Starting phenix.real_space_refine on Thu Feb 15 05:39:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/02_2024/7aua_11926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/02_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_11926/02_2024/7aua_11926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/02_2024/7aua_11926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/02_2024/7aua_11926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aua_11926/02_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12 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: 12 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: 5.34 Conformation dependent library (CDL) restraints added in 2.2 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: 2.44 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: 3.19 Time building geometry restraints manager: 5.10 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: 6682 20.70 - 41.40: 364 41.40 - 62.09: 38 62.09 - 82.79: 34 82.79 - 103.49: 12 Dihedral angle restraints: 7130 sinusoidal: 3092 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 7127 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: 13.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.040 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 32.990 Find NCS groups from input model: 0.590 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.280 ------------------------------------------------------------------------------- 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 : 13.954 103.488 4488 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 : 1.373 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.6669 time to fit residues: 213.1781 Evaluate side-chains 76 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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: 0.8304 moved from start: 0.1182 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= 0.147 Angle : 0.515 5.970 15820 Z= 0.264 Chirality : 0.043 0.142 1760 Planarity : 0.004 0.043 2008 Dihedral : 8.716 68.024 1820 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.83 % Allowed : 6.35 % Favored : 92.82 % 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: 1.41 (0.26), residues: 408 sheet: -0.84 (0.39), residues: 176 loop : 0.03 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 761 HIS 0.006 0.001 HIS A 872 PHE 0.013 0.001 PHE B 873 TYR 0.015 0.001 TYR B 808 ARG 0.007 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 108 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.292 Fit side-chains REVERT: A 391 LEU cc_start: 0.8537 (mp) cc_final: 0.8304 (mt) REVERT: A 533 MET cc_start: 0.8350 (mtp) cc_final: 0.8104 (mtt) REVERT: B 391 LEU cc_start: 0.8545 (mp) cc_final: 0.8311 (mt) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 1.4082 time to fit residues: 154.7953 Evaluate side-chains 82 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 249 VAL 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: 3.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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: 0.8414 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 11618 Z= 0.427 Angle : 0.622 6.173 15820 Z= 0.321 Chirality : 0.048 0.159 1760 Planarity : 0.005 0.040 2008 Dihedral : 7.981 56.395 1820 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.57 % Allowed : 8.66 % Favored : 89.77 % 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: 0.13 (0.22), residues: 1356 helix: 1.09 (0.26), residues: 410 sheet: -1.14 (0.38), residues: 164 loop : -0.09 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 266 HIS 0.005 0.002 HIS B 616 PHE 0.017 0.002 PHE A 452 TYR 0.014 0.002 TYR A 811 ARG 0.003 0.000 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 101 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.403 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 92 average time/residue: 1.4651 time to fit residues: 145.6615 Evaluate side-chains 83 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 517 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 83 optimal weight: 0.0010 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS 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: 0.8368 moved from start: 0.1971 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= 0.174 Angle : 0.498 5.341 15820 Z= 0.254 Chirality : 0.042 0.150 1760 Planarity : 0.004 0.038 2008 Dihedral : 6.863 54.745 1820 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.99 % Allowed : 10.07 % Favored : 88.94 % 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: 0.30 (0.22), residues: 1356 helix: 1.27 (0.26), residues: 412 sheet: -1.03 (0.38), residues: 164 loop : -0.01 (0.21), residues: 780 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 0.010 0.001 PHE A 857 TYR 0.011 0.001 TYR B 787 ARG 0.004 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 98 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.203 Fit side-chains REVERT: A 505 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8720 (tt) REVERT: B 505 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8722 (tt) outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 1.4407 time to fit residues: 146.7880 Evaluate side-chains 89 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.2119 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= 0.209 Angle : 0.502 7.104 15820 Z= 0.254 Chirality : 0.042 0.137 1760 Planarity : 0.004 0.037 2008 Dihedral : 6.174 54.829 1820 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.98 % Allowed : 10.07 % Favored : 87.95 % 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 (0.22), residues: 1356 helix: 1.38 (0.26), residues: 410 sheet: -0.98 (0.39), residues: 164 loop : 0.01 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 266 HIS 0.004 0.001 HIS A 872 PHE 0.011 0.001 PHE A 452 TYR 0.011 0.001 TYR B 787 ARG 0.003 0.000 ARG A 854 *********************** 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 112 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.221 Fit side-chains REVERT: A 391 LEU cc_start: 0.8620 (mp) cc_final: 0.8365 (mt) REVERT: A 505 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8739 (tt) REVERT: B 391 LEU cc_start: 0.8632 (mp) cc_final: 0.8362 (mt) REVERT: B 505 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8744 (tt) outliers start: 24 outliers final: 13 residues processed: 102 average time/residue: 1.4568 time to fit residues: 159.9143 Evaluate side-chains 95 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 306 VAL 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 517 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 306 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 Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 599 ASP 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: 5.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 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: 0.8396 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11618 Z= 0.322 Angle : 0.551 6.642 15820 Z= 0.280 Chirality : 0.044 0.137 1760 Planarity : 0.004 0.036 2008 Dihedral : 6.134 55.320 1820 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.98 % Allowed : 11.06 % Favored : 86.96 % 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: 1.21 (0.26), residues: 410 sheet: -0.99 (0.39), residues: 164 loop : -0.06 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 266 HIS 0.004 0.001 HIS A 616 PHE 0.014 0.002 PHE B 452 TYR 0.011 0.001 TYR B 811 ARG 0.005 0.000 ARG B 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 106 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 1.180 Fit side-chains REVERT: A 479 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9049 (p0) REVERT: A 505 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8780 (tt) REVERT: B 479 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.9064 (p0) REVERT: B 505 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8780 (tt) outliers start: 24 outliers final: 16 residues processed: 96 average time/residue: 1.2862 time to fit residues: 134.1177 Evaluate side-chains 98 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 700 LYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS 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 599 ASP Chi-restraints excluded: chain B residue 700 LYS 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: 0.5980 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 0.0470 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11618 Z= 0.187 Angle : 0.493 6.240 15820 Z= 0.250 Chirality : 0.042 0.136 1760 Planarity : 0.004 0.038 2008 Dihedral : 5.790 54.816 1820 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.65 % Allowed : 11.47 % Favored : 86.88 % 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: 0.37 (0.23), residues: 1356 helix: 1.33 (0.26), residues: 410 sheet: -0.99 (0.39), residues: 164 loop : 0.02 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 266 HIS 0.004 0.001 HIS A 872 PHE 0.010 0.001 PHE B 452 TYR 0.011 0.001 TYR A 787 ARG 0.004 0.000 ARG B 719 *********************** 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: 20 poor density : 84 time to evaluate : 1.274 Fit side-chains REVERT: A 505 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 505 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8736 (tt) outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 1.3517 time to fit residues: 144.2428 Evaluate side-chains 92 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 833 ASP Chi-restraints excluded: chain B residue 177 CYS 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 505 LEU 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: 0.1980 chunk 39 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11618 Z= 0.217 Angle : 0.495 5.337 15820 Z= 0.251 Chirality : 0.042 0.134 1760 Planarity : 0.004 0.037 2008 Dihedral : 5.701 55.129 1820 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.82 % Allowed : 11.30 % Favored : 86.88 % 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: 0.39 (0.23), residues: 1356 helix: 1.34 (0.26), residues: 410 sheet: -0.97 (0.39), residues: 164 loop : 0.05 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.004 0.001 HIS A 872 PHE 0.012 0.001 PHE A 452 TYR 0.011 0.001 TYR A 787 ARG 0.003 0.000 ARG B 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 107 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.296 Fit side-chains REVERT: A 479 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.9060 (p0) REVERT: A 505 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8759 (tt) REVERT: B 479 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.9076 (p0) REVERT: B 505 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8761 (tt) outliers start: 22 outliers final: 13 residues processed: 97 average time/residue: 1.3807 time to fit residues: 144.9171 Evaluate side-chains 99 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 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 256 LEU 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 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: 1.9990 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.0670 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 GLN ** 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: 0.8349 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11618 Z= 0.166 Angle : 0.480 5.186 15820 Z= 0.245 Chirality : 0.041 0.133 1760 Planarity : 0.004 0.038 2008 Dihedral : 5.510 54.701 1820 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 11.63 % Favored : 86.88 % 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: 0.44 (0.23), residues: 1356 helix: 1.39 (0.27), residues: 410 sheet: -0.99 (0.39), residues: 164 loop : 0.09 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 761 HIS 0.004 0.001 HIS A 872 PHE 0.010 0.001 PHE A 452 TYR 0.011 0.001 TYR A 787 ARG 0.004 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 107 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.329 Fit side-chains REVERT: A 479 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.9072 (p0) REVERT: A 505 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8712 (tt) REVERT: B 505 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8713 (tt) outliers start: 18 outliers final: 13 residues processed: 101 average time/residue: 1.2278 time to fit residues: 135.1509 Evaluate side-chains 96 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 505 LEU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS 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 505 LEU 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: 1.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 135 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 GLN ** 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: 0.8359 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11618 Z= 0.202 Angle : 0.502 8.940 15820 Z= 0.253 Chirality : 0.042 0.151 1760 Planarity : 0.004 0.037 2008 Dihedral : 5.499 54.916 1820 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.24 % Allowed : 12.38 % 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: 0.43 (0.23), residues: 1356 helix: 1.36 (0.27), residues: 410 sheet: -0.95 (0.39), residues: 164 loop : 0.08 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 266 HIS 0.004 0.001 HIS A 872 PHE 0.011 0.001 PHE B 452 TYR 0.011 0.001 TYR A 787 ARG 0.003 0.000 ARG B 719 ********************** 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 97 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.353 Fit side-chains REVERT: A 479 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9083 (p0) REVERT: A 505 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8743 (tt) REVERT: B 479 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.9099 (p0) REVERT: B 505 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 533 MET cc_start: 0.8186 (mtp) cc_final: 0.7839 (mmm) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 1.3322 time to fit residues: 134.5911 Evaluate side-chains 97 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 505 LEU Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 177 CYS 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 503 SER Chi-restraints excluded: chain B residue 505 LEU 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: 0.9980 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.116017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086901 restraints weight = 15757.984| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.32 r_work: 0.2831 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11618 Z= 0.179 Angle : 0.490 6.797 15820 Z= 0.248 Chirality : 0.041 0.146 1760 Planarity : 0.004 0.038 2008 Dihedral : 5.405 54.670 1820 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.40 % Allowed : 12.54 % Favored : 86.06 % 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: 1.42 (0.27), residues: 408 sheet: -0.96 (0.39), residues: 164 loop : 0.14 (0.22), residues: 784 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 0.015 0.001 PHE B 600 TYR 0.011 0.001 TYR A 787 ARG 0.003 0.000 ARG B 719 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3579.11 seconds wall clock time: 65 minutes 11.82 seconds (3911.82 seconds total)