Starting phenix.real_space_refine on Mon Jun 16 22:23:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tts_26122/06_2025/7tts_26122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tts_26122/06_2025/7tts_26122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tts_26122/06_2025/7tts_26122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tts_26122/06_2025/7tts_26122.map" model { file = "/net/cci-nas-00/data/ceres_data/7tts_26122/06_2025/7tts_26122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tts_26122/06_2025/7tts_26122.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.035 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 P 14 5.49 5 Mg 4 5.21 5 S 54 5.16 5 C 11438 2.51 5 N 3615 2.21 5 O 3668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18793 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2980 Classifications: {'peptide': 433} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "B" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3033 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 12, 'TRANS': 427} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "C" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3159 Classifications: {'peptide': 456} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "D" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3217 Classifications: {'peptide': 463} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 16, 'TRANS': 446} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "E" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3199 Classifications: {'peptide': 461} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 15, 'TRANS': 445} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "F" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2980 Classifications: {'peptide': 433} Incomplete info: {'backbone_only': 120} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 420} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "P" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.46, per 1000 atoms: 0.66 Number of scatterers: 18793 At special positions: 0 Unit cell: (133.6, 146.125, 140.28, 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) S 54 16.00 P 14 15.00 Mg 4 11.99 O 3668 8.00 N 3615 7.00 C 11438 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=0, symmetry=0 Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.6 seconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 15 sheets defined 62.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 309 through 336 Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.739A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 366 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 437 through 444 Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 460 through 474 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.683A pdb=" N HIS A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.664A pdb=" N GLY A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 590 Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 614 through 617 Processing helix chain 'A' and resid 618 through 641 removed outlier: 3.569A pdb=" N ARG A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 146 through 156 Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 179 through 189 Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.626A pdb=" N ALA B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 337 Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.563A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 366 Processing helix chain 'B' and resid 386 through 399 Processing helix chain 'B' and resid 412 through 415 removed outlier: 3.823A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 419 through 425 removed outlier: 4.281A pdb=" N PHE B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.680A pdb=" N LEU B 464 " --> pdb=" O HIS B 460 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 466' Processing helix chain 'B' and resid 466 through 474 removed outlier: 4.382A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 removed outlier: 3.709A pdb=" N GLN B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.673A pdb=" N LEU B 559 " --> pdb=" O ARG B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.784A pdb=" N GLY B 612 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 630 Processing helix chain 'B' and resid 630 through 640 Processing helix chain 'C' and resid 133 through 145 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 268 through 276 Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 309 through 337 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.528A pdb=" N GLU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 366 Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.870A pdb=" N ILE C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.617A pdb=" N LEU C 464 " --> pdb=" O HIS C 460 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 465' Processing helix chain 'C' and resid 466 through 474 removed outlier: 4.196A pdb=" N LEU C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 507 through 512 removed outlier: 4.204A pdb=" N GLU C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 553 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 572 through 596 Processing helix chain 'C' and resid 602 through 611 removed outlier: 4.196A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 630 removed outlier: 3.772A pdb=" N ILE C 622 " --> pdb=" O GLY C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'D' and resid 133 through 144 Processing helix chain 'D' and resid 146 through 157 Processing helix chain 'D' and resid 169 through 177 Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 268 through 277 Processing helix chain 'D' and resid 278 through 288 Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 309 through 336 Processing helix chain 'D' and resid 338 through 347 removed outlier: 3.642A pdb=" N HIS D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 366 Processing helix chain 'D' and resid 386 through 400 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.916A pdb=" N ILE D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 446 Processing helix chain 'D' and resid 456 through 459 Processing helix chain 'D' and resid 460 through 474 removed outlier: 4.003A pdb=" N ILE D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 514 Processing helix chain 'D' and resid 539 through 544 Processing helix chain 'D' and resid 544 through 554 removed outlier: 3.547A pdb=" N ILE D 548 " --> pdb=" O VAL D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 561 removed outlier: 3.554A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 602 through 611 Processing helix chain 'D' and resid 612 through 613 No H-bonds generated for 'chain 'D' and resid 612 through 613' Processing helix chain 'D' and resid 614 through 617 Processing helix chain 'D' and resid 618 through 630 removed outlier: 3.832A pdb=" N ILE D 622 " --> pdb=" O GLY D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 638 Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 146 through 156 Processing helix chain 'E' and resid 169 through 177 Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 268 through 276 Processing helix chain 'E' and resid 278 through 288 Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 309 through 335 removed outlier: 4.256A pdb=" N GLN E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG E 327 " --> pdb=" O GLN E 323 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 3.543A pdb=" N GLU E 345 " --> pdb=" O GLN E 341 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 367 Processing helix chain 'E' and resid 386 through 400 Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 416 through 419 Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.780A pdb=" N ILE E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 446 removed outlier: 3.575A pdb=" N LYS E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 Processing helix chain 'E' and resid 460 through 474 Processing helix chain 'E' and resid 498 through 517 Processing helix chain 'E' and resid 538 through 554 Proline residue: E 547 - end of helix Processing helix chain 'E' and resid 555 through 562 Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 602 through 611 Processing helix chain 'E' and resid 618 through 630 removed outlier: 3.785A pdb=" N ILE E 622 " --> pdb=" O GLY E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 639 removed outlier: 4.187A pdb=" N GLU E 639 " --> pdb=" O ALA E 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 144 Processing helix chain 'F' and resid 146 through 156 Processing helix chain 'F' and resid 169 through 177 Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 268 through 277 Processing helix chain 'F' and resid 278 through 288 Processing helix chain 'F' and resid 301 through 306 Processing helix chain 'F' and resid 309 through 337 removed outlier: 3.636A pdb=" N LYS F 313 " --> pdb=" O GLY F 309 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 removed outlier: 4.034A pdb=" N HIS F 346 " --> pdb=" O ARG F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 366 Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 410 through 414 Processing helix chain 'F' and resid 418 through 423 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 455 through 459 Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 468 through 471 Processing helix chain 'F' and resid 498 through 504 removed outlier: 4.219A pdb=" N ILE F 502 " --> pdb=" O ALA F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 548 through 554 Processing helix chain 'F' and resid 572 through 591 Processing helix chain 'F' and resid 593 through 597 Processing helix chain 'F' and resid 601 through 611 removed outlier: 3.635A pdb=" N ASP F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 630 removed outlier: 4.132A pdb=" N ILE F 622 " --> pdb=" O GLY F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 640 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.704A pdb=" N ILE A 407 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP A 454 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 409 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 451 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR A 494 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 453 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 376 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 566 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 378 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 477 Processing sheet with id=AA3, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.806A pdb=" N VAL B 376 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B 566 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 378 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE B 568 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 380 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 477 Processing sheet with id=AA5, first strand: chain 'B' and resid 598 through 601 removed outlier: 6.595A pdb=" N THR B 598 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 651 " --> pdb=" O THR B 598 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 600 " --> pdb=" O ILE B 651 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 406 through 410 removed outlier: 6.239A pdb=" N VAL C 451 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR C 494 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 453 " --> pdb=" O THR C 494 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 381 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 475 through 477 Processing sheet with id=AA8, first strand: chain 'C' and resid 598 through 601 removed outlier: 6.062A pdb=" N THR C 598 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE C 651 " --> pdb=" O THR C 598 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU C 600 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL C 653 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 406 through 410 removed outlier: 6.698A pdb=" N VAL D 376 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL D 566 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 378 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE D 568 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 380 " --> pdb=" O PHE D 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 598 through 600 removed outlier: 5.767A pdb=" N THR D 598 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU D 649 " --> pdb=" O THR D 598 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 600 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE D 651 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 406 through 410 removed outlier: 6.832A pdb=" N VAL E 376 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL E 566 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU E 378 " --> pdb=" O VAL E 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 475 through 477 Processing sheet with id=AB4, first strand: chain 'E' and resid 597 through 600 removed outlier: 6.112A pdb=" N THR E 598 " --> pdb=" O CYS E 647 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU E 649 " --> pdb=" O THR E 598 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU E 600 " --> pdb=" O LEU E 649 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ILE E 651 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 406 through 409 removed outlier: 6.364A pdb=" N VAL F 451 " --> pdb=" O ILE F 492 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR F 494 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE F 453 " --> pdb=" O THR F 494 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL F 376 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL F 566 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 378 " --> pdb=" O VAL F 566 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 474 through 477 removed outlier: 4.524A pdb=" N ILE F 484 " --> pdb=" O ARG F 475 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3192 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: 6.53 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 6709 1.34 - 1.48: 4537 1.48 - 1.63: 7741 1.63 - 1.78: 18 1.78 - 1.93: 79 Bond restraints: 19084 Sorted by residual: bond pdb=" O2B AGS B 802 " pdb=" PB AGS B 802 " ideal model delta sigma weight residual 1.531 1.239 0.292 1.60e-02 3.91e+03 3.33e+02 bond pdb=" O2A AGS B 802 " pdb=" PA AGS B 802 " ideal model delta sigma weight residual 1.531 1.264 0.267 1.60e-02 3.91e+03 2.79e+02 bond pdb=" C8 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.370 1.190 0.180 1.10e-02 8.26e+03 2.69e+02 bond pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.374 1.224 0.150 1.00e-02 1.00e+04 2.25e+02 bond pdb=" C3' AGS B 802 " pdb=" C4' AGS B 802 " ideal model delta sigma weight residual 1.526 1.390 0.136 1.10e-02 8.26e+03 1.54e+02 ... (remaining 19079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 25191 4.14 - 8.27: 174 8.27 - 12.41: 21 12.41 - 16.54: 10 16.54 - 20.68: 4 Bond angle restraints: 25400 Sorted by residual: angle pdb=" C4 AGS E 801 " pdb=" N9 AGS E 801 " pdb=" C8 AGS E 801 " ideal model delta sigma weight residual 105.70 115.48 -9.78 4.55e-01 4.83e+00 4.62e+02 angle pdb=" C4 AGS C 802 " pdb=" N9 AGS C 802 " pdb=" C8 AGS C 802 " ideal model delta sigma weight residual 105.70 115.39 -9.69 4.55e-01 4.83e+00 4.53e+02 angle pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " pdb=" C8 AGS B 802 " ideal model delta sigma weight residual 105.70 113.17 -7.47 4.55e-01 4.83e+00 2.70e+02 angle pdb=" N1 AGS B 802 " pdb=" C2 AGS B 802 " pdb=" N3 AGS B 802 " ideal model delta sigma weight residual 128.80 118.57 10.23 8.41e-01 1.41e+00 1.48e+02 angle pdb=" N7 AGS E 801 " pdb=" C8 AGS E 801 " pdb=" N9 AGS E 801 " ideal model delta sigma weight residual 114.03 105.71 8.32 6.99e-01 2.05e+00 1.42e+02 ... (remaining 25395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 10135 25.51 - 51.02: 318 51.02 - 76.54: 58 76.54 - 102.05: 7 102.05 - 127.56: 4 Dihedral angle restraints: 10522 sinusoidal: 4187 harmonic: 6335 Sorted by residual: dihedral pdb=" C4' ADP A 801 " pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -180.00 -52.79 -127.21 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" C2' ADP A 801 " pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C4 ADP A 801 " ideal model delta sinusoidal sigma weight residual 91.55 -143.32 -125.13 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" C VAL B 653 " pdb=" N VAL B 653 " pdb=" CA VAL B 653 " pdb=" CB VAL B 653 " ideal model delta harmonic sigma weight residual -122.00 -134.99 12.99 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 10519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2334 0.384 - 0.768: 3 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.920: 2 Chirality restraints: 2339 Sorted by residual: chirality pdb=" PB AGS B 802 " pdb=" O2B AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O3B AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.26 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" PA AGS B 802 " pdb=" O2A AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O5' AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.56 1.62 2.00e-01 2.50e+01 6.55e+01 chirality pdb=" C2' AGS B 802 " pdb=" C1' AGS B 802 " pdb=" C3' AGS B 802 " pdb=" O2' AGS B 802 " both_signs ideal model delta sigma weight residual False -2.67 -2.02 -0.66 2.00e-01 2.50e+01 1.07e+01 ... (remaining 2336 not shown) Planarity restraints: 3555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 423 " -0.102 2.00e-02 2.50e+03 6.39e-02 7.14e+01 pdb=" CG PHE B 423 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE B 423 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE B 423 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE B 423 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 423 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 423 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AGS D 801 " -0.088 2.00e-02 2.50e+03 4.45e-02 5.44e+01 pdb=" C2 AGS D 801 " 0.041 2.00e-02 2.50e+03 pdb=" C4 AGS D 801 " -0.018 2.00e-02 2.50e+03 pdb=" C5 AGS D 801 " -0.016 2.00e-02 2.50e+03 pdb=" C6 AGS D 801 " -0.006 2.00e-02 2.50e+03 pdb=" C8 AGS D 801 " 0.068 2.00e-02 2.50e+03 pdb=" N1 AGS D 801 " 0.020 2.00e-02 2.50e+03 pdb=" N3 AGS D 801 " -0.002 2.00e-02 2.50e+03 pdb=" N6 AGS D 801 " -0.062 2.00e-02 2.50e+03 pdb=" N7 AGS D 801 " 0.011 2.00e-02 2.50e+03 pdb=" N9 AGS D 801 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 601 " -0.084 2.00e-02 2.50e+03 4.55e-02 5.16e+01 pdb=" CG TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 601 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 601 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 601 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP B 601 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 601 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 601 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 601 " -0.059 2.00e-02 2.50e+03 ... (remaining 3552 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 77 2.41 - 3.03: 12872 3.03 - 3.66: 27884 3.66 - 4.28: 41713 4.28 - 4.90: 68532 Nonbonded interactions: 151078 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2G AGS B 802 " model vdw 1.788 2.170 nonbonded pdb=" O1B AGS D 801 " pdb="MG MG D 802 " model vdw 1.905 2.170 nonbonded pdb=" O1A AGS D 801 " pdb="MG MG D 802 " model vdw 2.012 2.170 nonbonded pdb=" OE2 GLU D 455 " pdb="MG MG D 802 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR E 388 " pdb="MG MG E 802 " model vdw 2.161 2.170 ... (remaining 151073 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 132 through 653) selection = (chain 'B' and (resid 132 through 515 or resid 539 through 653)) selection = (chain 'C' and (resid 132 through 515 or resid 539 through 653)) selection = (chain 'D' and (resid 132 through 515 or resid 539 through 653)) selection = (chain 'E' and (resid 132 through 515 or resid 539 through 653)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.250 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 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 : 0.008 0.292 19084 Z= 0.542 Angle : 0.995 20.677 25400 Z= 0.678 Chirality : 0.079 1.920 2339 Planarity : 0.005 0.080 3555 Dihedral : 12.972 127.559 6910 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 0.30 % Allowed : 1.28 % Favored : 98.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2650 helix: 1.81 (0.14), residues: 1449 sheet: 0.59 (0.32), residues: 263 loop : 0.74 (0.23), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.004 TRP B 601 HIS 0.012 0.001 HIS B 418 PHE 0.102 0.005 PHE B 423 TYR 0.075 0.002 TYR A 430 ARG 0.009 0.000 ARG D 620 Details of bonding type rmsd hydrogen bonds : bond 0.14953 ( 1092) hydrogen bonds : angle 6.73936 ( 3192) covalent geometry : bond 0.00830 (19084) covalent geometry : angle 0.99494 (25400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.9752 time to fit residues: 69.7233 Evaluate side-chains 53 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 40.0000 chunk 203 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 137 optimal weight: 110.0000 chunk 108 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 243 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN A 614 ASN A 632 ASN C 511 GLN C 595 HIS D 341 GLN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 HIS E 505 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.029466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.026286 restraints weight = 370572.440| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 5.83 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3753 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19084 Z= 0.147 Angle : 0.549 7.836 25400 Z= 0.291 Chirality : 0.040 0.150 2339 Planarity : 0.004 0.046 3555 Dihedral : 8.423 130.889 2955 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.24 % Allowed : 2.80 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.17), residues: 2650 helix: 2.30 (0.14), residues: 1468 sheet: 0.28 (0.31), residues: 270 loop : 1.15 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 601 HIS 0.017 0.001 HIS D 552 PHE 0.017 0.002 PHE C 540 TYR 0.009 0.001 TYR A 430 ARG 0.005 0.001 ARG D 546 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1092) hydrogen bonds : angle 5.44544 ( 3192) covalent geometry : bond 0.00301 (19084) covalent geometry : angle 0.54897 (25400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 2.109 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 56 average time/residue: 0.9159 time to fit residues: 62.5925 Evaluate side-chains 52 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 184 optimal weight: 40.0000 chunk 240 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 244 optimal weight: 40.0000 chunk 249 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 199 optimal weight: 50.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN C 624 HIS ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS F 552 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.029164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.026085 restraints weight = 373939.681| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 6.29 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3826 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19084 Z= 0.131 Angle : 0.500 6.784 25400 Z= 0.265 Chirality : 0.039 0.251 2339 Planarity : 0.004 0.046 3555 Dihedral : 8.249 128.978 2954 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Rotamer: Outliers : 0.24 % Allowed : 4.19 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.17), residues: 2650 helix: 2.47 (0.14), residues: 1477 sheet: 0.27 (0.30), residues: 286 loop : 1.25 (0.24), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 368 HIS 0.014 0.001 HIS D 552 PHE 0.023 0.002 PHE A 471 TYR 0.009 0.001 TYR A 397 ARG 0.010 0.001 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 1092) hydrogen bonds : angle 5.02905 ( 3192) covalent geometry : bond 0.00270 (19084) covalent geometry : angle 0.49995 (25400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 493 MET cc_start: 0.7625 (mpp) cc_final: 0.7204 (mpp) REVERT: E 467 MET cc_start: 0.8809 (mtt) cc_final: 0.8570 (ptp) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.8707 time to fit residues: 59.1517 Evaluate side-chains 53 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 23 optimal weight: 50.0000 chunk 201 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 320.0000 chunk 149 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 176 optimal weight: 30.0000 chunk 174 optimal weight: 30.0000 chunk 240 optimal weight: 5.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 578 GLN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 HIS E 595 HIS E 624 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.029051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.025981 restraints weight = 372523.673| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.88 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3893 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19084 Z= 0.143 Angle : 0.508 7.869 25400 Z= 0.268 Chirality : 0.038 0.145 2339 Planarity : 0.004 0.046 3555 Dihedral : 8.271 131.789 2954 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 0.18 % Allowed : 5.17 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.17), residues: 2650 helix: 2.52 (0.14), residues: 1481 sheet: 0.13 (0.31), residues: 271 loop : 1.13 (0.24), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 368 HIS 0.013 0.002 HIS E 433 PHE 0.017 0.002 PHE A 471 TYR 0.009 0.001 TYR D 430 ARG 0.003 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 1092) hydrogen bonds : angle 4.94367 ( 3192) covalent geometry : bond 0.00293 (19084) covalent geometry : angle 0.50829 (25400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 2.280 Fit side-chains revert: symmetry clash REVERT: E 467 MET cc_start: 0.8783 (mtt) cc_final: 0.8503 (mtt) outliers start: 3 outliers final: 0 residues processed: 55 average time/residue: 0.9045 time to fit residues: 61.8115 Evaluate side-chains 52 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 179 optimal weight: 40.0000 chunk 236 optimal weight: 50.0000 chunk 225 optimal weight: 30.0000 chunk 158 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 154 optimal weight: 40.0000 chunk 40 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.028849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.025895 restraints weight = 379336.336| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 5.36 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3869 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19084 Z= 0.147 Angle : 0.521 7.898 25400 Z= 0.273 Chirality : 0.039 0.157 2339 Planarity : 0.004 0.045 3555 Dihedral : 8.319 134.287 2954 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.83 % Rotamer: Outliers : 0.18 % Allowed : 5.53 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.17), residues: 2650 helix: 2.53 (0.14), residues: 1481 sheet: 0.02 (0.31), residues: 258 loop : 1.09 (0.23), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 368 HIS 0.011 0.002 HIS D 552 PHE 0.017 0.002 PHE E 453 TYR 0.011 0.001 TYR A 397 ARG 0.004 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 1092) hydrogen bonds : angle 4.92722 ( 3192) covalent geometry : bond 0.00298 (19084) covalent geometry : angle 0.52095 (25400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 2.245 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 1.1048 time to fit residues: 72.8615 Evaluate side-chains 53 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 493 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 100 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 95 optimal weight: 110.0000 chunk 0 optimal weight: 420.0000 chunk 123 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 97 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 243 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 228 optimal weight: 50.0000 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 552 HIS B 616 HIS C 366 ASN C 418 HIS D 578 GLN D 581 ASN D 616 HIS E 373 HIS ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 HIS F 511 GLN F 624 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.028486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.025483 restraints weight = 401710.562| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 5.98 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4172 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19084 Z= 0.229 Angle : 0.634 7.626 25400 Z= 0.336 Chirality : 0.041 0.169 2339 Planarity : 0.005 0.052 3555 Dihedral : 8.551 139.137 2954 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 0.61 % Allowed : 6.57 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.17), residues: 2650 helix: 2.22 (0.14), residues: 1489 sheet: -0.15 (0.33), residues: 243 loop : 0.86 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 368 HIS 0.019 0.002 HIS A 399 PHE 0.020 0.003 PHE B 553 TYR 0.017 0.002 TYR A 397 ARG 0.006 0.001 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1092) hydrogen bonds : angle 5.29122 ( 3192) covalent geometry : bond 0.00463 (19084) covalent geometry : angle 0.63434 (25400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 61 average time/residue: 0.9799 time to fit residues: 73.4718 Evaluate side-chains 51 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 95 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 179 optimal weight: 50.0000 chunk 1 optimal weight: 50.0000 chunk 76 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 176 optimal weight: 40.0000 chunk 219 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 ASN C 418 HIS ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.028146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.025600 restraints weight = 384294.250| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 4.66 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3823 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19084 Z= 0.127 Angle : 0.526 9.119 25400 Z= 0.272 Chirality : 0.039 0.147 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.348 143.345 2954 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 0.61 % Allowed : 6.93 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.17), residues: 2650 helix: 2.44 (0.14), residues: 1479 sheet: -0.17 (0.32), residues: 248 loop : 0.84 (0.23), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 368 HIS 0.011 0.001 HIS A 399 PHE 0.012 0.002 PHE E 453 TYR 0.012 0.001 TYR E 369 ARG 0.004 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 1092) hydrogen bonds : angle 5.09534 ( 3192) covalent geometry : bond 0.00263 (19084) covalent geometry : angle 0.52611 (25400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 467 MET cc_start: 0.8681 (ptp) cc_final: 0.8241 (mpt) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 1.1366 time to fit residues: 81.1050 Evaluate side-chains 54 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain F residue 504 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 44 optimal weight: 50.0000 chunk 146 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 235 optimal weight: 80.0000 chunk 215 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 180 optimal weight: 50.0000 chunk 159 optimal weight: 7.9990 chunk 229 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 ASN ** D 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.028165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.025419 restraints weight = 391227.312| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.05 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3898 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19084 Z= 0.126 Angle : 0.523 9.377 25400 Z= 0.271 Chirality : 0.039 0.160 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.288 142.273 2954 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 0.18 % Allowed : 7.60 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.17), residues: 2650 helix: 2.44 (0.14), residues: 1481 sheet: -0.20 (0.32), residues: 258 loop : 0.89 (0.23), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 368 HIS 0.009 0.001 HIS A 399 PHE 0.010 0.001 PHE C 540 TYR 0.011 0.001 TYR E 369 ARG 0.006 0.000 ARG C 417 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 1092) hydrogen bonds : angle 5.04586 ( 3192) covalent geometry : bond 0.00263 (19084) covalent geometry : angle 0.52344 (25400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 1.0777 time to fit residues: 71.0604 Evaluate side-chains 53 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain F residue 504 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 57 optimal weight: 4.9990 chunk 236 optimal weight: 50.0000 chunk 260 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 257 optimal weight: 30.0000 chunk 213 optimal weight: 0.4980 chunk 93 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 8 optimal weight: 320.0000 chunk 134 optimal weight: 6.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 ASN C 418 HIS ** D 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 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 = 0.3972 r_free = 0.3972 target = 0.028090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.025421 restraints weight = 392738.696| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 4.93 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3866 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19084 Z= 0.125 Angle : 0.539 12.249 25400 Z= 0.276 Chirality : 0.039 0.213 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.271 142.306 2954 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 0.30 % Allowed : 7.60 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.17), residues: 2650 helix: 2.45 (0.14), residues: 1480 sheet: -0.23 (0.32), residues: 258 loop : 0.95 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 368 HIS 0.009 0.001 HIS A 399 PHE 0.009 0.001 PHE C 540 TYR 0.011 0.001 TYR E 369 ARG 0.004 0.000 ARG E 510 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 1092) hydrogen bonds : angle 5.02860 ( 3192) covalent geometry : bond 0.00261 (19084) covalent geometry : angle 0.53948 (25400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 MET cc_start: 0.8128 (pmm) cc_final: 0.7847 (pmm) REVERT: F 467 MET cc_start: 0.8875 (ptp) cc_final: 0.8613 (pmm) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 1.6369 time to fit residues: 110.4328 Evaluate side-chains 53 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain F residue 504 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 16 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 136 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 11 optimal weight: 60.0000 chunk 169 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 HIS C 366 ASN C 393 GLN C 418 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 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 = 0.4043 r_free = 0.4043 target = 0.028373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.025439 restraints weight = 396216.514| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 5.84 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4198 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19084 Z= 0.168 Angle : 0.584 10.628 25400 Z= 0.304 Chirality : 0.040 0.182 2339 Planarity : 0.004 0.045 3555 Dihedral : 8.395 144.173 2954 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.24 % Allowed : 7.72 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.17), residues: 2650 helix: 2.34 (0.14), residues: 1485 sheet: -0.20 (0.33), residues: 250 loop : 0.88 (0.23), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 368 HIS 0.019 0.002 HIS B 399 PHE 0.013 0.002 PHE E 540 TYR 0.013 0.001 TYR E 369 ARG 0.025 0.001 ARG D 590 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 1092) hydrogen bonds : angle 5.14887 ( 3192) covalent geometry : bond 0.00346 (19084) covalent geometry : angle 0.58415 (25400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 2.298 Fit side-chains REVERT: F 467 MET cc_start: 0.9098 (ptp) cc_final: 0.8710 (mpp) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.9103 time to fit residues: 60.7803 Evaluate side-chains 52 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 418 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 119 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 205 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 186 optimal weight: 420.0000 chunk 149 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 ASN C 595 HIS ** D 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 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 = 0.3977 r_free = 0.3977 target = 0.028116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.025606 restraints weight = 392131.739| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 4.70 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3927 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19084 Z= 0.113 Angle : 0.554 10.976 25400 Z= 0.284 Chirality : 0.040 0.200 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.320 143.893 2954 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 0.18 % Allowed : 7.72 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.17), residues: 2650 helix: 2.41 (0.14), residues: 1481 sheet: -0.20 (0.32), residues: 256 loop : 0.93 (0.23), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 368 HIS 0.018 0.001 HIS C 418 PHE 0.011 0.001 PHE E 453 TYR 0.011 0.001 TYR E 369 ARG 0.007 0.001 ARG C 417 Details of bonding type rmsd hydrogen bonds : bond 0.02877 ( 1092) hydrogen bonds : angle 5.10315 ( 3192) covalent geometry : bond 0.00242 (19084) covalent geometry : angle 0.55443 (25400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10464.72 seconds wall clock time: 186 minutes 9.53 seconds (11169.53 seconds total)