Starting phenix.real_space_refine on Mon Aug 25 05:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3k_39746/08_2025/8z3k_39746_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3k_39746/08_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_39746/08_2025/8z3k_39746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3k_39746/08_2025/8z3k_39746.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3k_39746/08_2025/8z3k_39746_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3k_39746/08_2025/8z3k_39746_trim.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'TYR:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'PHE: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: {'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 2} 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, 'HIS:plan': 1, 'PHE:plan': 2} 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: {'ARG:plan': 4, 'TYR:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2} 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: 5.39, per 1000 atoms: 0.21 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: 1.82 Conformation dependent library (CDL) restraints added in 774.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.65 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: 3.90 Time building geometry restraints manager: 2.45 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: 10.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.710 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- 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 : 12.40 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (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 ARG 0.010 0.000 ARG A 172 TYR 0.015 0.001 TYR B 552 PHE 0.015 0.001 PHE B 97 TRP 0.033 0.001 TRP E 232 HIS 0.007 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00395 (26072) covalent geometry : angle 0.67167 (35554) hydrogen bonds : bond 0.24623 ( 1061) hydrogen bonds : angle 7.24500 ( 3084) metal coordination : bond 0.00078 ( 5) 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 : 0.651 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: 0.2499 time to fit residues: 64.9979 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 : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 0.0050 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.4552 ------------------------------------------------------------------------------- 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 570 ASN D 209 GLN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN E 525 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.066376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054701 restraints weight = 112148.985| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.64 r_work: 0.3094 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26079 Z= 0.141 Angle : 0.648 10.577 35554 Z= 0.324 Chirality : 0.041 0.178 3942 Planarity : 0.005 0.067 4660 Dihedral : 6.877 86.264 3805 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.83 % Favored : 91.61 % Rotamer: Outliers : 0.55 % Allowed : 7.05 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 3220 helix: 1.21 (0.13), residues: 1496 sheet: -2.60 (0.24), residues: 379 loop : -1.71 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 278 TYR 0.016 0.001 TYR C 521 PHE 0.020 0.002 PHE C 49 TRP 0.030 0.002 TRP E 232 HIS 0.006 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00313 (26072) covalent geometry : angle 0.64764 (35554) hydrogen bonds : bond 0.05069 ( 1061) hydrogen bonds : angle 5.04962 ( 3084) metal coordination : bond 0.00115 ( 5) Misc. bond : bond 0.00015 ( 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 134 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.975 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: 0.8984 (tp30) cc_final: 0.8485 (tp30) REVERT: A 313 GLU cc_start: 0.8622 (mp0) cc_final: 0.8322 (tm-30) REVERT: A 379 GLU cc_start: 0.9158 (tt0) cc_final: 0.8850 (pt0) REVERT: A 416 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8586 (mtt-85) REVERT: A 483 ARG cc_start: 0.8486 (ptm-80) cc_final: 0.8080 (ttt-90) REVERT: B 289 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9110 (mmmt) REVERT: B 444 TYR cc_start: 0.8664 (t80) cc_final: 0.7924 (t80) REVERT: B 448 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9046 (mmtp) REVERT: B 482 TRP cc_start: 0.8714 (t60) cc_final: 0.8500 (t60) REVERT: C 111 MET cc_start: 0.8747 (mmt) cc_final: 0.8430 (mpp) REVERT: C 140 MET cc_start: 0.8666 (pmm) cc_final: 0.8084 (mtt) REVERT: C 289 LYS cc_start: 0.9407 (mmtm) cc_final: 0.9012 (mmtm) REVERT: C 316 LYS cc_start: 0.9245 (mptt) cc_final: 0.8976 (mtpp) REVERT: D 527 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8853 (mmtp) REVERT: E 252 GLN cc_start: 0.8023 (mt0) cc_final: 0.7774 (mt0) REVERT: E 307 GLN cc_start: 0.8494 (tp-100) cc_final: 0.8257 (pm20) REVERT: E 487 ASP cc_start: 0.8627 (t0) cc_final: 0.8344 (t70) REVERT: F 289 LYS cc_start: 0.8431 (pttm) cc_final: 0.7920 (tptp) REVERT: F 316 LYS cc_start: 0.8881 (tptp) cc_final: 0.8645 (ttmm) REVERT: F 410 TYR cc_start: 0.8490 (p90) cc_final: 0.8202 (p90) outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 0.2429 time to fit residues: 45.6738 Evaluate side-chains 111 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 68 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 283 optimal weight: 0.0770 chunk 284 optimal weight: 0.0070 chunk 251 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 567 ASN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 601 GLN F 581 ASN F 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.066347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054695 restraints weight = 112292.801| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.65 r_work: 0.3097 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26079 Z= 0.126 Angle : 0.579 6.889 35554 Z= 0.290 Chirality : 0.040 0.197 3942 Planarity : 0.005 0.066 4660 Dihedral : 6.531 76.577 3805 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.45 % Favored : 91.99 % Rotamer: Outliers : 1.10 % Allowed : 10.07 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 3220 helix: 1.38 (0.14), residues: 1506 sheet: -2.48 (0.25), residues: 369 loop : -1.68 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 594 TYR 0.016 0.001 TYR D 360 PHE 0.025 0.001 PHE D 78 TRP 0.025 0.001 TRP E 239 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00285 (26072) covalent geometry : angle 0.57850 (35554) hydrogen bonds : bond 0.04287 ( 1061) hydrogen bonds : angle 4.59696 ( 3084) metal coordination : bond 0.00039 ( 5) Misc. bond : bond 0.00302 ( 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 140 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.763 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: 0.8876 (tp30) cc_final: 0.8524 (tp30) REVERT: A 220 MET cc_start: 0.8260 (pmm) cc_final: 0.7870 (pmm) REVERT: A 313 GLU cc_start: 0.8711 (mp0) cc_final: 0.8384 (tm-30) REVERT: A 379 GLU cc_start: 0.9174 (tt0) cc_final: 0.8852 (pt0) REVERT: A 416 ARG cc_start: 0.8802 (mtt180) cc_final: 0.8494 (mtt180) REVERT: A 483 ARG cc_start: 0.8480 (ptm-80) cc_final: 0.8175 (ttt-90) REVERT: B 289 LYS cc_start: 0.9325 (mmmm) cc_final: 0.9061 (mmmt) REVERT: B 317 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 448 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9084 (mmtp) REVERT: B 482 TRP cc_start: 0.8683 (t60) cc_final: 0.8450 (t60) REVERT: C 111 MET cc_start: 0.8773 (mmt) cc_final: 0.8423 (mpp) REVERT: C 140 MET cc_start: 0.8661 (pmm) cc_final: 0.8104 (mtm) REVERT: C 289 LYS cc_start: 0.9415 (mmtm) cc_final: 0.9028 (mmtm) REVERT: C 316 LYS cc_start: 0.9250 (mptt) cc_final: 0.8966 (mtpp) REVERT: D 527 LYS cc_start: 0.9048 (mmtp) cc_final: 0.8825 (mmtp) REVERT: E 220 MET cc_start: 0.2059 (ptt) cc_final: -0.0241 (tpt) REVERT: E 307 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8258 (pm20) REVERT: F 289 LYS cc_start: 0.8405 (pttm) cc_final: 0.7922 (tptp) REVERT: F 316 LYS cc_start: 0.8868 (tptp) cc_final: 0.8648 (ttmm) REVERT: F 410 TYR cc_start: 0.8492 (p90) cc_final: 0.8131 (p90) REVERT: F 560 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7595 (mp0) outliers start: 28 outliers final: 12 residues processed: 134 average time/residue: 0.2247 time to fit residues: 43.2218 Evaluate side-chains 116 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 B residue 184 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 32 VAL 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 D residue 206 ASP Chi-restraints excluded: chain E residue 232 TRP 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 47 optimal weight: 9.9990 chunk 118 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** C 567 ASN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3500 r_free = 0.3500 target = 0.064259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.052543 restraints weight = 113007.036| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.62 r_work: 0.3020 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 26079 Z= 0.246 Angle : 0.644 8.870 35554 Z= 0.324 Chirality : 0.043 0.182 3942 Planarity : 0.005 0.068 4660 Dihedral : 6.675 84.408 3805 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.26 % Favored : 91.21 % Rotamer: Outliers : 1.76 % Allowed : 11.56 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 3220 helix: 1.44 (0.14), residues: 1501 sheet: -2.56 (0.23), residues: 402 loop : -1.65 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.020 0.002 TYR C 521 PHE 0.027 0.002 PHE D 78 TRP 0.025 0.002 TRP E 232 HIS 0.007 0.001 HIS D 495 Details of bonding type rmsd covalent geometry : bond 0.00560 (26072) covalent geometry : angle 0.64425 (35554) hydrogen bonds : bond 0.04167 ( 1061) hydrogen bonds : angle 4.56082 ( 3084) metal coordination : bond 0.00230 ( 5) Misc. bond : bond 0.00392 ( 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 157 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.913 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: 0.8955 (tp30) cc_final: 0.8608 (tp30) REVERT: A 220 MET cc_start: 0.8340 (pmm) cc_final: 0.7894 (pmm) REVERT: A 313 GLU cc_start: 0.8866 (mp0) cc_final: 0.8542 (tm-30) REVERT: A 379 GLU cc_start: 0.9173 (tt0) cc_final: 0.8840 (pt0) REVERT: A 416 ARG cc_start: 0.8867 (mtt180) cc_final: 0.8509 (mtt-85) REVERT: A 483 ARG cc_start: 0.8463 (ptm-80) cc_final: 0.8192 (ptm-80) REVERT: B 289 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9091 (mmmt) REVERT: B 444 TYR cc_start: 0.8764 (t80) cc_final: 0.8201 (t80) REVERT: B 448 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9035 (mmtp) REVERT: C 140 MET cc_start: 0.8719 (pmm) cc_final: 0.8086 (mtm) REVERT: C 316 LYS cc_start: 0.9300 (mptt) cc_final: 0.9072 (mtpp) REVERT: C 444 TYR cc_start: 0.6801 (p90) cc_final: 0.6591 (p90) REVERT: C 447 GLU cc_start: 0.8578 (mp0) cc_final: 0.7860 (tm-30) REVERT: D 228 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8166 (p0) REVERT: D 527 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8905 (mmtp) REVERT: D 573 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7832 (mp) REVERT: E 220 MET cc_start: 0.2151 (ptt) cc_final: -0.0578 (tpt) REVERT: E 307 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8332 (pm20) REVERT: E 487 ASP cc_start: 0.8755 (t0) cc_final: 0.8483 (t70) REVERT: F 289 LYS cc_start: 0.8468 (pttm) cc_final: 0.7966 (tptp) REVERT: F 316 LYS cc_start: 0.8968 (tptp) cc_final: 0.8697 (ttmm) REVERT: F 410 TYR cc_start: 0.8476 (p90) cc_final: 0.8088 (p90) REVERT: F 560 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7576 (mp0) outliers start: 45 outliers final: 20 residues processed: 153 average time/residue: 0.2194 time to fit residues: 48.7910 Evaluate side-chains 127 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 183 VAL 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 B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL 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 D residue 573 ILE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 552 TYR Chi-restraints excluded: chain F residue 560 GLU 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 254 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ** 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 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN D 266 HIS D 427 HIS E 335 GLN ** E 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3498 r_free = 0.3498 target = 0.064222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052574 restraints weight = 112684.449| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.61 r_work: 0.3024 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26079 Z= 0.208 Angle : 0.607 8.941 35554 Z= 0.306 Chirality : 0.041 0.159 3942 Planarity : 0.005 0.064 4660 Dihedral : 6.660 88.818 3805 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.73 % Favored : 91.74 % Rotamer: Outliers : 2.51 % Allowed : 12.58 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.15), residues: 3220 helix: 1.48 (0.14), residues: 1515 sheet: -2.57 (0.24), residues: 394 loop : -1.72 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 172 TYR 0.016 0.001 TYR C 521 PHE 0.032 0.002 PHE D 78 TRP 0.025 0.001 TRP E 232 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00477 (26072) covalent geometry : angle 0.60742 (35554) hydrogen bonds : bond 0.03812 ( 1061) hydrogen bonds : angle 4.42973 ( 3084) metal coordination : bond 0.00178 ( 5) Misc. bond : bond 0.00731 ( 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 173 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 109 time to evaluate : 0.957 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: 0.8945 (tp30) cc_final: 0.8628 (tp30) REVERT: A 313 GLU cc_start: 0.8932 (mp0) cc_final: 0.8651 (tm-30) REVERT: A 379 GLU cc_start: 0.9171 (tt0) cc_final: 0.8823 (pt0) REVERT: A 416 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8575 (mtt-85) REVERT: A 483 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8193 (ptm-80) REVERT: B 289 LYS cc_start: 0.9371 (mmmm) cc_final: 0.9076 (mmmt) REVERT: B 317 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 444 TYR cc_start: 0.8689 (t80) cc_final: 0.8223 (t80) REVERT: B 448 LYS cc_start: 0.9420 (tmtt) cc_final: 0.9141 (mmtp) REVERT: C 140 MET cc_start: 0.8705 (pmm) cc_final: 0.8106 (mtt) REVERT: C 289 LYS cc_start: 0.9495 (mmtm) cc_final: 0.9066 (mmtm) REVERT: C 316 LYS cc_start: 0.9319 (mptt) cc_final: 0.9103 (mtpp) REVERT: D 86 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8398 (t80) REVERT: D 228 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8306 (p0) REVERT: D 573 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7807 (mp) REVERT: E 220 MET cc_start: 0.2200 (ptt) cc_final: -0.0154 (tpt) REVERT: E 307 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8326 (pm20) REVERT: E 338 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8121 (pt) REVERT: F 289 LYS cc_start: 0.8473 (pttm) cc_final: 0.7963 (tptp) REVERT: F 410 TYR cc_start: 0.8479 (p90) cc_final: 0.8026 (p90) REVERT: F 592 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8220 (tt) outliers start: 64 outliers final: 28 residues processed: 168 average time/residue: 0.1989 time to fit residues: 48.5656 Evaluate side-chains 137 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 183 VAL 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 B residue 184 VAL 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 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 206 ASP Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 385 ARG Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 232 TRP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 279 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 246 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 205 GLN F 397 ASN 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 = 0.064986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.053341 restraints weight = 112901.769| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.63 r_work: 0.3049 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26079 Z= 0.137 Angle : 0.587 13.689 35554 Z= 0.288 Chirality : 0.040 0.161 3942 Planarity : 0.005 0.065 4660 Dihedral : 6.466 85.448 3805 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.48 % Favored : 91.96 % Rotamer: Outliers : 2.08 % Allowed : 13.36 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.16), residues: 3220 helix: 1.60 (0.14), residues: 1515 sheet: -2.48 (0.25), residues: 366 loop : -1.71 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 594 TYR 0.018 0.001 TYR C 444 PHE 0.029 0.001 PHE D 78 TRP 0.026 0.001 TRP E 232 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00319 (26072) covalent geometry : angle 0.58676 (35554) hydrogen bonds : bond 0.03447 ( 1061) hydrogen bonds : angle 4.25608 ( 3084) metal coordination : bond 0.00144 ( 5) Misc. bond : bond 0.00091 ( 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 159 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 0.995 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: 0.8966 (tp30) cc_final: 0.8492 (tp30) REVERT: A 379 GLU cc_start: 0.9163 (tt0) cc_final: 0.8812 (pt0) REVERT: A 416 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8508 (mtt-85) REVERT: A 483 ARG cc_start: 0.8408 (ptm-80) cc_final: 0.8139 (ptm-80) REVERT: B 289 LYS cc_start: 0.9371 (mmmm) cc_final: 0.9080 (mmmt) REVERT: B 317 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8436 (mt) REVERT: B 444 TYR cc_start: 0.8680 (t80) cc_final: 0.8306 (t80) REVERT: B 448 LYS cc_start: 0.9400 (tmtt) cc_final: 0.9123 (mmtp) REVERT: C 140 MET cc_start: 0.8615 (pmm) cc_final: 0.8121 (mtt) REVERT: C 289 LYS cc_start: 0.9478 (mmtm) cc_final: 0.9058 (mmtm) REVERT: C 316 LYS cc_start: 0.9280 (mptt) cc_final: 0.9052 (mtpp) REVERT: C 447 GLU cc_start: 0.8519 (mp0) cc_final: 0.7780 (tm-30) REVERT: C 453 TYR cc_start: 0.8723 (m-80) cc_final: 0.8307 (m-80) REVERT: C 518 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8339 (pp) REVERT: D 80 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: D 228 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8213 (p0) REVERT: D 417 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7944 (t-90) REVERT: D 573 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7785 (mp) REVERT: E 220 MET cc_start: 0.2223 (ptt) cc_final: -0.0197 (tpt) REVERT: E 307 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8357 (pm20) REVERT: E 338 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8093 (pt) REVERT: F 234 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8685 (tp30) REVERT: F 289 LYS cc_start: 0.8482 (pttm) cc_final: 0.7980 (tptp) REVERT: F 316 LYS cc_start: 0.8889 (tptp) cc_final: 0.8594 (ttmm) REVERT: F 381 MET cc_start: 0.7857 (ptp) cc_final: 0.7305 (ptm) REVERT: F 410 TYR cc_start: 0.8471 (p90) cc_final: 0.8021 (p90) REVERT: F 527 LYS cc_start: 0.8759 (mppt) cc_final: 0.8205 (mtmm) outliers start: 53 outliers final: 27 residues processed: 151 average time/residue: 0.2247 time to fit residues: 48.5662 Evaluate side-chains 135 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL 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 386 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 80 GLU 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 573 ILE Chi-restraints excluded: chain E residue 232 TRP 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 552 TYR Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 601 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 282 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 276 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS D 205 GLN ** E 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 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 = 0.3506 r_free = 0.3506 target = 0.064480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052827 restraints weight = 112817.129| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.62 r_work: 0.3033 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26079 Z= 0.177 Angle : 0.604 12.736 35554 Z= 0.296 Chirality : 0.040 0.150 3942 Planarity : 0.005 0.063 4660 Dihedral : 6.386 85.462 3805 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.70 % Favored : 91.77 % Rotamer: Outliers : 2.23 % Allowed : 13.75 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 3220 helix: 1.65 (0.14), residues: 1511 sheet: -2.48 (0.24), residues: 373 loop : -1.69 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 172 TYR 0.017 0.001 TYR C 444 PHE 0.029 0.001 PHE D 78 TRP 0.027 0.001 TRP E 232 HIS 0.006 0.001 HIS F 462 Details of bonding type rmsd covalent geometry : bond 0.00410 (26072) covalent geometry : angle 0.60422 (35554) hydrogen bonds : bond 0.03491 ( 1061) hydrogen bonds : angle 4.24196 ( 3084) metal coordination : bond 0.00206 ( 5) Misc. bond : bond 0.00238 ( 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 163 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 0.980 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 166 ARG cc_start: 0.7882 (tpt170) cc_final: 0.7412 (tpt90) REVERT: A 219 GLU cc_start: 0.8954 (tp30) cc_final: 0.8485 (tp30) REVERT: A 379 GLU cc_start: 0.9167 (tt0) cc_final: 0.8814 (pt0) REVERT: A 416 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8581 (mtt-85) REVERT: A 483 ARG cc_start: 0.8445 (ptm-80) cc_final: 0.8176 (ptm-80) REVERT: B 289 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9096 (mmmt) REVERT: B 317 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 444 TYR cc_start: 0.8675 (t80) cc_final: 0.8324 (t80) REVERT: B 448 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9111 (mmtp) REVERT: C 111 MET cc_start: 0.8985 (tpp) cc_final: 0.8611 (tpp) REVERT: C 140 MET cc_start: 0.8605 (pmm) cc_final: 0.8095 (mtt) REVERT: C 289 LYS cc_start: 0.9505 (mmtm) cc_final: 0.9078 (mmtm) REVERT: C 316 LYS cc_start: 0.9303 (mptt) cc_final: 0.9091 (mtpp) REVERT: C 447 GLU cc_start: 0.8505 (mp0) cc_final: 0.7787 (tm-30) REVERT: C 453 TYR cc_start: 0.8740 (m-80) cc_final: 0.8326 (m-80) REVERT: C 518 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8358 (pp) REVERT: D 80 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: D 86 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8437 (t80) REVERT: D 228 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8291 (p0) REVERT: D 417 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7970 (t-90) REVERT: D 573 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7812 (mp) REVERT: E 220 MET cc_start: 0.2167 (ptt) cc_final: -0.0193 (tpt) REVERT: E 307 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8345 (pm20) REVERT: E 338 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8159 (pt) REVERT: F 234 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8686 (tp30) REVERT: F 289 LYS cc_start: 0.8551 (pttm) cc_final: 0.8017 (tptp) REVERT: F 316 LYS cc_start: 0.8936 (tptp) cc_final: 0.8621 (ttmm) REVERT: F 381 MET cc_start: 0.7874 (ptp) cc_final: 0.7328 (ptm) REVERT: F 410 TYR cc_start: 0.8487 (p90) cc_final: 0.8040 (p90) outliers start: 57 outliers final: 35 residues processed: 156 average time/residue: 0.2106 time to fit residues: 47.5481 Evaluate side-chains 142 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 A residue 519 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL 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 35 LEU 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 573 ILE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 232 TRP 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 519 CYS Chi-restraints excluded: chain F residue 552 TYR 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 168 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 144 optimal weight: 0.0070 chunk 230 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- 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 D 205 GLN D 489 ASN F 252 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052807 restraints weight = 112483.686| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.60 r_work: 0.3031 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 26079 Z= 0.185 Angle : 0.609 14.015 35554 Z= 0.298 Chirality : 0.041 0.201 3942 Planarity : 0.005 0.065 4660 Dihedral : 6.244 85.277 3805 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.95 % Favored : 91.52 % Rotamer: Outliers : 2.43 % Allowed : 13.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 3220 helix: 1.65 (0.14), residues: 1518 sheet: -2.46 (0.25), residues: 373 loop : -1.68 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 172 TYR 0.018 0.001 TYR C 444 PHE 0.031 0.001 PHE D 78 TRP 0.028 0.001 TRP E 232 HIS 0.006 0.001 HIS D 495 Details of bonding type rmsd covalent geometry : bond 0.00420 (26072) covalent geometry : angle 0.60852 (35554) hydrogen bonds : bond 0.03453 ( 1061) hydrogen bonds : angle 4.22640 ( 3084) metal coordination : bond 0.07821 ( 5) Misc. bond : bond 0.00221 ( 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 168 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 106 time to evaluate : 0.698 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 166 ARG cc_start: 0.7487 (tpt170) cc_final: 0.7063 (tpt170) REVERT: A 219 GLU cc_start: 0.8952 (tp30) cc_final: 0.8492 (tp30) REVERT: A 379 GLU cc_start: 0.9169 (tt0) cc_final: 0.8815 (pt0) REVERT: A 483 ARG cc_start: 0.8454 (ptm-80) cc_final: 0.8209 (ptm-80) REVERT: B 289 LYS cc_start: 0.9379 (mmmm) cc_final: 0.9109 (mmmt) REVERT: B 317 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8432 (mt) REVERT: B 444 TYR cc_start: 0.8653 (t80) cc_final: 0.8344 (t80) REVERT: B 448 LYS cc_start: 0.9410 (tmtt) cc_final: 0.9118 (mmtp) REVERT: C 111 MET cc_start: 0.8988 (tpp) cc_final: 0.8638 (tpp) REVERT: C 139 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8897 (mt) REVERT: C 140 MET cc_start: 0.8622 (pmm) cc_final: 0.8065 (mtt) REVERT: C 289 LYS cc_start: 0.9515 (mmtm) cc_final: 0.9087 (mmtm) REVERT: C 447 GLU cc_start: 0.8509 (mp0) cc_final: 0.7786 (tm-30) REVERT: C 453 TYR cc_start: 0.8750 (m-80) cc_final: 0.8347 (m-80) REVERT: C 518 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8361 (pp) REVERT: D 80 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: D 86 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8447 (t80) REVERT: D 417 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.7956 (t-90) REVERT: D 527 LYS cc_start: 0.9010 (mmtp) cc_final: 0.8804 (mmmt) REVERT: D 573 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7818 (mp) REVERT: E 220 MET cc_start: 0.2390 (ptt) cc_final: -0.0096 (tpt) REVERT: E 221 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6379 (pt) REVERT: E 260 LYS cc_start: 0.6542 (mppt) cc_final: 0.6300 (mppt) REVERT: E 307 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8336 (pm20) REVERT: E 338 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8174 (pt) REVERT: F 289 LYS cc_start: 0.8568 (pttm) cc_final: 0.8042 (tptp) REVERT: F 316 LYS cc_start: 0.8943 (tptp) cc_final: 0.8625 (ttmm) REVERT: F 410 TYR cc_start: 0.8476 (p90) cc_final: 0.8020 (p90) outliers start: 62 outliers final: 35 residues processed: 162 average time/residue: 0.1979 time to fit residues: 46.8029 Evaluate side-chains 145 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 A residue 519 CYS 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 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 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 521 TYR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 232 TRP 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 363 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 519 CYS Chi-restraints excluded: chain F residue 552 TYR Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 321 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 270 optimal weight: 0.0980 chunk 209 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 38 optimal weight: 0.0060 chunk 140 optimal weight: 0.3980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS C 342 HIS C 462 HIS ** F 462 HIS ** 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 = 0.3537 r_free = 0.3537 target = 0.065588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054032 restraints weight = 112282.711| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.62 r_work: 0.3073 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3035 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= 0.113 Angle : 0.583 15.301 35554 Z= 0.282 Chirality : 0.039 0.198 3942 Planarity : 0.004 0.063 4660 Dihedral : 6.072 82.577 3805 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.14 % Favored : 92.30 % Rotamer: Outliers : 1.88 % Allowed : 14.66 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 3220 helix: 1.73 (0.14), residues: 1517 sheet: -2.34 (0.25), residues: 371 loop : -1.64 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 172 TYR 0.032 0.001 TYR F 350 PHE 0.025 0.001 PHE D 78 TRP 0.026 0.001 TRP E 232 HIS 0.005 0.001 HIS F 462 Details of bonding type rmsd covalent geometry : bond 0.00264 (26072) covalent geometry : angle 0.58298 (35554) hydrogen bonds : bond 0.03087 ( 1061) hydrogen bonds : angle 4.07742 ( 3084) metal coordination : bond 0.00818 ( 5) Misc. bond : bond 0.00194 ( 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 155 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.994 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: 0.8888 (tp30) cc_final: 0.8416 (tp30) REVERT: A 379 GLU cc_start: 0.9148 (tt0) cc_final: 0.8800 (pt0) REVERT: A 483 ARG cc_start: 0.8423 (ptm-80) cc_final: 0.8182 (ptm-80) REVERT: B 289 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9108 (mmmt) REVERT: B 317 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 527 LYS cc_start: 0.8943 (mttt) cc_final: 0.8739 (mttt) REVERT: C 47 GLU cc_start: 0.8491 (tp30) cc_final: 0.8196 (tp30) REVERT: C 111 MET cc_start: 0.8956 (tpp) cc_final: 0.8624 (tpp) REVERT: C 139 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8894 (mt) REVERT: C 140 MET cc_start: 0.8546 (pmm) cc_final: 0.8090 (mtt) REVERT: C 289 LYS cc_start: 0.9492 (mmtm) cc_final: 0.9069 (mmtm) REVERT: C 447 GLU cc_start: 0.8453 (mp0) cc_final: 0.7722 (tm-30) REVERT: C 453 TYR cc_start: 0.8752 (m-80) cc_final: 0.8388 (m-80) REVERT: C 518 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8321 (pp) REVERT: D 80 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: D 86 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8377 (t80) REVERT: D 228 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8117 (p0) REVERT: D 417 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.7971 (t-90) REVERT: D 527 LYS cc_start: 0.8993 (mmtp) cc_final: 0.8771 (mmmt) REVERT: D 573 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7787 (mp) REVERT: E 220 MET cc_start: 0.2879 (ptt) cc_final: 0.0623 (tpt) REVERT: E 221 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6353 (pt) REVERT: E 338 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8155 (pt) REVERT: F 239 TRP cc_start: 0.8295 (t60) cc_final: 0.7997 (t60) REVERT: F 289 LYS cc_start: 0.8488 (pttm) cc_final: 0.8074 (tptp) REVERT: F 316 LYS cc_start: 0.8899 (tptp) cc_final: 0.8593 (ttmm) REVERT: F 381 MET cc_start: 0.7788 (ptp) cc_final: 0.7180 (ptm) REVERT: F 410 TYR cc_start: 0.8477 (p90) cc_final: 0.8015 (p90) outliers start: 48 outliers final: 26 residues processed: 151 average time/residue: 0.1976 time to fit residues: 43.9559 Evaluate side-chains 136 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 573 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 232 TRP 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 363 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 519 CYS Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 55 optimal weight: 0.5980 chunk 308 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 291 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 209 GLN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS C 342 HIS E 525 GLN E 601 GLN ** F 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.065284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.053712 restraints weight = 112260.436| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.62 r_work: 0.3059 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3114 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= 0.133 Angle : 0.603 21.035 35554 Z= 0.290 Chirality : 0.040 0.340 3942 Planarity : 0.005 0.088 4660 Dihedral : 6.283 84.029 3805 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.39 % Favored : 92.02 % Rotamer: Outliers : 1.49 % Allowed : 15.32 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 3220 helix: 1.81 (0.14), residues: 1509 sheet: -2.26 (0.25), residues: 368 loop : -1.61 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 594 TYR 0.028 0.001 TYR F 350 PHE 0.025 0.001 PHE D 78 TRP 0.027 0.001 TRP E 232 HIS 0.005 0.001 HIS F 462 Details of bonding type rmsd covalent geometry : bond 0.00312 (26072) covalent geometry : angle 0.60340 (35554) hydrogen bonds : bond 0.03149 ( 1061) hydrogen bonds : angle 4.07323 ( 3084) metal coordination : bond 0.00242 ( 5) Misc. bond : bond 0.00599 ( 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 139 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.879 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: 0.8899 (tp30) cc_final: 0.8437 (tp30) REVERT: A 379 GLU cc_start: 0.9168 (tt0) cc_final: 0.8826 (pt0) REVERT: A 483 ARG cc_start: 0.8437 (ptm-80) cc_final: 0.8089 (ttt-90) REVERT: B 289 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9109 (mmmt) REVERT: B 316 LYS cc_start: 0.9112 (pttp) cc_final: 0.8862 (ptmm) REVERT: B 448 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9061 (mmtp) REVERT: B 527 LYS cc_start: 0.8962 (mttt) cc_final: 0.8760 (mttt) REVERT: C 47 GLU cc_start: 0.8500 (tp30) cc_final: 0.8210 (tp30) REVERT: C 111 MET cc_start: 0.8953 (tpp) cc_final: 0.8629 (tpp) REVERT: C 139 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8921 (mt) REVERT: C 140 MET cc_start: 0.8569 (pmm) cc_final: 0.8064 (mtt) REVERT: C 289 LYS cc_start: 0.9488 (mmtm) cc_final: 0.9071 (mmtm) REVERT: C 315 MET cc_start: 0.8788 (mtt) cc_final: 0.8268 (mmm) REVERT: C 447 GLU cc_start: 0.8455 (mp0) cc_final: 0.7731 (tm-30) REVERT: C 453 TYR cc_start: 0.8762 (m-80) cc_final: 0.8371 (m-80) REVERT: C 518 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8318 (pp) REVERT: D 80 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: D 86 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8398 (t80) REVERT: D 242 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8444 (mm-30) REVERT: D 417 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7975 (t-90) REVERT: D 527 LYS cc_start: 0.9033 (mmtp) cc_final: 0.8808 (mmmt) REVERT: D 573 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7793 (mp) REVERT: E 220 MET cc_start: 0.2892 (ptt) cc_final: 0.0672 (tpt) REVERT: E 221 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6420 (pt) REVERT: E 338 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8127 (pt) REVERT: F 289 LYS cc_start: 0.8467 (pttm) cc_final: 0.8100 (tptp) REVERT: F 316 LYS cc_start: 0.8926 (tptp) cc_final: 0.8614 (ttmm) REVERT: F 381 MET cc_start: 0.7832 (ptp) cc_final: 0.7359 (ptm) REVERT: F 410 TYR cc_start: 0.8496 (p90) cc_final: 0.8026 (p90) outliers start: 38 outliers final: 27 residues processed: 136 average time/residue: 0.2042 time to fit residues: 40.7984 Evaluate side-chains 134 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 82 MET 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 385 ARG Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 519 CYS Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 232 TRP 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 363 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 519 CYS Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 582 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 67 optimal weight: 0.5980 chunk 265 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 319 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS 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 = 0.3531 r_free = 0.3531 target = 0.065412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.053829 restraints weight = 111820.428| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.61 r_work: 0.3065 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3173 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= 0.129 Angle : 0.599 19.757 35554 Z= 0.288 Chirality : 0.040 0.263 3942 Planarity : 0.005 0.086 4660 Dihedral : 6.212 84.405 3805 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.27 % Favored : 92.17 % Rotamer: Outliers : 1.49 % Allowed : 15.32 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 3220 helix: 1.83 (0.14), residues: 1513 sheet: -2.29 (0.25), residues: 371 loop : -1.58 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 594 TYR 0.029 0.001 TYR F 350 PHE 0.025 0.001 PHE D 78 TRP 0.023 0.001 TRP E 232 HIS 0.005 0.001 HIS F 462 Details of bonding type rmsd covalent geometry : bond 0.00304 (26072) covalent geometry : angle 0.59949 (35554) hydrogen bonds : bond 0.03072 ( 1061) hydrogen bonds : angle 4.04503 ( 3084) metal coordination : bond 0.00106 ( 5) Misc. bond : bond 0.00418 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5171.67 seconds wall clock time: 89 minutes 44.41 seconds (5384.41 seconds total)