Starting phenix.real_space_refine on Sun Aug 24 10:36:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tts_26122/08_2025/7tts_26122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tts_26122/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tts_26122/08_2025/7tts_26122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tts_26122/08_2025/7tts_26122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tts_26122/08_2025/7tts_26122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tts_26122/08_2025/7tts_26122.map" } resolution = 2.9 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= 0.006 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): 0.02s 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: 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: {'ASN:plan1': 10, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 8, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 4} 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: {'ASN:plan1': 10, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 8, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 4} 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: {'ASN:plan1': 10, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 8, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 4} 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: {'ASN:plan1': 10, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 8, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 4} 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: {'ASN:plan1': 10, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 8, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 4} 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: {'ASN:plan1': 10, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 8, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 4} 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: 5.28, per 1000 atoms: 0.28 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: 1.99 Conformation dependent library (CDL) restraints added in 964.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.75 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: 3.56 Time building geometry restraints manager: 2.50 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: 3.020 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.860 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.030 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- 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 : 5.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (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 ARG 0.009 0.000 ARG D 620 TYR 0.075 0.002 TYR A 430 PHE 0.102 0.005 PHE B 423 TRP 0.084 0.004 TRP B 601 HIS 0.012 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00830 (19084) covalent geometry : angle 0.99494 (25400) hydrogen bonds : bond 0.14953 ( 1092) hydrogen bonds : angle 6.73936 ( 3192) *********************** 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 : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.4852 time to fit residues: 34.2265 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 : 0.845 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 120.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.029477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.026422 restraints weight = 360515.803| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 5.74 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4241 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19084 Z= 0.130 Angle : 0.539 7.745 25400 Z= 0.285 Chirality : 0.040 0.155 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.381 130.532 2955 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.06 % 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 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: 2.49 (0.17), residues: 2650 helix: 2.33 (0.14), residues: 1462 sheet: 0.31 (0.31), residues: 269 loop : 1.12 (0.24), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 546 TYR 0.009 0.001 TYR A 397 PHE 0.015 0.001 PHE C 540 TRP 0.006 0.001 TRP B 601 HIS 0.017 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00269 (19084) covalent geometry : angle 0.53897 (25400) hydrogen bonds : bond 0.03914 ( 1092) hydrogen bonds : angle 5.39129 ( 3192) *********************** 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 : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 55 average time/residue: 0.4443 time to fit residues: 29.9255 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 : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 33 optimal weight: 20.0000 chunk 222 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 228 optimal weight: 100.0000 chunk 239 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 200 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 overall best weight: 13.7998 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 GLN C 624 HIS ** D 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 581 ASN D 595 HIS E 373 HIS E 595 HIS E 624 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS F 511 GLN F 552 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.028859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.025925 restraints weight = 392947.984| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 5.61 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3913 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19084 Z= 0.255 Angle : 0.691 8.882 25400 Z= 0.366 Chirality : 0.042 0.193 2339 Planarity : 0.005 0.053 3555 Dihedral : 8.689 129.723 2954 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer: Outliers : 0.49 % Allowed : 4.86 % 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 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: 2.12 (0.17), residues: 2650 helix: 2.04 (0.14), residues: 1479 sheet: 0.01 (0.31), residues: 274 loop : 0.99 (0.23), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 650 TYR 0.017 0.002 TYR B 430 PHE 0.024 0.003 PHE A 377 TRP 0.020 0.002 TRP B 368 HIS 0.017 0.003 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00513 (19084) covalent geometry : angle 0.69129 (25400) hydrogen bonds : bond 0.04258 ( 1092) hydrogen bonds : angle 5.37581 ( 3192) *********************** 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 59 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: F 467 MET cc_start: 0.8914 (ptp) cc_final: 0.8614 (pmm) outliers start: 8 outliers final: 1 residues processed: 57 average time/residue: 0.4193 time to fit residues: 29.4424 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 : 0.793 ------------------------------------------------------------------------------- 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 18 optimal weight: 40.0000 chunk 119 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** B 399 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 = 0.3978 r_free = 0.3978 target = 0.028420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.025754 restraints weight = 381603.536| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 4.88 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3811 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19084 Z= 0.134 Angle : 0.512 6.975 25400 Z= 0.272 Chirality : 0.039 0.141 2339 Planarity : 0.004 0.042 3555 Dihedral : 8.455 138.713 2954 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.41 (0.17), residues: 2650 helix: 2.33 (0.14), residues: 1482 sheet: -0.04 (0.31), residues: 269 loop : 1.05 (0.23), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 329 TYR 0.010 0.001 TYR D 430 PHE 0.014 0.002 PHE B 453 TRP 0.011 0.001 TRP E 368 HIS 0.011 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00277 (19084) covalent geometry : angle 0.51171 (25400) hydrogen bonds : bond 0.03304 ( 1092) hydrogen bonds : angle 5.18842 ( 3192) *********************** 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 52 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.976 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.4789 time to fit residues: 30.1719 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 : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 175 optimal weight: 50.0000 chunk 117 optimal weight: 8.9990 chunk 178 optimal weight: 620.0000 chunk 229 optimal weight: 50.0000 chunk 89 optimal weight: 40.0000 chunk 11 optimal weight: 0.2980 chunk 204 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 80.0000 chunk 192 optimal weight: 6.9990 chunk 237 optimal weight: 50.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.028719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.025705 restraints weight = 378640.975| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.98 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3945 moved from start: 0.3194 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= 0.129 Angle : 0.498 7.624 25400 Z= 0.262 Chirality : 0.039 0.135 2339 Planarity : 0.004 0.043 3555 Dihedral : 8.410 136.981 2954 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 0.36 % Allowed : 6.02 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.50 (0.17), residues: 2650 helix: 2.46 (0.14), residues: 1475 sheet: -0.11 (0.31), residues: 258 loop : 1.01 (0.23), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 329 TYR 0.010 0.001 TYR D 430 PHE 0.019 0.002 PHE A 471 TRP 0.010 0.001 TRP E 368 HIS 0.010 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00266 (19084) covalent geometry : angle 0.49776 (25400) hydrogen bonds : bond 0.03062 ( 1092) hydrogen bonds : angle 5.07422 ( 3192) *********************** 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 56 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.4657 time to fit residues: 31.5235 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 : 0.678 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN E 616 HIS F 624 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.028793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.025865 restraints weight = 382566.492| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 5.14 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3776 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19084 Z= 0.105 Angle : 0.484 7.809 25400 Z= 0.254 Chirality : 0.039 0.152 2339 Planarity : 0.003 0.044 3555 Dihedral : 8.340 137.382 2954 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.49 % Allowed : 6.38 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.57 (0.17), residues: 2650 helix: 2.52 (0.14), residues: 1479 sheet: -0.07 (0.31), residues: 258 loop : 1.01 (0.23), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 510 TYR 0.008 0.001 TYR D 430 PHE 0.025 0.001 PHE A 471 TRP 0.009 0.001 TRP E 368 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00221 (19084) covalent geometry : angle 0.48427 (25400) hydrogen bonds : bond 0.02816 ( 1092) hydrogen bonds : angle 4.95337 ( 3192) *********************** 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 58 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.4339 time to fit residues: 30.2878 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 : 0.856 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 191 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 chunk 227 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 HIS D 593 GLN D 616 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.028649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.025737 restraints weight = 385425.029| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.67 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3966 moved from start: 0.3606 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= 0.126 Angle : 0.502 8.102 25400 Z= 0.262 Chirality : 0.038 0.141 2339 Planarity : 0.003 0.044 3555 Dihedral : 8.350 138.276 2954 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 0.49 % Allowed : 6.87 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.60 (0.17), residues: 2650 helix: 2.52 (0.14), residues: 1482 sheet: -0.08 (0.31), residues: 268 loop : 1.08 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 590 TYR 0.009 0.001 TYR E 369 PHE 0.019 0.002 PHE A 471 TRP 0.012 0.001 TRP E 368 HIS 0.009 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00263 (19084) covalent geometry : angle 0.50209 (25400) hydrogen bonds : bond 0.02873 ( 1092) hydrogen bonds : angle 4.94150 ( 3192) *********************** 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 58 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 411 MET cc_start: 0.8575 (mpm) cc_final: 0.8191 (mpm) REVERT: F 467 MET cc_start: 0.8854 (ptp) cc_final: 0.8307 (mpt) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.4386 time to fit residues: 30.4694 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 : 0.669 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 122 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 232 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 249 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 247 optimal weight: 40.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.028149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.025541 restraints weight = 393855.538| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 4.84 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3901 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19084 Z= 0.141 Angle : 0.539 11.040 25400 Z= 0.279 Chirality : 0.039 0.205 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.307 141.708 2954 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.24 % Allowed : 7.54 % 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 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: 2.53 (0.17), residues: 2650 helix: 2.46 (0.14), residues: 1482 sheet: -0.10 (0.32), residues: 259 loop : 1.06 (0.23), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 590 TYR 0.010 0.001 TYR E 369 PHE 0.016 0.002 PHE A 471 TRP 0.016 0.001 TRP E 368 HIS 0.009 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00290 (19084) covalent geometry : angle 0.53917 (25400) hydrogen bonds : bond 0.02944 ( 1092) hydrogen bonds : angle 4.98149 ( 3192) *********************** 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 54 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.4912 time to fit residues: 31.7872 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 : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 19 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 8 optimal weight: 320.0000 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 199 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 179 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN C 595 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.028473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.025531 restraints weight = 394700.420| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 5.89 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4093 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19084 Z= 0.132 Angle : 0.540 10.118 25400 Z= 0.279 Chirality : 0.039 0.204 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.251 142.453 2954 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % 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 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: 2.51 (0.17), residues: 2650 helix: 2.45 (0.14), residues: 1482 sheet: -0.06 (0.33), residues: 249 loop : 1.00 (0.23), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 510 TYR 0.011 0.001 TYR E 369 PHE 0.016 0.002 PHE A 471 TRP 0.016 0.001 TRP E 368 HIS 0.008 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00275 (19084) covalent geometry : angle 0.53982 (25400) hydrogen bonds : bond 0.02907 ( 1092) hydrogen bonds : angle 5.00087 ( 3192) *********************** 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 53 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: F 467 MET cc_start: 0.8968 (ptp) cc_final: 0.8639 (pmm) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.4805 time to fit residues: 30.9204 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 : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 31 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 50.0000 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 85 optimal weight: 0.0570 chunk 92 optimal weight: 50.0000 overall best weight: 2.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.028522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.025506 restraints weight = 382116.092| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 5.54 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3985 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19084 Z= 0.097 Angle : 0.535 15.692 25400 Z= 0.271 Chirality : 0.039 0.185 2339 Planarity : 0.003 0.043 3555 Dihedral : 8.110 140.896 2954 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.12 % Allowed : 7.78 % 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 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: 2.57 (0.17), residues: 2650 helix: 2.51 (0.14), residues: 1475 sheet: -0.18 (0.31), residues: 275 loop : 1.11 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 510 TYR 0.009 0.001 TYR E 369 PHE 0.016 0.001 PHE A 586 TRP 0.010 0.001 TRP D 368 HIS 0.007 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00208 (19084) covalent geometry : angle 0.53529 (25400) hydrogen bonds : bond 0.02631 ( 1092) hydrogen bonds : angle 4.90548 ( 3192) ********************** 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 52 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: E 411 MET cc_start: 0.7973 (mpm) cc_final: 0.7615 (mpp) REVERT: F 467 MET cc_start: 0.8934 (ptp) cc_final: 0.8468 (mpt) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.4494 time to fit residues: 28.6419 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 : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 147 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 184 optimal weight: 50.0000 chunk 230 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 320.0000 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 50.0000 chunk 231 optimal weight: 50.0000 chunk 87 optimal weight: 320.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS C 366 ASN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.028357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.025408 restraints weight = 398417.043| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.73 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4093 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19084 Z= 0.152 Angle : 0.577 16.716 25400 Z= 0.295 Chirality : 0.039 0.201 2339 Planarity : 0.004 0.045 3555 Dihedral : 8.234 142.330 2954 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.18 % Allowed : 7.78 % 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 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: 2.52 (0.17), residues: 2650 helix: 2.49 (0.14), residues: 1479 sheet: -0.21 (0.32), residues: 259 loop : 1.04 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 590 TYR 0.012 0.001 TYR E 369 PHE 0.014 0.002 PHE A 586 TRP 0.017 0.001 TRP E 368 HIS 0.009 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00311 (19084) covalent geometry : angle 0.57679 (25400) hydrogen bonds : bond 0.02941 ( 1092) hydrogen bonds : angle 4.96732 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5133.80 seconds wall clock time: 88 minutes 55.29 seconds (5335.29 seconds total)