Starting phenix.real_space_refine (version: dev) on Fri May 13 23:30:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/05_2022/6ohy_20074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/05_2022/6ohy_20074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/05_2022/6ohy_20074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/05_2022/6ohy_20074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/05_2022/6ohy_20074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/05_2022/6ohy_20074.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 15192 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "E" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "A" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 491 Unusual residues: {'MAN': 4, 'BMA': 1, 'NAG': 29, 'FUC': 3} Classifications: {'undetermined': 37} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 37 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {'NAG': 3, 'FUC': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 491 Unusual residues: {'MAN': 4, 'BMA': 1, 'NAG': 29, 'FUC': 3} Classifications: {'undetermined': 37} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 37 Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {'NAG': 3, 'FUC': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 491 Unusual residues: {'MAN': 4, 'BMA': 1, 'NAG': 29, 'FUC': 3} Classifications: {'undetermined': 37} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 37 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {'NAG': 3, 'FUC': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 8.87, per 1000 atoms: 0.58 Number of scatterers: 15192 At special positions: 0 Unit cell: (133.62, 122.4, 121.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3177 8.00 N 2439 7.00 C 9474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=1.99 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 Links applied ALPHA1-3 " BMA A 621 " - " MAN A 623 " " MAN A 623 " - " MAN A 624 " " BMA C 621 " - " MAN C 623 " " MAN C 623 " - " MAN C 624 " " BMA D 621 " - " MAN D 623 " " MAN D 623 " - " MAN D 624 " ALPHA1-6 " BMA A 621 " - " MAN A 622 " " MAN A 623 " - " MAN A 625 " " BMA C 621 " - " MAN C 622 " " MAN C 623 " - " MAN C 625 " " BMA D 621 " - " MAN D 622 " " MAN D 623 " - " MAN D 625 " BETA1-4 " NAG A 603 " - " NAG A 604 " " NAG A 605 " - " NAG A 606 " " NAG A 608 " - " NAG A 609 " " NAG A 613 " - " NAG A 614 " " NAG A 615 " - " NAG A 616 " " NAG A 617 " - " NAG A 618 " " NAG A 619 " - " NAG A 620 " " NAG A 620 " - " BMA A 621 " " NAG A 630 " - " NAG A 631 " " NAG A 632 " - " NAG A 633 " " NAG A 635 " - " NAG A 636 " " NAG C 603 " - " NAG C 604 " " NAG C 605 " - " NAG C 606 " " NAG C 608 " - " NAG C 609 " " NAG C 613 " - " NAG C 614 " " NAG C 615 " - " NAG C 616 " " NAG C 617 " - " NAG C 618 " " NAG C 619 " - " NAG C 620 " " NAG C 620 " - " BMA C 621 " " NAG C 630 " - " NAG C 631 " " NAG C 632 " - " NAG C 633 " " NAG C 635 " - " NAG C 636 " " NAG D 603 " - " NAG D 604 " " NAG D 605 " - " NAG D 606 " " NAG D 608 " - " NAG D 609 " " NAG D 613 " - " NAG D 614 " " NAG D 615 " - " NAG D 616 " " NAG D 617 " - " NAG D 618 " " NAG D 619 " - " NAG D 620 " " NAG D 620 " - " BMA D 621 " " NAG D 630 " - " NAG D 631 " " NAG D 632 " - " NAG D 633 " " NAG D 635 " - " NAG D 636 " BETA1-6 " NAG A 601 " - " FUC A 602 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG A 608 " - " FUC A 610 " " NAG A 628 " - " FUC A 629 " " NAG B 701 " - " FUC B 702 " " NAG B 703 " - " FUC B 704 " " NAG C 601 " - " FUC C 602 " " NAG C 608 " - " FUC C 610 " " NAG C 628 " - " FUC C 629 " " NAG D 601 " - " FUC D 602 " " NAG D 608 " - " FUC D 610 " " NAG D 628 " - " FUC D 629 " " NAG E 701 " - " FUC E 702 " " NAG E 703 " - " FUC E 704 " " NAG F 701 " - " FUC F 702 " " NAG F 703 " - " FUC F 704 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 603 " - " ASN A 160 " " NAG A 605 " - " ASN A 156 " " NAG A 607 " - " ASN A 188 " " NAG A 608 " - " ASN A 197 " " NAG A 611 " - " ASN A 268 " " NAG A 612 " - " ASN A 301 " " NAG A 613 " - " ASN A 386 " " NAG A 615 " - " ASN A 236 " " NAG A 617 " - " ASN A 241 " " NAG A 619 " - " ASN A 262 " " NAG A 626 " - " ASN A 343 " " NAG A 627 " - " ASN A 358 " " NAG A 628 " - " ASN A 412 " " NAG A 630 " - " ASN A 392 " " NAG A 632 " - " ASN A 334 " " NAG A 634 " - " ASN A 442 " " NAG A 635 " - " ASN A 448 " " NAG A 637 " - " ASN A 464F" " NAG B 701 " - " ASN B 637 " " NAG B 703 " - " ASN B 616 " " NAG B 705 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 603 " - " ASN C 160 " " NAG C 605 " - " ASN C 156 " " NAG C 607 " - " ASN C 188 " " NAG C 608 " - " ASN C 197 " " NAG C 611 " - " ASN C 268 " " NAG C 612 " - " ASN C 301 " " NAG C 613 " - " ASN C 386 " " NAG C 615 " - " ASN C 236 " " NAG C 617 " - " ASN C 241 " " NAG C 619 " - " ASN C 262 " " NAG C 626 " - " ASN C 343 " " NAG C 627 " - " ASN C 358 " " NAG C 628 " - " ASN C 412 " " NAG C 630 " - " ASN C 392 " " NAG C 632 " - " ASN C 334 " " NAG C 634 " - " ASN C 442 " " NAG C 635 " - " ASN C 448 " " NAG C 637 " - " ASN C 464F" " NAG D 601 " - " ASN D 88 " " NAG D 603 " - " ASN D 160 " " NAG D 605 " - " ASN D 156 " " NAG D 607 " - " ASN D 188 " " NAG D 608 " - " ASN D 197 " " NAG D 611 " - " ASN D 268 " " NAG D 612 " - " ASN D 301 " " NAG D 613 " - " ASN D 386 " " NAG D 615 " - " ASN D 236 " " NAG D 617 " - " ASN D 241 " " NAG D 619 " - " ASN D 262 " " NAG D 626 " - " ASN D 343 " " NAG D 627 " - " ASN D 358 " " NAG D 628 " - " ASN D 412 " " NAG D 630 " - " ASN D 392 " " NAG D 632 " - " ASN D 334 " " NAG D 634 " - " ASN D 442 " " NAG D 635 " - " ASN D 448 " " NAG D 637 " - " ASN D 464F" " NAG E 701 " - " ASN E 637 " " NAG E 703 " - " ASN E 616 " " NAG E 705 " - " ASN E 625 " " NAG F 701 " - " ASN F 637 " " NAG F 703 " - " ASN F 616 " " NAG F 705 " - " ASN F 625 " Time building additional restraints: 7.51 Conformation dependent library (CDL) restraints added in 2.1 seconds 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 25.0% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.185A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.787A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.783A pdb=" N GLU A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.699A pdb=" N ILE A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.767A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.505A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.589A pdb=" N ALA B 533 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 4.230A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618A through 626 removed outlier: 3.668A pdb=" N TYR B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.897A pdb=" N ARG B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.546A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.794A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.184A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.788A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 148 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.782A pdb=" N GLU C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 3.698A pdb=" N ILE C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.766A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.506A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.590A pdb=" N ALA E 533 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 595 removed outlier: 4.230A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 618A through 626 removed outlier: 3.668A pdb=" N TYR E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.896A pdb=" N ARG E 633 " --> pdb=" O GLN E 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN E 636 " --> pdb=" O ASP E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 652 removed outlier: 3.545A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 660 removed outlier: 3.793A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.185A pdb=" N ASP D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.788A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 148 Processing helix chain 'D' and resid 334 through 354 removed outlier: 3.782A pdb=" N GLU D 347 " --> pdb=" O ASN D 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 397 removed outlier: 3.699A pdb=" N ILE D 396 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.766A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.505A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.590A pdb=" N ALA F 533 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 4.230A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618A through 626 removed outlier: 3.667A pdb=" N TYR F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.897A pdb=" N ARG F 633 " --> pdb=" O GLN F 629 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN F 636 " --> pdb=" O ASP F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.546A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 660 removed outlier: 3.793A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.679A pdb=" N LEU A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.703A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 93 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 5.113A pdb=" N ASN A 160 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 128 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL A 292 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN A 448 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL A 292 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN A 448 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 333 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 414 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A 382 " --> pdb=" O ARG A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 310 removed outlier: 6.545A pdb=" N THR A 303 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.678A pdb=" N LEU C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.703A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 93 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 removed outlier: 5.113A pdb=" N ASN C 160 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR C 128 " --> pdb=" O ASN C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN C 448 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN C 448 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 333 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 414 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE C 382 " --> pdb=" O ARG C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 302 through 310 removed outlier: 6.544A pdb=" N THR C 303 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.678A pdb=" N LEU D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.703A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 93 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 removed outlier: 5.113A pdb=" N ASN D 160 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR D 128 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=AC7, first strand: chain 'D' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL D 292 " --> pdb=" O THR D 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN D 448 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ASP D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL D 292 " --> pdb=" O THR D 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN D 448 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ASP D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 333 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 414 " --> pdb=" O ILE D 333 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE D 382 " --> pdb=" O ARG D 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 302 through 310 removed outlier: 6.545A pdb=" N THR D 303 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1215 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: 4.78 Time building geometry restraints manager: 7.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4537 1.34 - 1.46: 3790 1.46 - 1.58: 7006 1.58 - 1.70: 3 1.70 - 1.83: 135 Bond restraints: 15471 Sorted by residual: bond pdb=" C7 NAG D 604 " pdb=" N2 NAG D 604 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.10e-02 8.26e+03 6.00e+00 bond pdb=" C7 NAG C 604 " pdb=" N2 NAG C 604 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.10e-02 8.26e+03 5.88e+00 bond pdb=" C7 NAG A 604 " pdb=" N2 NAG A 604 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.10e-02 8.26e+03 5.74e+00 bond pdb=" C2 NAG A 604 " pdb=" N2 NAG A 604 " ideal model delta sigma weight residual 1.454 1.474 -0.020 1.00e-02 1.00e+04 3.99e+00 bond pdb=" C2 NAG D 604 " pdb=" N2 NAG D 604 " ideal model delta sigma weight residual 1.454 1.473 -0.019 1.00e-02 1.00e+04 3.63e+00 ... (remaining 15466 not shown) Histogram of bond angle deviations from ideal: 96.54 - 104.05: 199 104.05 - 111.55: 7615 111.55 - 119.05: 5625 119.05 - 126.56: 7290 126.56 - 134.06: 313 Bond angle restraints: 21042 Sorted by residual: angle pdb=" C2 NAG C 604 " pdb=" N2 NAG C 604 " pdb=" C7 NAG C 604 " ideal model delta sigma weight residual 123.12 134.05 -10.93 1.28e+00 6.08e-01 7.25e+01 angle pdb=" C2 NAG A 604 " pdb=" N2 NAG A 604 " pdb=" C7 NAG A 604 " ideal model delta sigma weight residual 123.12 134.01 -10.89 1.28e+00 6.08e-01 7.21e+01 angle pdb=" C2 NAG D 604 " pdb=" N2 NAG D 604 " pdb=" C7 NAG D 604 " ideal model delta sigma weight residual 123.12 133.98 -10.86 1.28e+00 6.08e-01 7.16e+01 angle pdb=" N PHE B 519 " pdb=" CA PHE B 519 " pdb=" C PHE B 519 " ideal model delta sigma weight residual 110.50 118.91 -8.41 1.41e+00 5.03e-01 3.56e+01 angle pdb=" N PHE E 519 " pdb=" CA PHE E 519 " pdb=" C PHE E 519 " ideal model delta sigma weight residual 110.50 118.86 -8.36 1.41e+00 5.03e-01 3.51e+01 ... (remaining 21037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.51: 8806 19.51 - 39.03: 325 39.03 - 58.54: 72 58.54 - 78.06: 10 78.06 - 97.57: 9 Dihedral angle restraints: 9222 sinusoidal: 4281 harmonic: 4941 Sorted by residual: dihedral pdb=" CA SER F 534 " pdb=" C SER F 534 " pdb=" N VAL F 535 " pdb=" CA VAL F 535 " ideal model delta harmonic sigma weight residual 180.00 131.35 48.65 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA SER B 534 " pdb=" C SER B 534 " pdb=" N VAL B 535 " pdb=" CA VAL B 535 " ideal model delta harmonic sigma weight residual 180.00 131.36 48.64 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA SER E 534 " pdb=" C SER E 534 " pdb=" N VAL E 535 " pdb=" CA VAL E 535 " ideal model delta harmonic sigma weight residual 180.00 131.37 48.63 0 5.00e+00 4.00e-02 9.46e+01 ... (remaining 9219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2472 0.095 - 0.189: 240 0.189 - 0.283: 18 0.283 - 0.378: 12 0.378 - 0.472: 9 Chirality restraints: 2751 Sorted by residual: chirality pdb=" C1 NAG F 701 " pdb=" ND2 ASN F 637 " pdb=" C2 NAG F 701 " pdb=" O5 NAG F 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CB ILE C 391 " pdb=" CA ILE C 391 " pdb=" CG1 ILE C 391 " pdb=" CG2 ILE C 391 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 637 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 2748 not shown) Planarity restraints: 2574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 534 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C SER B 534 " 0.046 2.00e-02 2.50e+03 pdb=" O SER B 534 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 535 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 534 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C SER E 534 " -0.046 2.00e-02 2.50e+03 pdb=" O SER E 534 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 535 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 534 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C SER F 534 " 0.046 2.00e-02 2.50e+03 pdb=" O SER F 534 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL F 535 " -0.016 2.00e-02 2.50e+03 ... (remaining 2571 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3962 2.81 - 3.33: 13306 3.33 - 3.86: 23997 3.86 - 4.38: 26125 4.38 - 4.90: 44042 Nonbonded interactions: 111432 Sorted by model distance: nonbonded pdb=" NH2 ARG D 503 " pdb=" OD1 ASN F 650 " model vdw 2.288 2.520 nonbonded pdb=" NH2 ARG A 503 " pdb=" OD1 ASN B 650 " model vdw 2.316 2.520 nonbonded pdb=" OH TYR E 586 " pdb=" NE2 GLN F 591 " model vdw 2.316 2.520 nonbonded pdb=" O PHE A 93 " pdb=" OH TYR A 233 " model vdw 2.331 2.440 nonbonded pdb=" O PHE D 93 " pdb=" OH TYR D 233 " model vdw 2.331 2.440 ... (remaining 111427 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' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9474 2.51 5 N 2439 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 6.090 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.140 Process input model: 41.350 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.006 0.054 15471 Z= 0.402 Angle : 0.980 11.968 21042 Z= 0.542 Chirality : 0.063 0.472 2751 Planarity : 0.007 0.060 2508 Dihedral : 11.074 97.571 5931 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.53 % Favored : 88.93 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -3.30 (0.17), residues: 1671 helix: -2.46 (0.20), residues: 333 sheet: -1.20 (0.25), residues: 306 loop : -2.52 (0.17), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 273 time to evaluate : 1.791 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 outliers start: 6 outliers final: 3 residues processed: 279 average time/residue: 0.2786 time to fit residues: 112.7545 Evaluate side-chains 133 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.685 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.1298 time to fit residues: 3.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 195 ASN A 249 HIS ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 195 ASN C 249 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN E 591 GLN D 103 GLN D 249 HIS ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN F 591 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15471 Z= 0.281 Angle : 0.719 9.963 21042 Z= 0.390 Chirality : 0.051 0.376 2751 Planarity : 0.005 0.062 2508 Dihedral : 9.545 95.846 2691 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.11 % Favored : 89.53 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.56 (0.19), residues: 1671 helix: -1.34 (0.24), residues: 345 sheet: -1.36 (0.24), residues: 348 loop : -2.01 (0.19), residues: 978 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 1.742 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 outliers start: 3 outliers final: 0 residues processed: 191 average time/residue: 0.2482 time to fit residues: 73.0283 Evaluate side-chains 128 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN C 195 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 15471 Z= 0.462 Angle : 0.796 10.136 21042 Z= 0.426 Chirality : 0.053 0.332 2751 Planarity : 0.005 0.054 2508 Dihedral : 9.505 94.054 2691 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.57 % Favored : 87.19 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -2.44 (0.19), residues: 1671 helix: -1.14 (0.25), residues: 345 sheet: -1.28 (0.24), residues: 348 loop : -1.98 (0.20), residues: 978 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.683 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 outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2554 time to fit residues: 69.0992 Evaluate side-chains 129 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 0.0020 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15471 Z= 0.190 Angle : 0.668 12.376 21042 Z= 0.356 Chirality : 0.050 0.354 2751 Planarity : 0.004 0.062 2508 Dihedral : 9.145 92.689 2691 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.31 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.12 (0.20), residues: 1671 helix: -0.78 (0.26), residues: 348 sheet: -1.20 (0.24), residues: 348 loop : -1.74 (0.20), residues: 975 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2464 time to fit residues: 69.9393 Evaluate side-chains 127 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.2980 chunk 92 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 0.0570 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 15471 Z= 0.248 Angle : 0.664 10.933 21042 Z= 0.353 Chirality : 0.049 0.318 2751 Planarity : 0.004 0.060 2508 Dihedral : 9.017 92.327 2691 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.99 % Favored : 89.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.05 (0.20), residues: 1671 helix: -0.52 (0.27), residues: 348 sheet: -1.14 (0.24), residues: 360 loop : -1.80 (0.20), residues: 963 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2245 time to fit residues: 60.4799 Evaluate side-chains 119 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 425 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15471 Z= 0.182 Angle : 0.632 13.163 21042 Z= 0.336 Chirality : 0.049 0.347 2751 Planarity : 0.004 0.057 2508 Dihedral : 8.844 91.522 2691 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1671 helix: -0.27 (0.27), residues: 348 sheet: -1.41 (0.24), residues: 378 loop : -1.64 (0.20), residues: 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.834 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 outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2403 time to fit residues: 65.0754 Evaluate side-chains 126 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 15471 Z= 0.303 Angle : 0.696 12.001 21042 Z= 0.366 Chirality : 0.049 0.301 2751 Planarity : 0.005 0.069 2508 Dihedral : 8.870 92.813 2691 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.89 % Favored : 88.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.00 (0.20), residues: 1671 helix: -0.30 (0.27), residues: 351 sheet: -1.38 (0.24), residues: 381 loop : -1.72 (0.20), residues: 939 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.723 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 outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2455 time to fit residues: 64.3793 Evaluate side-chains 115 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 10.0000 chunk 64 optimal weight: 0.0770 chunk 96 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15471 Z= 0.171 Angle : 0.624 12.322 21042 Z= 0.330 Chirality : 0.048 0.335 2751 Planarity : 0.004 0.073 2508 Dihedral : 8.686 91.021 2691 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1671 helix: 0.13 (0.28), residues: 351 sheet: -1.30 (0.23), residues: 396 loop : -1.71 (0.20), residues: 924 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.651 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 outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2272 time to fit residues: 62.6676 Evaluate side-chains 120 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464CGLN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 15471 Z= 0.311 Angle : 0.686 11.108 21042 Z= 0.361 Chirality : 0.048 0.299 2751 Planarity : 0.005 0.073 2508 Dihedral : 8.777 93.088 2691 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.71 % Favored : 89.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.20), residues: 1671 helix: -0.06 (0.27), residues: 357 sheet: -1.32 (0.24), residues: 387 loop : -1.78 (0.20), residues: 927 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2279 time to fit residues: 58.0972 Evaluate side-chains 109 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 15471 Z= 0.207 Angle : 0.639 11.638 21042 Z= 0.339 Chirality : 0.048 0.307 2751 Planarity : 0.005 0.073 2508 Dihedral : 8.670 91.705 2691 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.20), residues: 1671 helix: 0.05 (0.28), residues: 351 sheet: -1.26 (0.24), residues: 396 loop : -1.78 (0.20), residues: 924 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.703 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 outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2242 time to fit residues: 58.9559 Evaluate side-chains 117 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 0.0370 chunk 37 optimal weight: 0.4980 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.0370 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.8938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 203 GLN ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083042 restraints weight = 42207.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084908 restraints weight = 28886.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086236 restraints weight = 22248.650| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15471 Z= 0.184 Angle : 0.616 11.305 21042 Z= 0.326 Chirality : 0.047 0.309 2751 Planarity : 0.005 0.073 2508 Dihedral : 8.597 91.694 2691 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.69 % Favored : 90.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1671 helix: 0.08 (0.28), residues: 357 sheet: -1.23 (0.24), residues: 387 loop : -1.72 (0.20), residues: 927 =============================================================================== Job complete usr+sys time: 2403.44 seconds wall clock time: 45 minutes 25.46 seconds (2725.46 seconds total)