Starting phenix.real_space_refine on Tue Nov 19 10:10:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/11_2024/7tts_26122.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/11_2024/7tts_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/11_2024/7tts_26122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/11_2024/7tts_26122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/11_2024/7tts_26122.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/11_2024/7tts_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 13.99, per 1000 atoms: 0.74 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: 5.26 Conformation dependent library (CDL) restraints added in 2.9 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: 2.24 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: 6.44 Time building geometry restraints manager: 5.88 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: 7.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 45.780 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.040 ------------------------------------------------------------------------------- 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= 0.536 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 *********************** 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 : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 1.0139 time to fit residues: 72.8588 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 : 2.618 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 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= 0.202 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 *********************** 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 : 2.448 Fit side-chains revert: symmetry clash REVERT: B 602 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6711 (p0) REVERT: F 411 MET cc_start: -0.2432 (mpm) cc_final: -0.3036 (mpp) outliers start: 4 outliers final: 0 residues processed: 56 average time/residue: 1.0575 time to fit residues: 71.9389 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 : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 30.0000 chunk 75 optimal weight: 4.9990 chunk 202 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 195 optimal weight: 30.0000 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 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN C 578 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5666 moved from start: 0.1943 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= 0.189 Angle : 0.510 6.720 25400 Z= 0.270 Chirality : 0.039 0.202 2339 Planarity : 0.004 0.047 3555 Dihedral : 8.252 128.856 2954 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 0.24 % Allowed : 4.26 % Favored : 95.50 % 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: 2.68 (0.17), residues: 2650 helix: 2.47 (0.14), residues: 1478 sheet: 0.28 (0.30), residues: 286 loop : 1.27 (0.24), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 368 HIS 0.018 0.001 HIS A 399 PHE 0.024 0.002 PHE A 471 TYR 0.009 0.001 TYR B 430 ARG 0.010 0.001 ARG A 628 *********************** 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 : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.9489 time to fit residues: 64.7996 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 : 2.286 ------------------------------------------------------------------------------- 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 240 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 163 optimal weight: 0.6980 chunk 244 optimal weight: 40.0000 chunk 259 optimal weight: 40.0000 chunk 127 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 moved from start: 0.2324 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= 0.187 Angle : 0.495 8.337 25400 Z= 0.260 Chirality : 0.038 0.174 2339 Planarity : 0.003 0.047 3555 Dihedral : 8.244 131.597 2954 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 0.24 % Allowed : 5.11 % 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: 2.67 (0.17), residues: 2650 helix: 2.53 (0.14), residues: 1481 sheet: 0.11 (0.30), residues: 277 loop : 1.17 (0.24), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 368 HIS 0.015 0.001 HIS E 433 PHE 0.017 0.002 PHE A 471 TYR 0.008 0.001 TYR D 430 ARG 0.003 0.000 ARG D 628 *********************** 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 56 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 2.325 Fit side-chains REVERT: F 493 MET cc_start: 0.8082 (pmm) cc_final: 0.7882 (pmm) outliers start: 4 outliers final: 1 residues processed: 56 average time/residue: 0.9386 time to fit residues: 66.3071 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 : 2.407 ------------------------------------------------------------------------------- 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 215 optimal weight: 30.0000 chunk 147 optimal weight: 50.0000 chunk 3 optimal weight: 50.0000 chunk 192 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 179 optimal weight: 30.0000 chunk 0 optimal weight: 320.0000 chunk 132 optimal weight: 220.0000 chunk 232 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 HIS E 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.2768 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= 0.180 Angle : 0.497 7.255 25400 Z= 0.261 Chirality : 0.039 0.155 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.260 133.124 2954 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 0.18 % Allowed : 5.41 % Favored : 94.41 % 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: 2.70 (0.17), residues: 2650 helix: 2.58 (0.14), residues: 1479 sheet: 0.08 (0.31), residues: 268 loop : 1.16 (0.24), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 368 HIS 0.010 0.001 HIS D 552 PHE 0.014 0.002 PHE A 471 TYR 0.009 0.001 TYR D 430 ARG 0.003 0.000 ARG A 629 *********************** 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 : 2.131 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 0.9537 time to fit residues: 63.0778 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 : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 220.0000 chunk 233 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 21 optimal weight: 30.0000 chunk 85 optimal weight: 9.9990 chunk 136 optimal weight: 90.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 HIS F 624 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.3052 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= 0.182 Angle : 0.492 7.707 25400 Z= 0.259 Chirality : 0.038 0.147 2339 Planarity : 0.003 0.041 3555 Dihedral : 8.269 134.523 2954 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.83 % 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 (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: 2.68 (0.17), residues: 2650 helix: 2.58 (0.14), residues: 1480 sheet: -0.02 (0.31), residues: 271 loop : 1.14 (0.23), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 368 HIS 0.010 0.001 HIS B 399 PHE 0.015 0.001 PHE A 471 TYR 0.009 0.001 TYR D 430 ARG 0.003 0.000 ARG B 329 *********************** 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: 6 poor density : 52 time to evaluate : 2.221 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 0.9908 time to fit residues: 68.8126 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 : 2.336 ------------------------------------------------------------------------------- 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 249 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 147 optimal weight: 50.0000 chunk 189 optimal weight: 40.0000 chunk 146 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 161 optimal weight: 50.0000 chunk 157 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 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 : 0.003 0.050 19084 Z= 0.192 Angle : 0.514 8.103 25400 Z= 0.270 Chirality : 0.039 0.166 2339 Planarity : 0.003 0.042 3555 Dihedral : 8.316 136.140 2954 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 0.49 % Allowed : 6.26 % Favored : 93.25 % 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: 2.57 (0.14), residues: 1481 sheet: -0.04 (0.31), residues: 269 loop : 1.13 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 368 HIS 0.012 0.001 HIS C 399 PHE 0.012 0.002 PHE A 453 TYR 0.009 0.001 TYR D 430 ARG 0.003 0.000 ARG B 329 *********************** 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: 8 poor density : 52 time to evaluate : 2.326 Fit side-chains revert: symmetry clash REVERT: F 467 MET cc_start: 0.8167 (ptp) cc_final: 0.7839 (mpt) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.9571 time to fit residues: 67.0839 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 : 2.306 ------------------------------------------------------------------------------- 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 159 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 154 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 50 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 24 optimal weight: 0.0010 chunk 203 optimal weight: 7.9990 chunk 234 optimal weight: 40.0000 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.3478 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= 0.156 Angle : 0.505 10.830 25400 Z= 0.261 Chirality : 0.039 0.174 2339 Planarity : 0.003 0.042 3555 Dihedral : 8.246 137.186 2954 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.36 % Allowed : 6.50 % Favored : 93.13 % 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: 2.67 (0.17), residues: 2650 helix: 2.59 (0.14), residues: 1479 sheet: 0.01 (0.32), residues: 258 loop : 1.08 (0.23), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 368 HIS 0.012 0.001 HIS C 399 PHE 0.009 0.001 PHE B 406 TYR 0.008 0.001 TYR E 369 ARG 0.003 0.000 ARG E 510 *********************** 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 58 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 2.386 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.9460 time to fit residues: 67.5213 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 : 2.446 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 240 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 189 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 HIS C 366 ASN D 505 HIS E 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19084 Z= 0.236 Angle : 0.581 9.882 25400 Z= 0.303 Chirality : 0.039 0.195 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.321 140.878 2954 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.01 % 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: 2.52 (0.17), residues: 2650 helix: 2.47 (0.14), residues: 1478 sheet: -0.04 (0.33), residues: 249 loop : 1.01 (0.23), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 368 HIS 0.019 0.002 HIS B 399 PHE 0.015 0.002 PHE B 553 TYR 0.011 0.001 TYR E 369 ARG 0.005 0.001 ARG D 590 *********************** 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 56 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 2.342 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 1.0140 time to fit residues: 69.4627 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 : 2.323 ------------------------------------------------------------------------------- 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 254 optimal weight: 5.9990 chunk 155 optimal weight: 50.0000 chunk 120 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 266 optimal weight: 0.0070 chunk 245 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.4012 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= 0.161 Angle : 0.557 14.257 25400 Z= 0.285 Chirality : 0.040 0.189 2339 Planarity : 0.003 0.044 3555 Dihedral : 8.206 142.211 2954 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 0.12 % Allowed : 6.87 % Favored : 93.01 % 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: 2.52 (0.17), residues: 2650 helix: 2.48 (0.14), residues: 1482 sheet: -0.12 (0.32), residues: 258 loop : 1.00 (0.23), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 368 HIS 0.016 0.001 HIS B 399 PHE 0.017 0.001 PHE A 586 TYR 0.010 0.001 TYR E 369 ARG 0.004 0.000 ARG C 363 ********************** 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 : 2.447 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 1.0092 time to fit residues: 64.7528 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 : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 50.0000 chunk 65 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 chunk 218 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.028491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.025494 restraints weight = 391881.775| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.95 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4153 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19084 Z= 0.223 Angle : 0.604 15.297 25400 Z= 0.311 Chirality : 0.040 0.221 2339 Planarity : 0.004 0.045 3555 Dihedral : 8.317 143.465 2954 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.12 % Allowed : 7.23 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 2.42 (0.14), residues: 1485 sheet: -0.28 (0.32), residues: 259 loop : 0.96 (0.23), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 368 HIS 0.017 0.002 HIS B 399 PHE 0.015 0.002 PHE A 586 TYR 0.012 0.001 TYR E 369 ARG 0.005 0.001 ARG D 590 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: