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO E 388 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 388 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 388 " 0.028 5.00e-02 4.00e+02 ... (remaining 4657 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 251 2.55 - 3.14: 20869 3.14 - 3.73: 42130 3.73 - 4.31: 55239 4.31 - 4.90: 91703 Nonbonded interactions: 210192 Sorted by model distance: nonbonded pdb=" O GLY B 268 " pdb=" O1A ATP B 702 " model vdw 1.964 3.040 nonbonded pdb=" OD1 ASP D 228 " pdb=" OG SER D 623 " model vdw 2.089 3.040 nonbonded pdb=" OD2 ASP E 476 " pdb=" OG SER E 498 " model vdw 2.134 3.040 nonbonded pdb=" OG SER C 143 " pdb=" OE1 GLU C 147 " model vdw 2.173 3.040 nonbonded pdb=" NH2 ARG A 62 " pdb=" OE2 GLU A 190 " model vdw 2.174 3.120 ... (remaining 210187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 458 or (resid 459 through 460 and (name N or nam \ e CA or name C or name O or name CB )) or resid 461 through 532 or resid 549 thr \ ough 629)) selection = (chain 'B' and (resid 2 through 443 or (resid 444 through 460 and (name N or nam \ e CA or name C or name O or name CB )) or resid 461 through 532 or resid 549 thr \ ough 629)) selection = (chain 'C' and (resid 2 through 443 or (resid 444 through 460 and (name N or nam \ e CA or name C or name O or name CB )) or resid 461 through 532 or resid 549 thr \ ough 629)) selection = (chain 'D' and (resid 2 through 443 or (resid 444 through 460 and (name N or nam \ e CA or name C or name O or name CB )) or resid 461 through 532 or resid 549 thr \ ough 629)) } ncs_group { reference = (chain 'E' and (resid 221 through 384 or (resid 385 and (name N or name CA or na \ me C or name O or name CB )) or resid 386 through 445 or (resid 446 through 460 \ and (name N or name CA or name C or name O or name CB )) or resid 461 through 62 \ 7 or (resid 628 and (name N or name CA or name C or name O or name CB )) or resi \ d 629)) selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.170 Set scattering table: 0.260 Process input model: 65.560 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:3.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.006 0.646 26079 Z= 0.451 Angle : 0.672 22.724 35554 Z= 0.366 Chirality : 0.042 0.296 3942 Planarity : 0.005 0.069 4660 Dihedral : 13.549 84.490 9674 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.57 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3220 helix: 1.08 (0.14), residues: 1429 sheet: -2.65 (0.24), residues: 384 loop : -1.62 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 232 HIS 0.007 0.001 HIS B 264 PHE 0.015 0.001 PHE B 97 TYR 0.015 0.001 TYR B 552 ARG 0.010 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.24623 ( 1061) hydrogen bonds : angle 7.24500 ( 3084) metal coordination : bond 0.00078 ( 5) covalent geometry : bond 0.00395 (26072) covalent geometry : angle 0.67167 (35554) Misc. bond : bond 0.46431 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8747 (mppt) cc_final: 0.8449 (mmtm) REVERT: A 219 GLU cc_start: 0.8870 (tp30) cc_final: 0.8422 (tp30) REVERT: A 313 GLU cc_start: 0.8717 (mp0) cc_final: 0.8517 (tm-30) REVERT: A 379 GLU cc_start: 0.9022 (tt0) cc_final: 0.8709 (pt0) REVERT: A 416 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8020 (mtt180) REVERT: A 483 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7755 (ptm-80) REVERT: B 482 TRP cc_start: 0.8426 (t60) cc_final: 0.8155 (t60) REVERT: B 527 LYS cc_start: 0.8823 (mttm) cc_final: 0.8550 (mttt) REVERT: C 111 MET cc_start: 0.8612 (mmt) cc_final: 0.8351 (mmp) REVERT: C 314 TYR cc_start: 0.8630 (t80) cc_final: 0.8425 (t80) REVERT: C 316 LYS cc_start: 0.9291 (mptt) cc_final: 0.9013 (mtpp) REVERT: C 410 TYR cc_start: 0.8479 (p90) cc_final: 0.8127 (p90) REVERT: E 337 ARG cc_start: 0.7695 (tpt90) cc_final: 0.7324 (tmt-80) REVERT: E 487 ASP cc_start: 0.8458 (t0) cc_final: 0.8163 (t70) REVERT: E 623 SER cc_start: 0.8430 (p) cc_final: 0.8193 (m) REVERT: F 289 LYS cc_start: 0.8154 (pttm) cc_final: 0.7917 (tptp) REVERT: F 410 TYR cc_start: 0.8347 (p90) cc_final: 0.8064 (p90) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.5909 time to fit residues: 154.1189 Evaluate side-chains 109 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 7.9990 chunk 244 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 273 HIS A 427 HIS A 489 ASN B 489 ASN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN C 570 ASN D 209 GLN D 567 ASN E 335 GLN E 397 ASN E 525 GLN ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN ** F 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.065543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053816 restraints weight = 111968.454| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.63 r_work: 0.3062 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26079 Z= 0.176 Angle : 0.660 11.386 35554 Z= 0.332 Chirality : 0.042 0.206 3942 Planarity : 0.005 0.067 4660 Dihedral : 6.932 88.407 3805 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.26 % Favored : 91.18 % Rotamer: Outliers : 0.55 % Allowed : 7.29 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3220 helix: 1.21 (0.13), residues: 1492 sheet: -2.67 (0.24), residues: 388 loop : -1.71 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 232 HIS 0.006 0.001 HIS C 125 PHE 0.020 0.002 PHE C 49 TYR 0.019 0.001 TYR C 521 ARG 0.007 0.000 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.05382 ( 1061) hydrogen bonds : angle 5.12238 ( 3084) metal coordination : bond 0.00220 ( 5) covalent geometry : bond 0.00401 (26072) covalent geometry : angle 0.65959 (35554) Misc. bond : bond 0.00885 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8722 (mppt) cc_final: 0.8500 (mmtm) REVERT: A 219 GLU cc_start: 0.9027 (tp30) cc_final: 0.8513 (tp30) REVERT: A 313 GLU cc_start: 0.8687 (mp0) cc_final: 0.8361 (tm-30) REVERT: A 379 GLU cc_start: 0.9169 (tt0) cc_final: 0.8874 (pt0) REVERT: A 416 ARG cc_start: 0.8795 (mtt180) cc_final: 0.8555 (mtt-85) REVERT: A 483 ARG cc_start: 0.8466 (ptm-80) cc_final: 0.8027 (ttt-90) REVERT: B 289 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9107 (mmmt) REVERT: B 444 TYR cc_start: 0.8689 (t80) cc_final: 0.7880 (t80) REVERT: B 482 TRP cc_start: 0.8658 (t60) cc_final: 0.8428 (t60) REVERT: B 527 LYS cc_start: 0.8938 (mttm) cc_final: 0.8718 (mttt) REVERT: C 111 MET cc_start: 0.8750 (mmt) cc_final: 0.8444 (mpp) REVERT: C 140 MET cc_start: 0.8684 (pmm) cc_final: 0.8051 (mtm) REVERT: C 289 LYS cc_start: 0.9391 (mmtm) cc_final: 0.8966 (mmtm) REVERT: C 315 MET cc_start: 0.8853 (mtm) cc_final: 0.8582 (mtp) REVERT: C 316 LYS cc_start: 0.9288 (mptt) cc_final: 0.9022 (mtpp) REVERT: D 527 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8882 (mmtp) REVERT: E 252 GLN cc_start: 0.8041 (mt0) cc_final: 0.7791 (mt0) REVERT: E 487 ASP cc_start: 0.8613 (t0) cc_final: 0.8332 (t70) REVERT: F 289 LYS cc_start: 0.8468 (pttm) cc_final: 0.7916 (tptp) REVERT: F 410 TYR cc_start: 0.8491 (p90) cc_final: 0.8203 (p90) REVERT: F 594 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7262 (ttm-80) outliers start: 14 outliers final: 9 residues processed: 130 average time/residue: 0.5711 time to fit residues: 105.2077 Evaluate side-chains 115 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 552 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 317 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 HIS E 601 GLN ** F 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.065633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.053906 restraints weight = 111782.590| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.63 r_work: 0.3068 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26079 Z= 0.148 Angle : 0.590 7.449 35554 Z= 0.297 Chirality : 0.040 0.153 3942 Planarity : 0.005 0.066 4660 Dihedral : 6.648 81.544 3805 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.61 % Favored : 91.83 % Rotamer: Outliers : 1.18 % Allowed : 10.54 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3220 helix: 1.38 (0.14), residues: 1502 sheet: -2.59 (0.24), residues: 381 loop : -1.69 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 232 HIS 0.005 0.001 HIS C 75 PHE 0.027 0.002 PHE D 78 TYR 0.019 0.001 TYR C 521 ARG 0.004 0.000 ARG E 337 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 1061) hydrogen bonds : angle 4.61900 ( 3084) metal coordination : bond 0.00076 ( 5) covalent geometry : bond 0.00340 (26072) covalent geometry : angle 0.59000 (35554) Misc. bond : bond 0.00783 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8729 (mppt) cc_final: 0.8524 (mmtm) REVERT: A 219 GLU cc_start: 0.8915 (tp30) cc_final: 0.8460 (tp30) REVERT: A 313 GLU cc_start: 0.8713 (mp0) cc_final: 0.8408 (tm-30) REVERT: A 379 GLU cc_start: 0.9149 (tt0) cc_final: 0.8823 (pt0) REVERT: A 416 ARG cc_start: 0.8838 (mtt180) cc_final: 0.8481 (mtt-85) REVERT: A 483 ARG cc_start: 0.8429 (ptm-80) cc_final: 0.8194 (ptm-80) REVERT: B 289 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9110 (mmmt) REVERT: B 448 LYS cc_start: 0.9374 (tmtt) cc_final: 0.9099 (mmtp) REVERT: B 482 TRP cc_start: 0.8714 (t60) cc_final: 0.8499 (t60) REVERT: B 527 LYS cc_start: 0.8956 (mttm) cc_final: 0.8747 (mttt) REVERT: C 111 MET cc_start: 0.8796 (mmt) cc_final: 0.8425 (mpp) REVERT: C 140 MET cc_start: 0.8701 (pmm) cc_final: 0.8099 (mtm) REVERT: C 289 LYS cc_start: 0.9443 (mmtm) cc_final: 0.9042 (mmtm) REVERT: C 315 MET cc_start: 0.8827 (mtm) cc_final: 0.8569 (mtm) REVERT: C 316 LYS cc_start: 0.9283 (mptt) cc_final: 0.9021 (mtpp) REVERT: D 527 LYS cc_start: 0.9052 (mmtp) cc_final: 0.8834 (mmtp) REVERT: E 220 MET cc_start: 0.2042 (ptt) cc_final: -0.0730 (tpt) REVERT: E 307 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8264 (pm20) REVERT: E 315 MET cc_start: 0.9195 (mtm) cc_final: 0.8746 (mtm) REVERT: E 487 ASP cc_start: 0.8622 (t0) cc_final: 0.8337 (t70) REVERT: F 289 LYS cc_start: 0.8433 (pttm) cc_final: 0.7938 (tptp) REVERT: F 316 LYS cc_start: 0.8861 (tptp) cc_final: 0.8613 (ttmm) REVERT: F 381 MET cc_start: 0.7732 (ptp) cc_final: 0.7350 (ptm) REVERT: F 410 TYR cc_start: 0.8462 (p90) cc_final: 0.8116 (p90) REVERT: F 560 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: F 594 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7406 (tpp-160) outliers start: 30 outliers final: 11 residues processed: 142 average time/residue: 0.5309 time to fit residues: 109.7314 Evaluate side-chains 118 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 552 TYR Chi-restraints excluded: chain F residue 560 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 286 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 277 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** F 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.064954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.053257 restraints weight = 113081.969| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.65 r_work: 0.3044 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26079 Z= 0.181 Angle : 0.599 8.904 35554 Z= 0.300 Chirality : 0.041 0.148 3942 Planarity : 0.005 0.067 4660 Dihedral : 6.493 83.144 3805 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.04 % Favored : 91.43 % Rotamer: Outliers : 1.61 % Allowed : 11.79 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3220 helix: 1.48 (0.14), residues: 1503 sheet: -2.56 (0.24), residues: 386 loop : -1.68 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 232 HIS 0.007 0.001 HIS E 395 PHE 0.027 0.002 PHE D 78 TYR 0.018 0.001 TYR C 444 ARG 0.004 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1061) hydrogen bonds : angle 4.46932 ( 3084) metal coordination : bond 0.00142 ( 5) covalent geometry : bond 0.00419 (26072) covalent geometry : angle 0.59884 (35554) Misc. bond : bond 0.00173 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.8914 (tp30) cc_final: 0.8566 (tp30) REVERT: A 220 MET cc_start: 0.8290 (pmm) cc_final: 0.7943 (pmm) REVERT: A 313 GLU cc_start: 0.8832 (mp0) cc_final: 0.8502 (tm-30) REVERT: A 379 GLU cc_start: 0.9155 (tt0) cc_final: 0.8822 (pt0) REVERT: A 416 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8575 (mtt-85) REVERT: A 483 ARG cc_start: 0.8437 (ptm-80) cc_final: 0.8187 (ptm-80) REVERT: B 289 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9120 (mmmt) REVERT: B 298 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8379 (pp) REVERT: B 317 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 448 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9041 (mmtp) REVERT: B 527 LYS cc_start: 0.8989 (mttm) cc_final: 0.8744 (mttt) REVERT: C 140 MET cc_start: 0.8717 (pmm) cc_final: 0.8087 (mtm) REVERT: C 315 MET cc_start: 0.8854 (mtm) cc_final: 0.8609 (mtm) REVERT: C 316 LYS cc_start: 0.9287 (mptt) cc_final: 0.9029 (mtpp) REVERT: C 444 TYR cc_start: 0.6817 (p90) cc_final: 0.6543 (p90) REVERT: C 447 GLU cc_start: 0.8476 (mp0) cc_final: 0.7818 (tm-30) REVERT: D 228 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8141 (p0) REVERT: D 527 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8872 (mmtp) REVERT: E 220 MET cc_start: 0.1591 (ptt) cc_final: -0.0611 (tpt) REVERT: E 307 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8281 (pm20) REVERT: E 338 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8157 (pt) REVERT: E 487 ASP cc_start: 0.8737 (t0) cc_final: 0.8466 (t70) REVERT: F 289 LYS cc_start: 0.8481 (pttm) cc_final: 0.7977 (tptp) REVERT: F 316 LYS cc_start: 0.8955 (tptp) cc_final: 0.8658 (ttmm) REVERT: F 381 MET cc_start: 0.7776 (ptp) cc_final: 0.7382 (ptm) REVERT: F 410 TYR cc_start: 0.8483 (p90) cc_final: 0.8107 (p90) REVERT: F 527 LYS cc_start: 0.8658 (mppt) cc_final: 0.8139 (mtmm) outliers start: 41 outliers final: 20 residues processed: 151 average time/residue: 0.5115 time to fit residues: 112.2722 Evaluate side-chains 127 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 582 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 242 optimal weight: 0.0670 chunk 188 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.0070 chunk 274 optimal weight: 9.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.065535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.053899 restraints weight = 112580.059| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.63 r_work: 0.3068 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26079 Z= 0.128 Angle : 0.565 10.789 35554 Z= 0.281 Chirality : 0.039 0.141 3942 Planarity : 0.004 0.064 4660 Dihedral : 6.199 81.373 3805 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.33 % Favored : 92.14 % Rotamer: Outliers : 2.04 % Allowed : 12.66 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3220 helix: 1.59 (0.14), residues: 1504 sheet: -2.47 (0.25), residues: 371 loop : -1.68 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 482 HIS 0.005 0.001 HIS E 395 PHE 0.025 0.001 PHE D 78 TYR 0.013 0.001 TYR C 444 ARG 0.009 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 1061) hydrogen bonds : angle 4.27820 ( 3084) metal coordination : bond 0.00105 ( 5) covalent geometry : bond 0.00297 (26072) covalent geometry : angle 0.56505 (35554) Misc. bond : bond 0.00215 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.8904 (tp30) cc_final: 0.8524 (tp30) REVERT: A 313 GLU cc_start: 0.8829 (mp0) cc_final: 0.8522 (tm-30) REVERT: A 379 GLU cc_start: 0.9148 (tt0) cc_final: 0.8804 (pt0) REVERT: A 416 ARG cc_start: 0.8848 (mtt180) cc_final: 0.8504 (mtt-85) REVERT: A 483 ARG cc_start: 0.8431 (ptm-80) cc_final: 0.8180 (ptm-80) REVERT: B 289 LYS cc_start: 0.9342 (mmmm) cc_final: 0.9078 (mmmt) REVERT: B 317 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8553 (mp) REVERT: B 444 TYR cc_start: 0.8666 (t80) cc_final: 0.8261 (t80) REVERT: B 448 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9073 (mmtp) REVERT: B 527 LYS cc_start: 0.8978 (mttm) cc_final: 0.8762 (mttt) REVERT: C 140 MET cc_start: 0.8638 (pmm) cc_final: 0.8143 (mtt) REVERT: C 289 LYS cc_start: 0.9462 (mmtm) cc_final: 0.9070 (mmtm) REVERT: C 315 MET cc_start: 0.8838 (mtm) cc_final: 0.8517 (mtp) REVERT: C 316 LYS cc_start: 0.9289 (mptt) cc_final: 0.9036 (mtpp) REVERT: D 228 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8148 (p0) REVERT: E 220 MET cc_start: 0.2043 (ptt) cc_final: -0.0147 (tpt) REVERT: E 232 TRP cc_start: 0.5368 (p90) cc_final: 0.4706 (p90) REVERT: E 307 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8315 (pm20) REVERT: E 338 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8097 (pt) REVERT: E 350 TYR cc_start: 0.7756 (t80) cc_final: 0.7526 (t80) REVERT: F 289 LYS cc_start: 0.8437 (pttm) cc_final: 0.7938 (tptp) REVERT: F 316 LYS cc_start: 0.8927 (tptp) cc_final: 0.8631 (ttmm) REVERT: F 381 MET cc_start: 0.7762 (ptp) cc_final: 0.7258 (ptm) REVERT: F 410 TYR cc_start: 0.8480 (p90) cc_final: 0.8063 (p90) REVERT: F 592 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8156 (tt) outliers start: 52 outliers final: 22 residues processed: 155 average time/residue: 0.4744 time to fit residues: 108.1702 Evaluate side-chains 126 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 592 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 312 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 254 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS D 427 HIS F 397 ASN ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 581 ASN ** F 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.065452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.053817 restraints weight = 112338.711| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.64 r_work: 0.3064 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26079 Z= 0.133 Angle : 0.579 15.098 35554 Z= 0.282 Chirality : 0.039 0.166 3942 Planarity : 0.004 0.066 4660 Dihedral : 6.078 83.159 3805 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.55 % Favored : 91.93 % Rotamer: Outliers : 2.00 % Allowed : 13.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 3220 helix: 1.67 (0.14), residues: 1510 sheet: -2.36 (0.25), residues: 364 loop : -1.66 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 302 HIS 0.005 0.001 HIS F 462 PHE 0.028 0.001 PHE D 78 TYR 0.013 0.001 TYR C 444 ARG 0.003 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 1061) hydrogen bonds : angle 4.18912 ( 3084) metal coordination : bond 0.00134 ( 5) covalent geometry : bond 0.00309 (26072) covalent geometry : angle 0.57873 (35554) Misc. bond : bond 0.00354 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.8938 (tp30) cc_final: 0.8469 (tp30) REVERT: A 313 GLU cc_start: 0.8877 (mp0) cc_final: 0.8590 (tm-30) REVERT: A 379 GLU cc_start: 0.9160 (tt0) cc_final: 0.8823 (pt0) REVERT: A 416 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8567 (mtt-85) REVERT: A 483 ARG cc_start: 0.8421 (ptm-80) cc_final: 0.8167 (ptm-80) REVERT: B 289 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9074 (mmmt) REVERT: B 317 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 444 TYR cc_start: 0.8639 (t80) cc_final: 0.8300 (t80) REVERT: B 448 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9081 (mmtp) REVERT: B 527 LYS cc_start: 0.8976 (mttm) cc_final: 0.8756 (mttt) REVERT: C 47 GLU cc_start: 0.8550 (tp30) cc_final: 0.8263 (tp30) REVERT: C 140 MET cc_start: 0.8584 (pmm) cc_final: 0.8135 (mtt) REVERT: C 289 LYS cc_start: 0.9472 (mmtm) cc_final: 0.9089 (mmtm) REVERT: C 316 LYS cc_start: 0.9298 (mptt) cc_final: 0.9037 (mtpp) REVERT: C 444 TYR cc_start: 0.6783 (p90) cc_final: 0.6528 (p90) REVERT: C 447 GLU cc_start: 0.8477 (mp0) cc_final: 0.7737 (tm-30) REVERT: C 453 TYR cc_start: 0.8757 (m-80) cc_final: 0.8311 (m-80) REVERT: C 518 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8338 (pp) REVERT: D 80 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: D 228 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8192 (p0) REVERT: D 417 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7960 (t-90) REVERT: E 220 MET cc_start: 0.2137 (ptt) cc_final: -0.0166 (tpt) REVERT: E 232 TRP cc_start: 0.5378 (p90) cc_final: 0.4496 (p90) REVERT: E 302 TRP cc_start: 0.7182 (t-100) cc_final: 0.6778 (t-100) REVERT: E 338 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8077 (pt) REVERT: F 234 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8676 (tp30) REVERT: F 289 LYS cc_start: 0.8442 (pttm) cc_final: 0.7924 (tptp) REVERT: F 316 LYS cc_start: 0.8937 (tptp) cc_final: 0.8641 (ttmm) REVERT: F 381 MET cc_start: 0.7731 (ptp) cc_final: 0.7247 (ptm) REVERT: F 410 TYR cc_start: 0.8479 (p90) cc_final: 0.8069 (p90) REVERT: F 527 LYS cc_start: 0.8809 (mppt) cc_final: 0.8271 (mtmm) REVERT: F 592 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8097 (tt) outliers start: 51 outliers final: 31 residues processed: 154 average time/residue: 0.4780 time to fit residues: 107.9154 Evaluate side-chains 141 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 592 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 176 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 204 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS C 462 HIS ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.065509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.053896 restraints weight = 112837.057| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.64 r_work: 0.3065 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26079 Z= 0.132 Angle : 0.577 14.243 35554 Z= 0.281 Chirality : 0.039 0.159 3942 Planarity : 0.004 0.064 4660 Dihedral : 6.051 85.003 3805 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.11 % Favored : 92.33 % Rotamer: Outliers : 2.04 % Allowed : 13.64 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 3220 helix: 1.72 (0.14), residues: 1513 sheet: -2.36 (0.25), residues: 365 loop : -1.64 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 302 HIS 0.005 0.001 HIS F 462 PHE 0.027 0.001 PHE D 78 TYR 0.015 0.001 TYR E 340 ARG 0.006 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 1061) hydrogen bonds : angle 4.12349 ( 3084) metal coordination : bond 0.00131 ( 5) covalent geometry : bond 0.00309 (26072) covalent geometry : angle 0.57714 (35554) Misc. bond : bond 0.00331 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.8900 (tp30) cc_final: 0.8439 (tp30) REVERT: A 313 GLU cc_start: 0.8864 (mp0) cc_final: 0.8601 (tm-30) REVERT: A 379 GLU cc_start: 0.9166 (tt0) cc_final: 0.8818 (pt0) REVERT: A 416 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8549 (mtt-85) REVERT: A 483 ARG cc_start: 0.8421 (ptm-80) cc_final: 0.8171 (ptm-80) REVERT: B 220 MET cc_start: 0.8042 (ppp) cc_final: 0.7813 (ppp) REVERT: B 289 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9069 (mmmt) REVERT: B 317 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8464 (mt) REVERT: B 444 TYR cc_start: 0.8622 (t80) cc_final: 0.8353 (t80) REVERT: B 448 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9087 (mmtp) REVERT: B 527 LYS cc_start: 0.8973 (mttm) cc_final: 0.8762 (mttt) REVERT: C 47 GLU cc_start: 0.8582 (tp30) cc_final: 0.8279 (tp30) REVERT: C 111 MET cc_start: 0.8973 (tpp) cc_final: 0.8633 (tpp) REVERT: C 140 MET cc_start: 0.8564 (pmm) cc_final: 0.8120 (mtt) REVERT: C 289 LYS cc_start: 0.9479 (mmtm) cc_final: 0.9061 (mmtm) REVERT: C 316 LYS cc_start: 0.9272 (mptt) cc_final: 0.9017 (mtpp) REVERT: C 447 GLU cc_start: 0.8444 (mp0) cc_final: 0.7697 (tm-30) REVERT: C 448 LYS cc_start: 0.8938 (mmpt) cc_final: 0.8378 (mmpt) REVERT: C 453 TYR cc_start: 0.8767 (m-80) cc_final: 0.8336 (m-80) REVERT: C 518 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8343 (pp) REVERT: D 80 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: D 86 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8374 (t80) REVERT: D 228 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8233 (p0) REVERT: D 417 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7927 (t-90) REVERT: D 527 LYS cc_start: 0.8966 (mmtp) cc_final: 0.8742 (mmmt) REVERT: E 220 MET cc_start: 0.2206 (ptt) cc_final: 0.0077 (tpt) REVERT: E 232 TRP cc_start: 0.5283 (p90) cc_final: 0.4259 (p90) REVERT: E 338 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8115 (pt) REVERT: F 234 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8688 (tp30) REVERT: F 289 LYS cc_start: 0.8507 (pttm) cc_final: 0.7996 (tptp) REVERT: F 316 LYS cc_start: 0.8941 (tptp) cc_final: 0.8647 (ttmm) REVERT: F 381 MET cc_start: 0.7741 (ptp) cc_final: 0.7262 (ptm) REVERT: F 410 TYR cc_start: 0.8475 (p90) cc_final: 0.8017 (p90) REVERT: F 592 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8103 (tt) outliers start: 52 outliers final: 29 residues processed: 156 average time/residue: 0.5031 time to fit residues: 114.6729 Evaluate side-chains 136 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 592 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 107 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 149 optimal weight: 0.0770 chunk 83 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 0.0040 chunk 118 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS F 264 HIS ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.065963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054407 restraints weight = 112032.676| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.63 r_work: 0.3082 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26079 Z= 0.112 Angle : 0.574 14.488 35554 Z= 0.278 Chirality : 0.039 0.161 3942 Planarity : 0.005 0.083 4660 Dihedral : 5.958 85.930 3805 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.30 % Favored : 92.17 % Rotamer: Outliers : 2.12 % Allowed : 14.15 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 3220 helix: 1.77 (0.14), residues: 1513 sheet: -2.27 (0.25), residues: 365 loop : -1.64 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP E 302 HIS 0.006 0.001 HIS F 462 PHE 0.028 0.001 PHE D 78 TYR 0.012 0.001 TYR C 444 ARG 0.005 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 1061) hydrogen bonds : angle 4.05467 ( 3084) metal coordination : bond 0.00100 ( 5) covalent geometry : bond 0.00261 (26072) covalent geometry : angle 0.57423 (35554) Misc. bond : bond 0.00237 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.8854 (tp30) cc_final: 0.8369 (tp30) REVERT: A 313 GLU cc_start: 0.8858 (mp0) cc_final: 0.8581 (tm-30) REVERT: A 379 GLU cc_start: 0.9151 (tt0) cc_final: 0.8805 (pt0) REVERT: A 416 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8497 (mtt-85) REVERT: A 483 ARG cc_start: 0.8404 (ptm-80) cc_final: 0.8157 (ptm-80) REVERT: B 289 LYS cc_start: 0.9328 (mmmm) cc_final: 0.9055 (mmmt) REVERT: B 317 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8483 (mt) REVERT: B 448 LYS cc_start: 0.9379 (tmtt) cc_final: 0.9101 (mmtp) REVERT: B 482 TRP cc_start: 0.8663 (t60) cc_final: 0.8267 (t60) REVERT: C 47 GLU cc_start: 0.8533 (tp30) cc_final: 0.8223 (tp30) REVERT: C 111 MET cc_start: 0.8955 (tpp) cc_final: 0.8640 (tpp) REVERT: C 139 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8962 (mt) REVERT: C 140 MET cc_start: 0.8523 (pmm) cc_final: 0.8086 (mtt) REVERT: C 289 LYS cc_start: 0.9450 (mmtm) cc_final: 0.9037 (mmtm) REVERT: C 316 LYS cc_start: 0.9254 (mptt) cc_final: 0.8904 (mtpp) REVERT: C 447 GLU cc_start: 0.8435 (mp0) cc_final: 0.7692 (tm-30) REVERT: C 453 TYR cc_start: 0.8740 (m-80) cc_final: 0.8332 (m-80) REVERT: C 518 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8291 (pp) REVERT: D 80 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: D 86 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8351 (t80) REVERT: D 228 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8205 (p0) REVERT: D 417 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7912 (t-90) REVERT: D 527 LYS cc_start: 0.9016 (mmtp) cc_final: 0.8776 (mmmt) REVERT: E 220 MET cc_start: 0.2210 (ptt) cc_final: 0.0107 (tpt) REVERT: E 221 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6308 (pt) REVERT: E 232 TRP cc_start: 0.5134 (p90) cc_final: 0.4140 (p90) REVERT: E 338 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8097 (pt) REVERT: E 381 MET cc_start: 0.7326 (mmm) cc_final: 0.7052 (mmm) REVERT: F 234 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8699 (tp30) REVERT: F 289 LYS cc_start: 0.8442 (pttm) cc_final: 0.8080 (tptp) REVERT: F 316 LYS cc_start: 0.8933 (tptp) cc_final: 0.8636 (ttmm) REVERT: F 381 MET cc_start: 0.7711 (ptp) cc_final: 0.7122 (ptm) REVERT: F 410 TYR cc_start: 0.8478 (p90) cc_final: 0.8018 (p90) REVERT: F 527 LYS cc_start: 0.8830 (mppt) cc_final: 0.8265 (mtmm) outliers start: 54 outliers final: 29 residues processed: 154 average time/residue: 0.5081 time to fit residues: 113.8549 Evaluate side-chains 141 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 592 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 47 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 270 optimal weight: 0.4980 chunk 207 optimal weight: 0.3980 chunk 261 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 HIS D 489 ASN ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052735 restraints weight = 113195.751| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.61 r_work: 0.3026 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26079 Z= 0.214 Angle : 0.645 17.244 35554 Z= 0.314 Chirality : 0.042 0.326 3942 Planarity : 0.005 0.075 4660 Dihedral : 6.334 87.102 3805 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.14 % Favored : 91.34 % Rotamer: Outliers : 1.92 % Allowed : 14.50 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 3220 helix: 1.70 (0.14), residues: 1519 sheet: -2.33 (0.25), residues: 387 loop : -1.64 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 302 HIS 0.006 0.001 HIS C 75 PHE 0.029 0.002 PHE D 78 TYR 0.015 0.002 TYR E 340 ARG 0.007 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 1061) hydrogen bonds : angle 4.21291 ( 3084) metal coordination : bond 0.00291 ( 5) covalent geometry : bond 0.00492 (26072) covalent geometry : angle 0.64545 (35554) Misc. bond : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.8951 (tp30) cc_final: 0.8464 (tp30) REVERT: A 313 GLU cc_start: 0.8943 (mp0) cc_final: 0.8657 (tm-30) REVERT: A 379 GLU cc_start: 0.9167 (tt0) cc_final: 0.8831 (pt0) REVERT: A 483 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.8251 (ptm-80) REVERT: B 289 LYS cc_start: 0.9379 (mmmm) cc_final: 0.9113 (mmmt) REVERT: B 317 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8490 (mt) REVERT: B 448 LYS cc_start: 0.9388 (tmtt) cc_final: 0.9076 (mmtp) REVERT: C 111 MET cc_start: 0.8954 (tpp) cc_final: 0.8650 (tpp) REVERT: C 139 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8934 (mt) REVERT: C 140 MET cc_start: 0.8593 (pmm) cc_final: 0.8099 (mtt) REVERT: C 316 LYS cc_start: 0.9243 (mptt) cc_final: 0.8895 (mtpp) REVERT: C 447 GLU cc_start: 0.8511 (mp0) cc_final: 0.7750 (tm-30) REVERT: C 448 LYS cc_start: 0.8964 (mmpt) cc_final: 0.8408 (mmpt) REVERT: C 453 TYR cc_start: 0.8812 (m-80) cc_final: 0.8397 (m-80) REVERT: C 518 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8339 (pp) REVERT: D 80 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: D 417 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.7958 (t-90) REVERT: E 220 MET cc_start: 0.2736 (ptt) cc_final: 0.0535 (tpt) REVERT: E 221 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6515 (pt) REVERT: E 260 LYS cc_start: 0.6515 (mppt) cc_final: 0.6188 (mppt) REVERT: E 338 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8172 (pt) REVERT: F 289 LYS cc_start: 0.8569 (pttm) cc_final: 0.8064 (tptp) REVERT: F 316 LYS cc_start: 0.9001 (tptp) cc_final: 0.8700 (ttmm) REVERT: F 381 MET cc_start: 0.7951 (ptp) cc_final: 0.7568 (ptm) REVERT: F 410 TYR cc_start: 0.8483 (p90) cc_final: 0.8031 (p90) REVERT: F 527 LYS cc_start: 0.8816 (mppt) cc_final: 0.8225 (mtmm) outliers start: 49 outliers final: 32 residues processed: 153 average time/residue: 0.4890 time to fit residues: 109.2468 Evaluate side-chains 139 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 592 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 10 optimal weight: 0.8980 chunk 178 optimal weight: 0.4980 chunk 234 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS C 52 HIS C 342 HIS ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.065285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.053727 restraints weight = 112684.824| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.62 r_work: 0.3060 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 26079 Z= 0.138 Angle : 0.608 16.831 35554 Z= 0.293 Chirality : 0.040 0.309 3942 Planarity : 0.005 0.068 4660 Dihedral : 6.351 86.603 3805 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.67 % Favored : 91.80 % Rotamer: Outliers : 1.57 % Allowed : 14.77 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 3220 helix: 1.78 (0.14), residues: 1513 sheet: -2.29 (0.26), residues: 355 loop : -1.60 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP E 302 HIS 0.007 0.001 HIS E 395 PHE 0.029 0.001 PHE D 78 TYR 0.018 0.001 TYR C 444 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 1061) hydrogen bonds : angle 4.10055 ( 3084) metal coordination : bond 0.09333 ( 5) covalent geometry : bond 0.00306 (26072) covalent geometry : angle 0.60751 (35554) Misc. bond : bond 0.00506 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.8870 (tp30) cc_final: 0.8407 (tp30) REVERT: A 313 GLU cc_start: 0.8880 (mp0) cc_final: 0.8670 (tm-30) REVERT: A 379 GLU cc_start: 0.9164 (tt0) cc_final: 0.8830 (pt0) REVERT: A 483 ARG cc_start: 0.8431 (ptm-80) cc_final: 0.8173 (ptm-80) REVERT: B 289 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9089 (mmmt) REVERT: B 317 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8491 (mt) REVERT: B 448 LYS cc_start: 0.9389 (tmtt) cc_final: 0.9064 (mmtp) REVERT: C 47 GLU cc_start: 0.8486 (tp30) cc_final: 0.8188 (tp30) REVERT: C 111 MET cc_start: 0.8939 (tpp) cc_final: 0.8697 (tpp) REVERT: C 139 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8928 (mt) REVERT: C 140 MET cc_start: 0.8545 (pmm) cc_final: 0.8088 (mtt) REVERT: C 289 LYS cc_start: 0.9370 (mmmm) cc_final: 0.9030 (mmtm) REVERT: C 316 LYS cc_start: 0.9250 (mptt) cc_final: 0.8978 (mtpp) REVERT: C 447 GLU cc_start: 0.8475 (mp0) cc_final: 0.7734 (tm-30) REVERT: C 448 LYS cc_start: 0.8972 (mmpt) cc_final: 0.8314 (mmmt) REVERT: C 453 TYR cc_start: 0.8766 (m-80) cc_final: 0.8363 (m-80) REVERT: C 518 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8306 (pp) REVERT: D 80 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: D 417 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7972 (t-90) REVERT: E 220 MET cc_start: 0.2764 (ptt) cc_final: 0.0533 (tpt) REVERT: E 221 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6481 (pt) REVERT: E 260 LYS cc_start: 0.6496 (mppt) cc_final: 0.6197 (mppt) REVERT: E 338 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8152 (pt) REVERT: E 340 TYR cc_start: 0.7681 (t80) cc_final: 0.7445 (t80) REVERT: F 289 LYS cc_start: 0.8526 (pttm) cc_final: 0.8069 (tptp) REVERT: F 316 LYS cc_start: 0.8975 (tptp) cc_final: 0.8672 (ttmm) REVERT: F 381 MET cc_start: 0.7906 (ptp) cc_final: 0.7524 (ptm) REVERT: F 410 TYR cc_start: 0.8477 (p90) cc_final: 0.8020 (p90) outliers start: 40 outliers final: 32 residues processed: 140 average time/residue: 0.5000 time to fit residues: 103.0091 Evaluate side-chains 141 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 592 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 267 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 HIS ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053015 restraints weight = 112486.060| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.58 r_work: 0.3035 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26079 Z= 0.186 Angle : 0.631 16.134 35554 Z= 0.305 Chirality : 0.041 0.224 3942 Planarity : 0.005 0.063 4660 Dihedral : 6.325 82.795 3805 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.23 % Favored : 91.24 % Rotamer: Outliers : 1.80 % Allowed : 14.69 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 3220 helix: 1.74 (0.14), residues: 1520 sheet: -2.36 (0.25), residues: 362 loop : -1.61 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP E 302 HIS 0.006 0.001 HIS A 417 PHE 0.029 0.001 PHE D 78 TYR 0.033 0.001 TYR F 350 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 1061) hydrogen bonds : angle 4.16306 ( 3084) metal coordination : bond 0.00965 ( 5) covalent geometry : bond 0.00431 (26072) covalent geometry : angle 0.63135 (35554) Misc. bond : bond 0.00422 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12259.12 seconds wall clock time: 213 minutes 25.68 seconds (12805.68 seconds total)