Starting phenix.real_space_refine on Fri Jan 19 11:39:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/01_2024/7aua_11926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/01_2024/7aua_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_11926/01_2024/7aua_11926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/01_2024/7aua_11926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/01_2024/7aua_11926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/01_2024/7aua_11926_updated.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-1.21-5211/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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: 6.44, 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: 4.68 Conformation dependent library (CDL) restraints added in 2.1 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: 2.55 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: 3.40 Time building geometry restraints manager: 4.96 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 - 20.70: 6598 20.70 - 41.40: 348 41.40 - 62.09: 36 62.09 - 82.79: 34 82.79 - 103.49: 12 Dihedral angle restraints: 7028 sinusoidal: 2990 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 7025 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: 4.990 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: 10.450 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.990 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.220 ------------------------------------------------------------------------------- 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 : 13.929 103.488 4386 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 % Allowed : 0.17 % Favored : 99.83 % 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: -0.20 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 266 HIS 0.005 0.001 HIS B 872 PHE 0.019 0.002 PHE A 600 TYR 0.018 0.002 TYR A 808 ARG 0.004 0.001 ARG B 822 *********************** 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 : 1.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.6716 time to fit residues: 214.0640 Evaluate side-chains 76 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 346 GLN B 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11618 Z= 0.152 Angle : 0.510 5.826 15820 Z= 0.263 Chirality : 0.043 0.138 1760 Planarity : 0.004 0.044 2008 Dihedral : 8.529 70.672 1718 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.66 % Allowed : 6.19 % Favored : 93.15 % 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: 0.42 (0.22), residues: 1356 helix: 1.42 (0.26), residues: 408 sheet: -0.84 (0.39), residues: 176 loop : 0.02 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 761 HIS 0.006 0.001 HIS A 872 PHE 0.014 0.001 PHE B 873 TYR 0.014 0.001 TYR A 808 ARG 0.008 0.000 ARG A 854 *********************** 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 104 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.340 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 100 average time/residue: 1.3952 time to fit residues: 150.4991 Evaluate side-chains 83 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 824 MET 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: 2.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 11618 Z= 0.477 Angle : 0.651 7.245 15820 Z= 0.335 Chirality : 0.049 0.157 1760 Planarity : 0.005 0.040 2008 Dihedral : 7.758 56.705 1718 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.73 % Allowed : 8.25 % Favored : 90.02 % 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: 0.05 (0.22), residues: 1356 helix: 1.03 (0.26), residues: 408 sheet: -1.18 (0.38), residues: 164 loop : -0.15 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 266 HIS 0.006 0.002 HIS A 616 PHE 0.019 0.003 PHE A 857 TYR 0.015 0.002 TYR B 811 ARG 0.003 0.001 ARG A 602 *********************** 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 103 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.336 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 92 average time/residue: 1.3885 time to fit residues: 138.4447 Evaluate side-chains 86 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 0.0050 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11618 Z= 0.180 Angle : 0.496 5.395 15820 Z= 0.254 Chirality : 0.043 0.153 1760 Planarity : 0.004 0.040 2008 Dihedral : 6.411 54.685 1718 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.16 % Allowed : 9.57 % Favored : 89.27 % 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: 1.24 (0.26), residues: 410 sheet: -1.04 (0.38), residues: 164 loop : -0.06 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 516 HIS 0.004 0.001 HIS A 872 PHE 0.011 0.001 PHE A 206 TYR 0.011 0.001 TYR B 787 ARG 0.003 0.000 ARG B 854 *********************** 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 103 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.245 Fit side-chains REVERT: A 505 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8727 (tt) REVERT: B 505 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8728 (tt) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 1.4993 time to fit residues: 159.7520 Evaluate side-chains 94 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.0020 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11618 Z= 0.191 Angle : 0.494 7.063 15820 Z= 0.252 Chirality : 0.042 0.137 1760 Planarity : 0.004 0.038 2008 Dihedral : 5.562 54.689 1718 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.49 % Allowed : 10.81 % Favored : 87.71 % 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: 0.40 (0.22), residues: 1356 helix: 1.43 (0.26), residues: 410 sheet: -0.98 (0.39), residues: 164 loop : -0.00 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 266 HIS 0.004 0.001 HIS B 872 PHE 0.010 0.001 PHE A 452 TYR 0.011 0.001 TYR A 787 ARG 0.005 0.000 ARG A 719 *********************** 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 105 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.342 Fit side-chains REVERT: A 505 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8720 (tt) REVERT: B 505 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8730 (tt) outliers start: 18 outliers final: 7 residues processed: 98 average time/residue: 1.4246 time to fit residues: 150.8772 Evaluate side-chains 92 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8381 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11618 Z= 0.260 Angle : 0.519 6.290 15820 Z= 0.264 Chirality : 0.043 0.137 1760 Planarity : 0.004 0.038 2008 Dihedral : 5.351 54.962 1718 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.06 % Allowed : 10.64 % Favored : 87.29 % 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: 0.34 (0.23), residues: 1356 helix: 1.35 (0.26), residues: 410 sheet: -0.95 (0.39), residues: 164 loop : -0.04 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 266 HIS 0.004 0.001 HIS B 872 PHE 0.013 0.002 PHE B 452 TYR 0.011 0.001 TYR B 787 ARG 0.003 0.000 ARG A 719 *********************** 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 110 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.460 Fit side-chains REVERT: A 479 ASN cc_start: 0.9310 (OUTLIER) cc_final: 0.9061 (p0) REVERT: A 505 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8765 (tt) REVERT: B 245 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8489 (mtt) REVERT: B 479 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.9056 (p0) REVERT: B 505 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8767 (tt) outliers start: 25 outliers final: 16 residues processed: 99 average time/residue: 1.3102 time to fit residues: 140.7551 Evaluate side-chains 104 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 833 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 651 GLN ** 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: 0.8347 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11618 Z= 0.147 Angle : 0.469 4.802 15820 Z= 0.238 Chirality : 0.041 0.135 1760 Planarity : 0.004 0.039 2008 Dihedral : 4.986 54.505 1718 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.49 % Allowed : 11.72 % Favored : 86.80 % 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: 1.48 (0.26), residues: 410 sheet: -0.91 (0.39), residues: 164 loop : 0.04 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 761 HIS 0.004 0.001 HIS A 872 PHE 0.009 0.001 PHE B 452 TYR 0.011 0.001 TYR B 787 ARG 0.003 0.000 ARG B 854 *********************** 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 105 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.211 Fit side-chains REVERT: A 505 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8701 (tt) REVERT: B 245 MET cc_start: 0.8902 (mtp) cc_final: 0.8451 (mtt) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 1.3111 time to fit residues: 139.4027 Evaluate side-chains 100 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 833 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.5980 chunk 39 optimal weight: 0.0370 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.8343 moved from start: 0.2441 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= 0.155 Angle : 0.469 5.778 15820 Z= 0.237 Chirality : 0.041 0.140 1760 Planarity : 0.004 0.039 2008 Dihedral : 4.844 54.598 1718 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.73 % Allowed : 11.72 % Favored : 86.55 % 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: 0.53 (0.23), residues: 1356 helix: 1.57 (0.27), residues: 408 sheet: -0.87 (0.39), residues: 164 loop : 0.07 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 761 HIS 0.004 0.001 HIS A 872 PHE 0.013 0.001 PHE B 600 TYR 0.011 0.001 TYR B 787 ARG 0.002 0.000 ARG A 719 *********************** 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 111 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.163 Fit side-chains REVERT: A 479 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.9043 (p0) REVERT: B 245 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: B 479 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9047 (p0) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 1.2111 time to fit residues: 132.0940 Evaluate side-chains 101 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 833 ASP 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: 3.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.0050 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 0.0040 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- 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: 0.8333 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11618 Z= 0.147 Angle : 0.462 5.227 15820 Z= 0.234 Chirality : 0.041 0.145 1760 Planarity : 0.004 0.039 2008 Dihedral : 4.691 54.472 1718 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.49 % Allowed : 12.13 % Favored : 86.39 % 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: 0.57 (0.23), residues: 1356 helix: 1.60 (0.27), residues: 408 sheet: -0.89 (0.39), residues: 164 loop : 0.09 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 761 HIS 0.004 0.001 HIS A 872 PHE 0.014 0.001 PHE A 600 TYR 0.011 0.001 TYR B 787 ARG 0.002 0.000 ARG A 719 *********************** 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 111 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.371 Fit side-chains REVERT: A 479 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9038 (p0) REVERT: B 245 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8415 (mtt) REVERT: B 475 MET cc_start: 0.8542 (mpt) cc_final: 0.8309 (mmt) REVERT: B 479 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9020 (p0) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 1.2425 time to fit residues: 140.9625 Evaluate side-chains 103 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 833 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.0040 chunk 135 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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** ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11618 Z= 0.241 Angle : 0.514 8.247 15820 Z= 0.258 Chirality : 0.042 0.145 1760 Planarity : 0.004 0.037 2008 Dihedral : 4.869 55.247 1718 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.49 % Allowed : 12.62 % Favored : 85.89 % 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: 1.45 (0.27), residues: 410 sheet: -0.91 (0.39), residues: 164 loop : 0.06 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 266 HIS 0.004 0.001 HIS A 872 PHE 0.013 0.002 PHE A 452 TYR 0.011 0.001 TYR B 787 ARG 0.002 0.000 ARG B 535 ********************** 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: 18 poor density : 87 time to evaluate : 1.361 Fit side-chains REVERT: A 479 ASN cc_start: 0.9310 (OUTLIER) cc_final: 0.9064 (p0) REVERT: B 245 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8425 (mtt) REVERT: B 475 MET cc_start: 0.8616 (mpt) cc_final: 0.8382 (mmt) REVERT: B 479 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.9031 (p0) REVERT: B 505 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8678 (tt) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 1.3734 time to fit residues: 144.1011 Evaluate side-chains 101 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 833 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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** ** A 872 HIS ** 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 = 0.3415 r_free = 0.3415 target = 0.115108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086201 restraints weight = 15888.615| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.30 r_work: 0.2817 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2567 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= 0.209 Angle : 0.497 6.993 15820 Z= 0.252 Chirality : 0.042 0.146 1760 Planarity : 0.004 0.038 2008 Dihedral : 4.815 54.909 1718 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.65 % Allowed : 12.79 % Favored : 85.56 % 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: 1.46 (0.27), residues: 406 sheet: -0.98 (0.39), residues: 164 loop : 0.09 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 266 HIS 0.005 0.001 HIS A 872 PHE 0.012 0.001 PHE B 600 TYR 0.011 0.001 TYR B 787 ARG 0.002 0.000 ARG B 854 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.07 seconds wall clock time: 65 minutes 45.39 seconds (3945.39 seconds total)