Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 03:36:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/04_2023/7aua_11926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/04_2023/7aua_11926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/04_2023/7aua_11926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/04_2023/7aua_11926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/04_2023/7aua_11926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/04_2023/7aua_11926_updated.pdb" } resolution = 2.93 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 56 5.16 5 C 7276 2.51 5 N 1896 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B ARG 546": "NH1" <-> "NH2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B GLU 734": "OE1" <-> "OE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 774": "NH1" <-> "NH2" Residue "B ARG 854": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11300 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5546 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5546 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.41, per 1000 atoms: 0.57 Number of scatterers: 11300 At special positions: 0 Unit cell: (94.785, 99.045, 104.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 56 16.00 P 4 15.00 O 2066 8.00 N 1896 7.00 C 7276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 182 " distance=2.04 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 793 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 879 " distance=2.03 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 182 " distance=2.04 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 879 " 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN A 790 " " NAG E 1 " - " ASN B 592 " " NAG F 1 " - " ASN B 790 " Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 10 sheets defined 33.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 206 through 209 No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 418 through 427 removed outlier: 4.206A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.547A pdb=" N VAL A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 487 through 499 removed outlier: 4.209A pdb=" N THR A 491 " --> pdb=" O PRO A 488 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N HIS A 494 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 495 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 523 through 537 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.692A pdb=" N THR A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 625 through 630 removed outlier: 4.386A pdb=" N PHE A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.657A pdb=" N ALA A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.573A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 751 through 763 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 819 through 827 Processing helix chain 'A' and resid 832 through 844 Processing helix chain 'A' and resid 870 through 887 removed outlier: 3.917A pdb=" N ARG A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 206 through 209 No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 375 through 389 Processing helix chain 'B' and resid 418 through 427 removed outlier: 4.206A pdb=" N LEU B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.546A pdb=" N VAL B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 487 through 499 removed outlier: 4.208A pdb=" N THR B 491 " --> pdb=" O PRO B 488 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N HIS B 494 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 495 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.692A pdb=" N THR B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.386A pdb=" N PHE B 629 " --> pdb=" O SER B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 642 Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.657A pdb=" N ALA B 652 " --> pdb=" O LYS B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.573A pdb=" N LEU B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 751 through 763 Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 819 through 827 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 870 through 887 removed outlier: 3.917A pdb=" N ARG B 876 " --> pdb=" O HIS B 872 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.204A pdb=" N LEU A 237 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET A 297 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN A 277 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA A 299 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 344 through 346 removed outlier: 6.558A pdb=" N LEU A 395 " --> pdb=" O PHE A 345 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.017A pdb=" N VAL A 460 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 433 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 462 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 715 through 719 removed outlier: 6.591A pdb=" N VAL A 692 " --> pdb=" O MET A 716 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 718 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 694 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL A 693 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 665 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 695 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET A 667 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 739 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A 666 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 741 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU A 668 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 743 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 775 through 779 Processing sheet with id= F, first strand: chain 'B' and resid 196 through 198 removed outlier: 6.203A pdb=" N LEU B 237 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET B 297 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN B 277 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 299 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.558A pdb=" N LEU B 395 " --> pdb=" O PHE B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.016A pdb=" N VAL B 460 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE B 433 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 462 " --> pdb=" O ILE B 433 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 715 through 719 removed outlier: 6.591A pdb=" N VAL B 692 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL B 718 " --> pdb=" O VAL B 692 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 694 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL B 693 " --> pdb=" O PHE B 663 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 665 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL B 695 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET B 667 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 739 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL B 666 " --> pdb=" O ALA B 739 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU B 741 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU B 668 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE B 743 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 775 through 779 282 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 5.15 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: 3586 1.34 - 1.46: 2953 1.46 - 1.59: 4991 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 11618 Sorted by residual: bond pdb=" C HIS B 555 " pdb=" N ARG B 556 " ideal model delta sigma weight residual 1.330 1.533 -0.204 1.32e-02 5.74e+03 2.38e+02 bond pdb=" C HIS A 555 " pdb=" N ARG A 556 " ideal model delta sigma weight residual 1.330 1.533 -0.204 1.32e-02 5.74e+03 2.38e+02 bond pdb=" O1B UDP A1002 " pdb=" PB UDP A1002 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" O1B UDP B1002 " pdb=" PB UDP B1002 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" N PHE B 918 " pdb=" CA PHE B 918 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.14e-02 7.69e+03 6.76e+00 ... (remaining 11613 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.95: 360 105.95 - 112.95: 6214 112.95 - 119.96: 3887 119.96 - 126.96: 5175 126.96 - 133.97: 184 Bond angle restraints: 15820 Sorted by residual: angle pdb=" O1B UDP B1002 " pdb=" PB UDP B1002 " pdb=" O3A UDP B1002 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O1B UDP A1002 " pdb=" PB UDP A1002 " pdb=" O3A UDP A1002 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O3A UDP A1002 " pdb=" PB UDP A1002 " pdb=" O3B UDP A1002 " ideal model delta sigma weight residual 112.01 102.98 9.03 1.00e+00 1.00e+00 8.16e+01 angle pdb=" O3A UDP B1002 " pdb=" PB UDP B1002 " pdb=" O3B UDP B1002 " ideal model delta sigma weight residual 112.01 103.00 9.01 1.00e+00 1.00e+00 8.11e+01 angle pdb=" CA TYR A 808 " pdb=" CB TYR A 808 " pdb=" CG TYR A 808 " ideal model delta sigma weight residual 113.90 117.96 -4.06 1.80e+00 3.09e-01 5.08e+00 ... (remaining 15815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6278 17.25 - 34.51: 438 34.51 - 51.76: 72 51.76 - 69.01: 18 69.01 - 86.27: 16 Dihedral angle restraints: 6822 sinusoidal: 2784 harmonic: 4038 Sorted by residual: dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS A 188 " pdb=" SG CYS A 188 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CA ARG A 267 " pdb=" C ARG A 267 " pdb=" N THR A 268 " pdb=" CA THR A 268 " ideal model delta harmonic sigma weight residual -180.00 -152.10 -27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 6819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1752 0.147 - 0.293: 6 0.293 - 0.440: 0 0.440 - 0.586: 0 0.586 - 0.733: 2 Chirality restraints: 1760 Sorted by residual: chirality pdb=" CG LEU A 251 " pdb=" CB LEU A 251 " pdb=" CD1 LEU A 251 " pdb=" CD2 LEU A 251 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU B 251 " pdb=" CB LEU B 251 " pdb=" CD1 LEU B 251 " pdb=" CD2 LEU B 251 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1757 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 817 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A 818 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 818 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 818 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 817 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 818 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 818 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 818 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 609 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 610 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.021 5.00e-02 4.00e+02 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 30 2.43 - 3.05: 7308 3.05 - 3.66: 15963 3.66 - 4.28: 25560 4.28 - 4.90: 43214 Nonbonded interactions: 92075 Sorted by model distance: nonbonded pdb="MN MN A1001 " pdb=" O2A UDP A1002 " model vdw 1.809 2.320 nonbonded pdb="MN MN B1001 " pdb=" O2A UDP B1002 " model vdw 1.809 2.320 nonbonded pdb="MN MN B1001 " pdb=" O2B UDP B1002 " model vdw 1.970 2.320 nonbonded pdb="MN MN A1001 " pdb=" O2B UDP A1002 " model vdw 1.970 2.320 nonbonded pdb=" OG1 THR B 617 " pdb=" OD1 ASP B 620 " model vdw 2.143 2.440 ... (remaining 92070 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 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.970 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.070 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.204 11618 Z= 0.497 Angle : 0.639 9.176 15820 Z= 0.356 Chirality : 0.052 0.733 1760 Planarity : 0.004 0.047 2008 Dihedral : 12.693 86.268 4180 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.20 (0.22), residues: 1356 helix: 0.73 (0.26), residues: 432 sheet: -1.32 (0.40), residues: 160 loop : -0.28 (0.21), residues: 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.6029 time to fit residues: 205.0537 Evaluate side-chains 76 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.0030 chunk 41 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11618 Z= 0.145 Angle : 0.509 5.979 15820 Z= 0.262 Chirality : 0.042 0.139 1760 Planarity : 0.004 0.043 2008 Dihedral : 4.425 24.566 1512 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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 (0.22), residues: 1356 helix: 1.42 (0.26), residues: 408 sheet: -0.84 (0.39), residues: 176 loop : 0.03 (0.22), residues: 772 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.367 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 1.4786 time to fit residues: 162.6699 Evaluate side-chains 82 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.6096 time to fit residues: 5.3930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 346 GLN B 219 GLN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 11618 Z= 0.369 Angle : 0.583 8.038 15820 Z= 0.300 Chirality : 0.046 0.140 1760 Planarity : 0.005 0.037 2008 Dihedral : 4.650 24.255 1512 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.24 (0.22), residues: 1356 helix: 1.15 (0.26), residues: 412 sheet: -1.09 (0.39), residues: 164 loop : 0.00 (0.21), residues: 780 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.431 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 88 average time/residue: 1.4334 time to fit residues: 136.4911 Evaluate side-chains 81 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.7993 time to fit residues: 6.2277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 HIS ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 11618 Z= 0.283 Angle : 0.530 7.995 15820 Z= 0.271 Chirality : 0.044 0.141 1760 Planarity : 0.004 0.037 2008 Dihedral : 4.464 23.762 1512 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.25 (0.22), residues: 1356 helix: 1.15 (0.26), residues: 412 sheet: -1.06 (0.38), residues: 164 loop : 0.00 (0.22), residues: 780 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.243 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 99 average time/residue: 1.3504 time to fit residues: 145.1709 Evaluate side-chains 91 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 0.2020 time to fit residues: 2.9801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 HIS ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11618 Z= 0.195 Angle : 0.504 7.669 15820 Z= 0.255 Chirality : 0.042 0.147 1760 Planarity : 0.004 0.037 2008 Dihedral : 4.292 21.442 1512 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.36 (0.22), residues: 1356 helix: 1.32 (0.26), residues: 410 sheet: -0.95 (0.39), residues: 164 loop : 0.01 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.321 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 98 average time/residue: 1.3247 time to fit residues: 141.2412 Evaluate side-chains 87 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.2105 time to fit residues: 2.7974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 11618 Z= 0.323 Angle : 0.550 6.272 15820 Z= 0.281 Chirality : 0.044 0.138 1760 Planarity : 0.004 0.036 2008 Dihedral : 4.418 20.859 1512 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.24 (0.22), residues: 1356 helix: 1.18 (0.26), residues: 410 sheet: -1.01 (0.39), residues: 164 loop : -0.04 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.361 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 1.4289 time to fit residues: 151.1631 Evaluate side-chains 95 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 7 average time/residue: 0.3624 time to fit residues: 6.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11618 Z= 0.170 Angle : 0.487 8.457 15820 Z= 0.247 Chirality : 0.041 0.136 1760 Planarity : 0.004 0.037 2008 Dihedral : 4.160 19.090 1512 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.38 (0.23), residues: 1356 helix: 1.33 (0.26), residues: 410 sheet: -0.96 (0.39), residues: 164 loop : 0.04 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.243 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 1.3334 time to fit residues: 141.2772 Evaluate side-chains 96 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 6 average time/residue: 0.1755 time to fit residues: 3.0720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 11618 Z= 0.164 Angle : 0.471 5.754 15820 Z= 0.239 Chirality : 0.041 0.148 1760 Planarity : 0.004 0.038 2008 Dihedral : 4.002 16.947 1512 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.46 (0.23), residues: 1356 helix: 1.40 (0.27), residues: 410 sheet: -0.94 (0.39), residues: 164 loop : 0.09 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.494 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 96 average time/residue: 1.3597 time to fit residues: 142.1204 Evaluate side-chains 97 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 6 average time/residue: 0.4050 time to fit residues: 4.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11618 Z= 0.190 Angle : 0.483 5.472 15820 Z= 0.245 Chirality : 0.041 0.136 1760 Planarity : 0.004 0.037 2008 Dihedral : 3.989 16.778 1512 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.47 (0.23), residues: 1356 helix: 1.43 (0.27), residues: 410 sheet: -0.93 (0.40), residues: 164 loop : 0.08 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.341 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 1.2686 time to fit residues: 131.3735 Evaluate side-chains 97 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 5 average time/residue: 0.3801 time to fit residues: 4.1944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 135 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 11618 Z= 0.151 Angle : 0.469 8.888 15820 Z= 0.236 Chirality : 0.041 0.135 1760 Planarity : 0.004 0.038 2008 Dihedral : 3.886 16.036 1512 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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 (0.23), residues: 1356 helix: 1.47 (0.27), residues: 410 sheet: -0.91 (0.40), residues: 164 loop : 0.09 (0.22), residues: 782 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.290 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 103 average time/residue: 1.2783 time to fit residues: 143.3261 Evaluate side-chains 94 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1656 time to fit residues: 2.0635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 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 = 0.3423 r_free = 0.3423 target = 0.115628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086621 restraints weight = 15810.503| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.31 r_work: 0.2825 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11618 Z= 0.203 Angle : 0.501 8.507 15820 Z= 0.252 Chirality : 0.042 0.152 1760 Planarity : 0.004 0.037 2008 Dihedral : 3.940 17.513 1512 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.48 (0.23), residues: 1356 helix: 1.41 (0.27), residues: 410 sheet: -0.89 (0.40), residues: 164 loop : 0.10 (0.22), residues: 782 =============================================================================== Job complete usr+sys time: 3377.76 seconds wall clock time: 61 minutes 11.63 seconds (3671.63 seconds total)