Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 21:18:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297_trim_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/6mzb_9297/08_2023/6mzb_9297_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzb_9297/08_2023/6mzb_9297_trim_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 ------------------------------------------------------------------------------- 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= 0.157 sd= 1.341 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 8991 2.51 5 N 2367 2.21 5 O 2605 1.98 5 H 13839 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 27905 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 12982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 12982 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 31, 'TRANS': 775} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 13314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 820, 13306 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 820, 13306 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 13450 Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 796 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 1 Chain: "D" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 763 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain breaks: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 345 " occ=0.50 ... (12 atoms not shown) pdb=" HA3BGLY A 345 " occ=0.50 Time building chain proxies: 16.12, per 1000 atoms: 0.58 Number of scatterers: 27905 At special positions: 0 Unit cell: (165.048, 122.728, 119.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 97 16.00 P 2 15.00 Mg 2 11.99 O 2605 8.00 N 2367 7.00 C 8991 6.00 H 13839 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 92 " 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=0, symmetry=0 Time building additional restraints: 22.60 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 599 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 561 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 597 " 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 5 sheets defined 47.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'B' and resid 48 through 65 removed outlier: 3.713A pdb=" N GLN B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.593A pdb=" N LYS B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.679A pdb=" N ALA B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.819A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 246 Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 345 through 348 No H-bonds generated for 'chain 'B' and resid 345 through 348' Processing helix chain 'B' and resid 412 through 456 removed outlier: 3.940A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASN B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 469 through 472 No H-bonds generated for 'chain 'B' and resid 469 through 472' Processing helix chain 'B' and resid 482 through 492 removed outlier: 3.758A pdb=" N LYS B 487 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.892A pdb=" N VAL B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 550 Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'B' and resid 584 through 595 removed outlier: 3.871A pdb=" N MET B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 removed outlier: 3.801A pdb=" N MET B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 611' Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 626 through 636 removed outlier: 3.773A pdb=" N LEU B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.627A pdb=" N LYS B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 687 removed outlier: 3.854A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 699 removed outlier: 3.586A pdb=" N VAL B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 718 removed outlier: 3.637A pdb=" N THR B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 718 " --> pdb=" O MET B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 745 removed outlier: 3.782A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 750 No H-bonds generated for 'chain 'B' and resid 747 through 750' Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 761 through 763 No H-bonds generated for 'chain 'B' and resid 761 through 763' Processing helix chain 'B' and resid 765 through 777 Proline residue: B 768 - end of helix removed outlier: 3.629A pdb=" N ASP B 776 " --> pdb=" O GLY B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 789 removed outlier: 3.901A pdb=" N SER B 787 " --> pdb=" O TYR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 822 Proline residue: B 795 - end of helix Processing helix chain 'A' and resid 12 through 15 No H-bonds generated for 'chain 'A' and resid 12 through 15' Processing helix chain 'A' and resid 20 through 34 removed outlier: 3.909A pdb=" N LEU A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.958A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.602A pdb=" N PHE A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.674A pdb=" N LEU A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 169' Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.597A pdb=" N GLU A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 222 through 249 removed outlier: 4.009A pdb=" N GLY A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 247 " --> pdb=" O TRP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 414 through 457 removed outlier: 3.788A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Proline residue: A 434 - end of helix removed outlier: 3.614A pdb=" N GLU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 441 " --> pdb=" O TYR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 4.146A pdb=" N GLN A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 467' Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 489 through 492 No H-bonds generated for 'chain 'A' and resid 489 through 492' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.664A pdb=" N TYR A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 539 through 552 removed outlier: 3.606A pdb=" N SER A 550 " --> pdb=" O MET A 546 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 586 through 597 removed outlier: 3.644A pdb=" N THR A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 626 through 635 Processing helix chain 'A' and resid 652 through 669 removed outlier: 3.602A pdb=" N HIS A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 664 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.795A pdb=" N LEU A 703 " --> pdb=" O TYR A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.911A pdb=" N THR A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 728 through 753 removed outlier: 4.653A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 763 through 779 removed outlier: 5.088A pdb=" N ASP A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 3.983A pdb=" N VAL A 774 " --> pdb=" O LYS A 771 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 775 " --> pdb=" O LEU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 791 removed outlier: 3.607A pdb=" N SER A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 826 removed outlier: 3.580A pdb=" N GLY A 801 " --> pdb=" O MET A 798 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 804 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 811 " --> pdb=" O GLU A 808 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR A 816 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing sheet with id= A, first strand: chain 'B' and resid 92 through 96 removed outlier: 3.754A pdb=" N SER B 93 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 175 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 151 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= C, first strand: chain 'B' and resid 384 through 387 removed outlier: 4.238A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 328 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 105 through 112 removed outlier: 6.542A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.548A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.641A pdb=" N VAL A 318 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 279 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 318 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A 277 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP A 320 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR A 275 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 398 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 390 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL A 400 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET A 388 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 386 " --> pdb=" O THR A 402 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1251 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: 9.54 Time building geometry restraints manager: 23.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13809 1.02 - 1.22: 31 1.22 - 1.42: 6045 1.42 - 1.62: 8176 1.62 - 1.82: 162 Bond restraints: 28223 Sorted by residual: bond pdb=" O2P 35G A 903 " pdb=" P 35G A 903 " ideal model delta sigma weight residual 1.648 1.469 0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" C4 35G B 903 " pdb=" N3 35G B 903 " ideal model delta sigma weight residual 1.492 1.345 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C4 35G A 903 " pdb=" N3 35G A 903 " ideal model delta sigma weight residual 1.492 1.346 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C2 35G B 903 " pdb=" N3 35G B 903 " ideal model delta sigma weight residual 1.462 1.330 0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C2 35G A 903 " pdb=" N3 35G A 903 " ideal model delta sigma weight residual 1.462 1.331 0.131 2.00e-02 2.50e+03 4.31e+01 ... (remaining 28218 not shown) Histogram of bond angle deviations from ideal: 68.89 - 82.08: 4 82.08 - 95.28: 0 95.28 - 108.47: 9044 108.47 - 121.66: 36760 121.66 - 134.85: 5221 Bond angle restraints: 51029 Sorted by residual: angle pdb=" O2P 35G A 903 " pdb=" P 35G A 903 " pdb=" O5' 35G A 903 " ideal model delta sigma weight residual 108.00 68.89 39.11 3.00e+00 1.11e-01 1.70e+02 angle pdb=" O1P 35G A 903 " pdb=" P 35G A 903 " pdb=" O2P 35G A 903 " ideal model delta sigma weight residual 119.60 80.79 38.81 3.00e+00 1.11e-01 1.67e+02 angle pdb=" O1P 35G B 903 " pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " ideal model delta sigma weight residual 119.60 80.85 38.75 3.00e+00 1.11e-01 1.67e+02 angle pdb=" O1P 35G B 903 " pdb=" P 35G B 903 " pdb=" O5' 35G B 903 " ideal model delta sigma weight residual 108.00 69.83 38.17 3.00e+00 1.11e-01 1.62e+02 angle pdb=" O2P 35G B 903 " pdb=" P 35G B 903 " pdb=" O5' 35G B 903 " ideal model delta sigma weight residual 108.00 134.85 -26.85 3.00e+00 1.11e-01 8.01e+01 ... (remaining 51024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.93: 10511 19.93 - 39.87: 756 39.87 - 59.80: 88 59.80 - 79.74: 21 79.74 - 99.67: 10 Dihedral angle restraints: 11386 sinusoidal: 5308 harmonic: 6078 Sorted by residual: dihedral pdb=" CB CYS B 84 " pdb=" SG CYS B 84 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual -86.00 -175.31 89.31 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CA HIS C 75 " pdb=" C HIS C 75 " pdb=" N LEU C 76 " pdb=" CA LEU C 76 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 598 " pdb=" C ASP B 598 " pdb=" N ILE B 599 " pdb=" CA ILE B 599 " ideal model delta harmonic sigma weight residual 180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 11383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.436: 2120 0.436 - 0.872: 0 0.872 - 1.308: 0 1.308 - 1.743: 0 1.743 - 2.179: 1 Chirality restraints: 2121 Sorted by residual: chirality pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " pdb=" O3' 35G B 903 " pdb=" O5' 35G B 903 " both_signs ideal model delta sigma weight residual True 3.39 1.21 2.18 2.00e-01 2.50e+01 1.19e+02 chirality pdb=" CA THR A 796 " pdb=" N THR A 796 " pdb=" C THR A 796 " pdb=" CB THR A 796 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" P 35G A 903 " pdb=" O2P 35G A 903 " pdb=" O3' 35G A 903 " pdb=" O5' 35G A 903 " both_signs ideal model delta sigma weight residual True 3.39 3.23 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 2118 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 35G A 903 " 0.062 2.00e-02 2.50e+03 2.56e-02 1.97e+01 pdb=" C2 35G A 903 " -0.003 2.00e-02 2.50e+03 pdb=" C4 35G A 903 " -0.010 2.00e-02 2.50e+03 pdb=" C5 35G A 903 " -0.009 2.00e-02 2.50e+03 pdb=" C6 35G A 903 " 0.011 2.00e-02 2.50e+03 pdb=" C8 35G A 903 " -0.030 2.00e-02 2.50e+03 pdb=" N1 35G A 903 " 0.012 2.00e-02 2.50e+03 pdb=" N2 35G A 903 " -0.023 2.00e-02 2.50e+03 pdb=" N3 35G A 903 " -0.010 2.00e-02 2.50e+03 pdb=" N7 35G A 903 " -0.025 2.00e-02 2.50e+03 pdb=" N9 35G A 903 " -0.013 2.00e-02 2.50e+03 pdb=" O6 35G A 903 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 798 " -0.019 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" N LEU A 799 " 0.061 2.00e-02 2.50e+03 pdb=" CA LEU A 799 " -0.015 2.00e-02 2.50e+03 pdb=" H LEU A 799 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 27 " -0.056 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO C 28 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 28 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 28 " -0.046 5.00e-02 4.00e+02 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 962 2.15 - 2.76: 52168 2.76 - 3.37: 77601 3.37 - 3.99: 97667 3.99 - 4.60: 156276 Nonbonded interactions: 384674 Sorted by model distance: nonbonded pdb=" HG1 THR A 693 " pdb=" OE1 GLN A 694 " model vdw 1.533 1.850 nonbonded pdb=" HE1 TRP B 290 " pdb=" OE2 GLU A 709 " model vdw 1.567 1.850 nonbonded pdb=" O VAL A 685 " pdb=" HG SER A 688 " model vdw 1.576 1.850 nonbonded pdb=" O GLY A 801 " pdb="HD22 ASN A 805 " model vdw 1.583 1.850 nonbonded pdb=" OD1 ASN A 645 " pdb=" H PHE A 647 " model vdw 1.595 1.850 ... (remaining 384669 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 'C' and (resid 10 through 39 or resid 72 through 87)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.070 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: 0.410 Extract box with map and model: 4.370 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 97.410 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.005 0.179 14384 Z= 0.337 Angle : 0.848 39.110 19448 Z= 0.363 Chirality : 0.061 2.179 2121 Planarity : 0.004 0.084 2504 Dihedral : 14.629 99.674 5389 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 0.13 % 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: -0.51 (0.21), residues: 1712 helix: 0.66 (0.20), residues: 821 sheet: -0.86 (0.48), residues: 129 loop : -1.35 (0.22), residues: 762 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 546 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 544 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 544 average time/residue: 0.6627 time to fit residues: 502.3472 Evaluate side-chains 365 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN A 361 ASN A 608 ASN A 804 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 14384 Z= 0.343 Angle : 0.739 31.089 19448 Z= 0.360 Chirality : 0.058 1.847 2121 Planarity : 0.005 0.056 2504 Dihedral : 4.973 68.051 1867 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer Outliers : 1.82 % 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: -0.73 (0.21), residues: 1712 helix: 0.50 (0.19), residues: 816 sheet: -0.77 (0.46), residues: 142 loop : -1.51 (0.22), residues: 754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 363 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 379 average time/residue: 0.6493 time to fit residues: 352.3851 Evaluate side-chains 374 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 352 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3487 time to fit residues: 16.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 167 optimal weight: 0.0980 chunk 137 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14384 Z= 0.175 Angle : 0.679 30.789 19448 Z= 0.319 Chirality : 0.056 1.831 2121 Planarity : 0.004 0.064 2504 Dihedral : 4.859 70.993 1867 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer Outliers : 0.59 % 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: -0.60 (0.21), residues: 1712 helix: 0.54 (0.19), residues: 822 sheet: -0.64 (0.46), residues: 142 loop : -1.39 (0.22), residues: 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 361 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 362 average time/residue: 0.6690 time to fit residues: 342.5920 Evaluate side-chains 360 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 355 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3406 time to fit residues: 5.9829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14384 Z= 0.262 Angle : 0.695 31.431 19448 Z= 0.330 Chirality : 0.056 1.810 2121 Planarity : 0.004 0.078 2504 Dihedral : 4.873 68.320 1867 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.39 % Rotamer Outliers : 1.04 % 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: -0.74 (0.21), residues: 1712 helix: 0.43 (0.19), residues: 840 sheet: -0.59 (0.46), residues: 142 loop : -1.54 (0.22), residues: 730 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 351 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 359 average time/residue: 0.6478 time to fit residues: 328.4483 Evaluate side-chains 352 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 341 time to evaluate : 2.528 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3177 time to fit residues: 9.6660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 0.0020 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 14384 Z= 0.152 Angle : 0.667 30.715 19448 Z= 0.308 Chirality : 0.055 1.826 2121 Planarity : 0.004 0.078 2504 Dihedral : 4.741 69.094 1867 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer Outliers : 0.85 % 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: -0.50 (0.21), residues: 1712 helix: 0.63 (0.19), residues: 834 sheet: -0.50 (0.45), residues: 145 loop : -1.40 (0.23), residues: 733 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 368 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 355 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 357 average time/residue: 0.6453 time to fit residues: 328.6800 Evaluate side-chains 354 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 345 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4260 time to fit residues: 9.1951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN A 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 14384 Z= 0.350 Angle : 0.718 32.032 19448 Z= 0.346 Chirality : 0.057 1.812 2121 Planarity : 0.005 0.082 2504 Dihedral : 4.904 67.998 1867 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.37 % Favored : 92.51 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.21), residues: 1712 helix: 0.41 (0.19), residues: 842 sheet: -0.56 (0.46), residues: 144 loop : -1.61 (0.22), residues: 726 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 334 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 340 average time/residue: 0.6520 time to fit residues: 314.7883 Evaluate side-chains 341 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 329 time to evaluate : 2.447 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3151 time to fit residues: 9.9763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 14384 Z= 0.244 Angle : 0.690 31.165 19448 Z= 0.326 Chirality : 0.056 1.813 2121 Planarity : 0.004 0.086 2504 Dihedral : 4.919 69.070 1867 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.27 % Rotamer Outliers : 0.59 % 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: -0.72 (0.21), residues: 1712 helix: 0.46 (0.19), residues: 845 sheet: -0.58 (0.46), residues: 145 loop : -1.57 (0.22), residues: 722 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 334 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 340 average time/residue: 0.6445 time to fit residues: 308.9095 Evaluate side-chains 338 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 332 time to evaluate : 2.321 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3421 time to fit residues: 6.5475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 14384 Z= 0.229 Angle : 0.688 31.216 19448 Z= 0.324 Chirality : 0.056 1.816 2121 Planarity : 0.004 0.081 2504 Dihedral : 4.872 69.175 1867 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.08 % Favored : 92.86 % Rotamer Outliers : 0.39 % 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: -0.68 (0.21), residues: 1712 helix: 0.54 (0.19), residues: 838 sheet: -0.56 (0.46), residues: 145 loop : -1.60 (0.22), residues: 729 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 339 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 342 average time/residue: 0.6584 time to fit residues: 317.3897 Evaluate side-chains 339 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 335 time to evaluate : 2.418 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2969 time to fit residues: 5.3025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 14384 Z= 0.213 Angle : 0.688 31.096 19448 Z= 0.323 Chirality : 0.056 1.817 2121 Planarity : 0.004 0.076 2504 Dihedral : 4.862 68.975 1867 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.73 % Favored : 93.21 % Rotamer Outliers : 0.20 % 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: -0.67 (0.21), residues: 1712 helix: 0.55 (0.19), residues: 838 sheet: -0.52 (0.46), residues: 145 loop : -1.59 (0.22), residues: 729 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 337 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 338 average time/residue: 0.6776 time to fit residues: 325.6428 Evaluate side-chains 336 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 2.562 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4254 time to fit residues: 4.7071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.0010 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS A 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14384 Z= 0.180 Angle : 0.680 30.866 19448 Z= 0.317 Chirality : 0.055 1.820 2121 Planarity : 0.004 0.075 2504 Dihedral : 4.754 68.531 1867 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer Outliers : 0.20 % 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: -0.55 (0.21), residues: 1712 helix: 0.64 (0.19), residues: 836 sheet: -0.45 (0.46), residues: 145 loop : -1.52 (0.23), residues: 731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 339 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 340 average time/residue: 0.6643 time to fit residues: 319.2228 Evaluate side-chains 336 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3422 time to fit residues: 4.1816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.0070 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 ASN ** 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 = 0.3380 r_free = 0.3380 target = 0.087631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078037 restraints weight = 96705.893| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.72 r_work: 0.3073 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14384 Z= 0.156 Angle : 0.676 30.577 19448 Z= 0.313 Chirality : 0.055 1.822 2121 Planarity : 0.004 0.073 2504 Dihedral : 4.645 67.574 1867 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.27 % Rotamer Outliers : 0.33 % 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: -0.43 (0.21), residues: 1712 helix: 0.74 (0.19), residues: 835 sheet: -0.34 (0.46), residues: 145 loop : -1.48 (0.23), residues: 732 =============================================================================== Job complete usr+sys time: 7665.18 seconds wall clock time: 135 minutes 58.75 seconds (8158.75 seconds total)