Starting phenix.real_space_refine on Wed Feb 14 09:17:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/02_2024/7she_25125_updated.pdb" } resolution = 3.4 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= 0.021 sd= 0.072 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 60 5.16 5 C 6036 2.51 5 N 1394 2.21 5 O 1498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 579": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8990 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4131 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 23, 'TRANS': 517} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4136 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 415 Unusual residues: {'CLR': 11, 'EIJ': 1, 'PEE': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 308 Unusual residues: {'CLR': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 5.41, per 1000 atoms: 0.60 Number of scatterers: 8990 At special positions: 0 Unit cell: (60.237, 101.268, 173.727, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 2 15.00 O 1498 8.00 N 1394 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 272 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 352 " distance=2.04 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 392 " distance=2.16 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 402 " distance=2.04 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 354 " distance=2.04 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 352 " distance=2.04 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 395 " - pdb=" SG CYS B 402 " distance=2.03 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 573 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.6 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 4 sheets defined 39.3% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 67 through 75 removed outlier: 4.054A pdb=" N ALA A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 88 through 92 removed outlier: 4.184A pdb=" N SER A 91 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 92 " --> pdb=" O GLY A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 92' Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.726A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 127 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.505A pdb=" N TRP A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 414 through 440 removed outlier: 3.582A pdb=" N ALA A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 448 No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.768A pdb=" N THR A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 473 No H-bonds generated for 'chain 'A' and resid 470 through 473' Processing helix chain 'A' and resid 480 through 495 removed outlier: 4.762A pdb=" N ARG A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 removed outlier: 3.696A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.523A pdb=" N ALA A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 633 removed outlier: 3.655A pdb=" N MET A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.996A pdb=" N LEU A 646 " --> pdb=" O TRP A 642 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.769A pdb=" N ALA B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 121 through 138 removed outlier: 4.394A pdb=" N PHE B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.621A pdb=" N ASP B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 417 No H-bonds generated for 'chain 'B' and resid 414 through 417' Processing helix chain 'B' and resid 421 through 424 No H-bonds generated for 'chain 'B' and resid 421 through 424' Processing helix chain 'B' and resid 426 through 440 removed outlier: 3.597A pdb=" N ASP B 431 " --> pdb=" O CYS B 427 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 453 through 460 removed outlier: 3.610A pdb=" N THR B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 470 through 474 removed outlier: 4.346A pdb=" N PHE B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 474' Processing helix chain 'B' and resid 479 through 513 removed outlier: 4.432A pdb=" N LEU B 484 " --> pdb=" O ARG B 480 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 485 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 490 " --> pdb=" O TRP B 486 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 500 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 501 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 548 removed outlier: 3.603A pdb=" N ALA B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 533 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.515A pdb=" N LEU B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 591 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 removed outlier: 3.634A pdb=" N ALA B 614 " --> pdb=" O PRO B 610 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 633 removed outlier: 4.109A pdb=" N PHE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 650 No H-bonds generated for 'chain 'B' and resid 647 through 650' Processing helix chain 'B' and resid 664 through 667 No H-bonds generated for 'chain 'B' and resid 664 through 667' Processing sheet with id= A, first strand: chain 'A' and resid 174 through 176 Processing sheet with id= B, first strand: chain 'A' and resid 190 through 192 removed outlier: 4.510A pdb=" N VAL A 190 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 204 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.301A pdb=" N GLY A 562 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 174 through 176 removed outlier: 4.430A pdb=" N GLY B 302 " --> pdb=" O ILE B 289 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 615 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: 2.88 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 9 1.09 - 1.27: 1293 1.27 - 1.46: 3198 1.46 - 1.64: 4669 1.64 - 1.83: 92 Bond restraints: 9261 Sorted by residual: bond pdb=" C TRP A 642 " pdb=" O TRP A 642 " ideal model delta sigma weight residual 1.236 0.903 0.333 1.32e-02 5.74e+03 6.36e+02 bond pdb=" C PHE A 570 " pdb=" O PHE A 570 " ideal model delta sigma weight residual 1.234 0.952 0.282 1.18e-02 7.18e+03 5.71e+02 bond pdb=" C PRO A 476 " pdb=" O PRO A 476 " ideal model delta sigma weight residual 1.235 0.928 0.307 1.30e-02 5.92e+03 5.59e+02 bond pdb=" N PRO A 374 " pdb=" CA PRO A 374 " ideal model delta sigma weight residual 1.470 1.686 -0.216 1.01e-02 9.80e+03 4.56e+02 bond pdb=" N PRO B 374 " pdb=" CA PRO B 374 " ideal model delta sigma weight residual 1.469 1.691 -0.222 1.28e-02 6.10e+03 3.01e+02 ... (remaining 9256 not shown) Histogram of bond angle deviations from ideal: 83.49 - 98.96: 38 98.96 - 114.43: 6073 114.43 - 129.91: 6501 129.91 - 145.38: 98 145.38 - 160.85: 2 Bond angle restraints: 12712 Sorted by residual: angle pdb=" N TYR B 390 " pdb=" CA TYR B 390 " pdb=" C TYR B 390 " ideal model delta sigma weight residual 113.50 160.85 -47.35 1.23e+00 6.61e-01 1.48e+03 angle pdb=" N GLN A 516 " pdb=" CA GLN A 516 " pdb=" C GLN A 516 " ideal model delta sigma weight residual 113.23 152.37 -39.14 1.22e+00 6.72e-01 1.03e+03 angle pdb=" N ALA A 403 " pdb=" CA ALA A 403 " pdb=" C ALA A 403 " ideal model delta sigma weight residual 110.97 139.54 -28.57 1.09e+00 8.42e-01 6.87e+02 angle pdb=" N VAL B 391 " pdb=" CA VAL B 391 " pdb=" CB VAL B 391 " ideal model delta sigma weight residual 110.65 87.74 22.91 1.13e+00 7.83e-01 4.11e+02 angle pdb=" N ALA B 389 " pdb=" CA ALA B 389 " pdb=" C ALA B 389 " ideal model delta sigma weight residual 109.54 136.84 -27.30 1.37e+00 5.33e-01 3.97e+02 ... (remaining 12707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 6223 34.73 - 69.45: 238 69.45 - 104.18: 28 104.18 - 138.91: 22 138.91 - 173.63: 2 Dihedral angle restraints: 6513 sinusoidal: 3366 harmonic: 3147 Sorted by residual: dihedral pdb=" C CYS A 402 " pdb=" N CYS A 402 " pdb=" CA CYS A 402 " pdb=" CB CYS A 402 " ideal model delta harmonic sigma weight residual -122.60 -164.59 41.99 0 2.50e+00 1.60e-01 2.82e+02 dihedral pdb=" N CYS A 402 " pdb=" C CYS A 402 " pdb=" CA CYS A 402 " pdb=" CB CYS A 402 " ideal model delta harmonic sigma weight residual 122.80 164.18 -41.38 0 2.50e+00 1.60e-01 2.74e+02 dihedral pdb=" C CYS B 99 " pdb=" N CYS B 99 " pdb=" CA CYS B 99 " pdb=" CB CYS B 99 " ideal model delta harmonic sigma weight residual -122.60 -88.09 -34.51 0 2.50e+00 1.60e-01 1.91e+02 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.062: 1507 1.062 - 2.124: 3 2.124 - 3.186: 0 3.186 - 4.249: 0 4.249 - 5.311: 4 Chirality restraints: 1514 Sorted by residual: chirality pdb=" C8 CLR A 803 " pdb=" C14 CLR A 803 " pdb=" C7 CLR A 803 " pdb=" C9 CLR A 803 " both_signs ideal model delta sigma weight residual False 2.69 -2.62 5.31 2.00e-01 2.50e+01 7.05e+02 chirality pdb=" C8 CLR B 802 " pdb=" C14 CLR B 802 " pdb=" C7 CLR B 802 " pdb=" C9 CLR B 802 " both_signs ideal model delta sigma weight residual False 2.69 -2.62 5.31 2.00e-01 2.50e+01 7.05e+02 chirality pdb=" C17 CLR B 808 " pdb=" C13 CLR B 808 " pdb=" C16 CLR B 808 " pdb=" C20 CLR B 808 " both_signs ideal model delta sigma weight residual False 2.55 -2.57 5.12 2.00e-01 2.50e+01 6.55e+02 ... (remaining 1511 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 EIJ A 802 " 0.181 2.00e-02 2.50e+03 1.79e-01 3.21e+02 pdb=" C09 EIJ A 802 " -0.187 2.00e-02 2.50e+03 pdb=" C10 EIJ A 802 " -0.171 2.00e-02 2.50e+03 pdb=" C11 EIJ A 802 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EIJ A 802 " 0.161 2.00e-02 2.50e+03 1.61e-01 2.58e+02 pdb=" C06 EIJ A 802 " -0.161 2.00e-02 2.50e+03 pdb=" C07 EIJ A 802 " -0.160 2.00e-02 2.50e+03 pdb=" C08 EIJ A 802 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.181 5.00e-02 4.00e+02 2.48e-01 9.81e+01 pdb=" N PRO A 120 " -0.424 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.164 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.079 5.00e-02 4.00e+02 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 8 2.18 - 2.86: 3073 2.86 - 3.54: 11672 3.54 - 4.22: 18802 4.22 - 4.90: 32185 Nonbonded interactions: 65740 Sorted by model distance: nonbonded pdb=" O GLN A 516 " pdb=" CG GLN A 516 " model vdw 1.502 3.440 nonbonded pdb=" SG CYS A 395 " pdb=" O CYS A 402 " model vdw 1.783 3.400 nonbonded pdb=" O PRO A 407 " pdb=" CD1 LEU A 568 " model vdw 1.866 3.460 nonbonded pdb=" N PHE A 474 " pdb=" O PHE A 474 " model vdw 1.930 2.496 nonbonded pdb=" CE1 TYR B 103 " pdb=" CB ALA B 106 " model vdw 2.091 3.760 ... (remaining 65735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 66 through 205 or resid 261 through 352 or (resid 353 and \ (name N or name CA or name C or name O or name CB )) or resid 354 through 378 or \ (resid 379 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 0 through 670 or resid 803 through 811)) selection = (chain 'B' and (resid 66 through 292 or resid 298 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 331 or \ (resid 332 through 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 359 or (resid 360 and (name N or name CA or name C or name \ O or name CB )) or resid 361 through 362 or (resid 363 through 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 670 or resid 8 \ 03 through 811)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 13.300 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.120 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.013 0.333 9261 Z= 0.921 Angle : 1.851 47.349 12712 Z= 1.127 Chirality : 0.284 5.311 1514 Planarity : 0.013 0.248 1448 Dihedral : 18.015 173.633 4436 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 1.88 % Allowed : 14.08 % Favored : 84.04 % Rotamer: Outliers : 1.41 % Allowed : 0.71 % Favored : 97.88 % Cbeta Deviations : 2.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.10 % 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: -4.29 (0.23), residues: 1065 helix: -2.12 (0.23), residues: 462 sheet: -1.40 (0.58), residues: 78 loop : -3.87 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 642 HIS 0.005 0.001 HIS A 92 PHE 0.077 0.002 PHE A 570 TYR 0.064 0.003 TYR B 269 ARG 0.005 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 VAL cc_start: 0.6445 (m) cc_final: 0.6226 (p) REVERT: A 602 THR cc_start: 0.8597 (p) cc_final: 0.8227 (m) REVERT: B 309 ASN cc_start: 0.7855 (t0) cc_final: 0.7421 (t0) outliers start: 12 outliers final: 5 residues processed: 157 average time/residue: 0.2846 time to fit residues: 58.3477 Evaluate side-chains 103 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 476 PRO Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 521 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 204 GLN ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9261 Z= 0.256 Angle : 0.804 10.260 12712 Z= 0.383 Chirality : 0.045 0.289 1514 Planarity : 0.007 0.136 1448 Dihedral : 13.426 162.382 2679 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 1.13 % Allowed : 14.93 % Favored : 83.94 % Rotamer: Outliers : 0.71 % Allowed : 7.88 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.29 % 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: -3.90 (0.24), residues: 1065 helix: -1.58 (0.23), residues: 476 sheet: -1.31 (0.55), residues: 86 loop : -3.95 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 323 HIS 0.007 0.001 HIS B 131 PHE 0.015 0.002 PHE A 423 TYR 0.014 0.002 TYR B 277 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: B 309 ASN cc_start: 0.7801 (t0) cc_final: 0.7456 (t0) REVERT: B 429 LEU cc_start: 0.8239 (tt) cc_final: 0.8036 (tt) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.2272 time to fit residues: 32.8989 Evaluate side-chains 93 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.0010 chunk 87 optimal weight: 0.0050 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9261 Z= 0.175 Angle : 0.654 9.327 12712 Z= 0.322 Chirality : 0.041 0.231 1514 Planarity : 0.006 0.114 1448 Dihedral : 11.685 156.833 2666 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.15 % Favored : 85.63 % Rotamer: Outliers : 1.18 % Allowed : 10.35 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % 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: -3.56 (0.24), residues: 1065 helix: -1.18 (0.24), residues: 481 sheet: -0.99 (0.58), residues: 80 loop : -3.94 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 265 HIS 0.005 0.001 HIS B 331 PHE 0.015 0.001 PHE A 423 TYR 0.008 0.001 TYR A 277 ARG 0.002 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.4078 (mmp) cc_final: 0.3677 (mmt) REVERT: B 171 ILE cc_start: 0.7657 (tt) cc_final: 0.7388 (tt) REVERT: B 309 ASN cc_start: 0.7673 (t0) cc_final: 0.7359 (t0) REVERT: B 429 LEU cc_start: 0.8133 (tt) cc_final: 0.7780 (tp) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.2130 time to fit residues: 29.8363 Evaluate side-chains 89 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9261 Z= 0.215 Angle : 0.679 9.912 12712 Z= 0.335 Chirality : 0.042 0.206 1514 Planarity : 0.006 0.105 1448 Dihedral : 11.027 138.988 2666 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 1.03 % Allowed : 13.62 % Favored : 85.35 % Rotamer: Outliers : 2.12 % Allowed : 10.94 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % 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: -3.37 (0.25), residues: 1065 helix: -0.96 (0.24), residues: 499 sheet: -1.34 (0.55), residues: 81 loop : -3.92 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.010 0.001 HIS B 331 PHE 0.018 0.001 PHE A 467 TYR 0.010 0.001 TYR B 473 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 309 ASN cc_start: 0.7799 (t0) cc_final: 0.7533 (t0) REVERT: B 310 LEU cc_start: 0.7132 (tp) cc_final: 0.6926 (tp) REVERT: B 429 LEU cc_start: 0.8165 (tt) cc_final: 0.7817 (tp) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 0.2271 time to fit residues: 33.0822 Evaluate side-chains 96 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 538 PHE Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.0070 chunk 77 optimal weight: 50.0000 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9261 Z= 0.272 Angle : 0.709 8.072 12712 Z= 0.351 Chirality : 0.043 0.203 1514 Planarity : 0.006 0.100 1448 Dihedral : 10.682 118.238 2666 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.71 % Favored : 85.07 % Rotamer: Outliers : 2.12 % Allowed : 12.59 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.25), residues: 1065 helix: -0.91 (0.23), residues: 499 sheet: -0.91 (0.58), residues: 77 loop : -3.91 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 265 HIS 0.005 0.001 HIS B 131 PHE 0.022 0.002 PHE A 467 TYR 0.012 0.001 TYR B 473 ARG 0.005 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 309 ASN cc_start: 0.7943 (t0) cc_final: 0.7694 (t0) REVERT: B 429 LEU cc_start: 0.8296 (tt) cc_final: 0.7923 (tp) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.2703 time to fit residues: 38.2575 Evaluate side-chains 102 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 538 PHE Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9261 Z= 0.217 Angle : 0.666 10.025 12712 Z= 0.333 Chirality : 0.041 0.198 1514 Planarity : 0.006 0.088 1448 Dihedral : 10.036 114.537 2666 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.43 % Favored : 85.82 % Rotamer: Outliers : 2.12 % Allowed : 12.35 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.25), residues: 1065 helix: -0.82 (0.24), residues: 499 sheet: -0.78 (0.57), residues: 82 loop : -3.81 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 265 HIS 0.006 0.001 HIS B 131 PHE 0.017 0.001 PHE A 467 TYR 0.009 0.001 TYR B 473 ARG 0.003 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 THR cc_start: 0.5384 (p) cc_final: 0.5074 (p) REVERT: A 529 MET cc_start: 0.7795 (mtp) cc_final: 0.7539 (mtp) REVERT: B 126 LEU cc_start: 0.7299 (tp) cc_final: 0.7050 (tt) REVERT: B 305 LYS cc_start: 0.7251 (mmtt) cc_final: 0.6910 (tttt) REVERT: B 309 ASN cc_start: 0.7885 (t0) cc_final: 0.7646 (t0) REVERT: B 429 LEU cc_start: 0.8189 (tt) cc_final: 0.7817 (tp) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.2199 time to fit residues: 31.1004 Evaluate side-chains 99 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 538 PHE Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9261 Z= 0.220 Angle : 0.665 9.408 12712 Z= 0.332 Chirality : 0.041 0.195 1514 Planarity : 0.006 0.092 1448 Dihedral : 9.607 113.077 2666 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.99 % Favored : 85.26 % Rotamer: Outliers : 2.59 % Allowed : 12.71 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.25), residues: 1065 helix: -0.71 (0.24), residues: 499 sheet: -0.71 (0.58), residues: 82 loop : -3.81 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 265 HIS 0.007 0.001 HIS B 131 PHE 0.018 0.001 PHE A 467 TYR 0.010 0.001 TYR B 473 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 THR cc_start: 0.5450 (p) cc_final: 0.5120 (p) REVERT: A 529 MET cc_start: 0.7807 (mtp) cc_final: 0.7554 (mtp) REVERT: A 572 MET cc_start: 0.8785 (ppp) cc_final: 0.8091 (ptt) REVERT: B 126 LEU cc_start: 0.7399 (tp) cc_final: 0.7126 (tt) REVERT: B 305 LYS cc_start: 0.7161 (mmtt) cc_final: 0.6838 (tttt) REVERT: B 309 ASN cc_start: 0.7977 (t0) cc_final: 0.7721 (t0) REVERT: B 429 LEU cc_start: 0.8196 (tt) cc_final: 0.7827 (tp) outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 0.2340 time to fit residues: 33.2117 Evaluate side-chains 102 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 0.0070 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9261 Z= 0.189 Angle : 0.648 9.912 12712 Z= 0.325 Chirality : 0.040 0.196 1514 Planarity : 0.005 0.082 1448 Dihedral : 9.331 111.009 2666 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.24 % Favored : 86.01 % Rotamer: Outliers : 2.00 % Allowed : 13.76 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.25), residues: 1065 helix: -0.58 (0.24), residues: 500 sheet: -0.74 (0.57), residues: 83 loop : -3.81 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 156 HIS 0.007 0.001 HIS B 131 PHE 0.013 0.001 PHE A 467 TYR 0.008 0.001 TYR B 473 ARG 0.007 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 THR cc_start: 0.5309 (p) cc_final: 0.5021 (p) REVERT: A 529 MET cc_start: 0.7817 (mtp) cc_final: 0.7583 (mtp) REVERT: A 572 MET cc_start: 0.8763 (ppp) cc_final: 0.8082 (ptt) REVERT: B 126 LEU cc_start: 0.7399 (tp) cc_final: 0.7131 (tt) REVERT: B 284 THR cc_start: 0.7379 (m) cc_final: 0.7164 (m) REVERT: B 305 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6775 (tttt) REVERT: B 429 LEU cc_start: 0.8135 (tt) cc_final: 0.7772 (tp) outliers start: 17 outliers final: 16 residues processed: 96 average time/residue: 0.2302 time to fit residues: 30.4075 Evaluate side-chains 99 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 87 optimal weight: 0.2980 chunk 91 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9261 Z= 0.197 Angle : 0.655 14.380 12712 Z= 0.327 Chirality : 0.041 0.246 1514 Planarity : 0.005 0.086 1448 Dihedral : 9.116 109.708 2666 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.55 % Favored : 84.69 % Rotamer: Outliers : 1.88 % Allowed : 14.12 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.26), residues: 1065 helix: -0.44 (0.24), residues: 497 sheet: -0.64 (0.59), residues: 81 loop : -3.84 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 156 HIS 0.007 0.001 HIS B 131 PHE 0.016 0.001 PHE A 467 TYR 0.009 0.001 TYR B 473 ARG 0.006 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 THR cc_start: 0.5332 (p) cc_final: 0.5055 (p) REVERT: A 529 MET cc_start: 0.7789 (mtp) cc_final: 0.7544 (mtp) REVERT: A 572 MET cc_start: 0.8764 (ppp) cc_final: 0.8099 (ptt) REVERT: B 126 LEU cc_start: 0.7426 (tp) cc_final: 0.7180 (tt) REVERT: B 305 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6738 (tttt) REVERT: B 429 LEU cc_start: 0.8168 (tt) cc_final: 0.7803 (tp) outliers start: 16 outliers final: 16 residues processed: 98 average time/residue: 0.2500 time to fit residues: 33.0831 Evaluate side-chains 100 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9261 Z= 0.193 Angle : 0.649 14.560 12712 Z= 0.323 Chirality : 0.041 0.242 1514 Planarity : 0.005 0.082 1448 Dihedral : 8.875 107.078 2666 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.43 % Favored : 85.82 % Rotamer: Outliers : 1.76 % Allowed : 13.88 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.26), residues: 1065 helix: -0.35 (0.24), residues: 499 sheet: -0.74 (0.58), residues: 81 loop : -3.84 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 265 HIS 0.008 0.001 HIS B 131 PHE 0.015 0.001 PHE A 467 TYR 0.008 0.001 TYR B 473 ARG 0.005 0.000 ARG A 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 THR cc_start: 0.5316 (p) cc_final: 0.5027 (p) REVERT: A 529 MET cc_start: 0.7799 (mtp) cc_final: 0.7553 (mtp) REVERT: A 572 MET cc_start: 0.8761 (ppp) cc_final: 0.8100 (ptt) REVERT: B 126 LEU cc_start: 0.7454 (tp) cc_final: 0.7177 (tt) REVERT: B 284 THR cc_start: 0.7368 (m) cc_final: 0.7167 (m) REVERT: B 305 LYS cc_start: 0.6981 (mmtt) cc_final: 0.6618 (tttt) REVERT: B 429 LEU cc_start: 0.8168 (tt) cc_final: 0.7797 (tp) outliers start: 15 outliers final: 15 residues processed: 96 average time/residue: 0.2144 time to fit residues: 29.0521 Evaluate side-chains 99 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 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 = 0.4107 r_free = 0.4107 target = 0.145617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114116 restraints weight = 14866.870| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.65 r_work: 0.3187 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9261 Z= 0.198 Angle : 0.653 14.681 12712 Z= 0.324 Chirality : 0.041 0.246 1514 Planarity : 0.005 0.085 1448 Dihedral : 8.770 106.488 2666 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.27 % Favored : 85.07 % Rotamer: Outliers : 1.88 % Allowed : 13.76 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.26), residues: 1065 helix: -0.29 (0.24), residues: 500 sheet: -0.71 (0.59), residues: 81 loop : -3.83 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 156 HIS 0.008 0.001 HIS B 131 PHE 0.013 0.001 PHE B 467 TYR 0.009 0.001 TYR B 473 ARG 0.004 0.000 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.93 seconds wall clock time: 38 minutes 49.92 seconds (2329.92 seconds total)