Starting phenix.real_space_refine on Mon Dec 30 11:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t7h_41092/12_2024/8t7h_41092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t7h_41092/12_2024/8t7h_41092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t7h_41092/12_2024/8t7h_41092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t7h_41092/12_2024/8t7h_41092.map" model { file = "/net/cci-nas-00/data/ceres_data/8t7h_41092/12_2024/8t7h_41092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t7h_41092/12_2024/8t7h_41092.cif" } resolution = 3.3 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= 0.005 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 8288 2.51 5 N 2247 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13100 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5614 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 741} Chain breaks: 2 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 421 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 268 Chain: "B" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5618 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 741} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 634 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 268 Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 920 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 922 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.28, per 1000 atoms: 0.63 Number of scatterers: 13100 At special positions: 0 Unit cell: (87.769, 121.099, 211.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2461 8.00 N 2247 7.00 C 8288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 2.0 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 43.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.658A pdb=" N ALA A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.518A pdb=" N GLU A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.728A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.523A pdb=" N TYR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.859A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.061A pdb=" N ASP A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.560A pdb=" N TRP A 307 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.880A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 344 No H-bonds generated for 'chain 'A' and resid 343 through 344' Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.727A pdb=" N ASN A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.693A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.932A pdb=" N TYR A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.658A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 673 removed outlier: 3.592A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.673A pdb=" N SER A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 715 Processing helix chain 'A' and resid 736 through 761 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 765 through 789 removed outlier: 5.714A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 797 through 827 removed outlier: 4.313A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.960A pdb=" N ILE B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.629A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.762A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.509A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 237 removed outlier: 3.915A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 4.194A pdb=" N ASP B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.529A pdb=" N TRP B 307 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.875A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 344 No H-bonds generated for 'chain 'B' and resid 343 through 344' Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.725A pdb=" N ASN B 349 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.697A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 577 through 604 removed outlier: 4.060A pdb=" N TYR B 604 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 633 removed outlier: 3.637A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 673 Proline residue: B 655 - end of helix removed outlier: 3.573A pdb=" N SER B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 Processing helix chain 'B' and resid 736 through 761 Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 765 through 789 removed outlier: 5.706A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 827 removed outlier: 3.504A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.544A pdb=" N SER C 33 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 34 " --> pdb=" O PHE C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 34' Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.516A pdb=" N SER D 33 " --> pdb=" O THR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 217 removed outlier: 3.712A pdb=" N ALA A 275 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 325 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 removed outlier: 4.145A pdb=" N LEU A 731 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.389A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 241 through 242 removed outlier: 6.587A pdb=" N CYS B 241 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA B 216 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL B 273 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 275 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 325 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 446 through 447 Processing sheet with id=AB4, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB6, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AB7, first strand: chain 'B' and resid 570 through 571 removed outlier: 4.019A pdb=" N LEU B 731 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 6 through 9 Processing sheet with id=AB9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.912A pdb=" N MET C 36 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA C 52 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 9 Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.918A pdb=" N MET D 36 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA D 52 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP D 38 " --> pdb=" O VAL D 50 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2170 1.31 - 1.43: 3633 1.43 - 1.56: 7433 1.56 - 1.69: 0 1.69 - 1.82: 152 Bond restraints: 13388 Sorted by residual: bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.365 1.438 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C05 QUS B 901 " pdb=" N15 QUS B 901 " ideal model delta sigma weight residual 1.365 1.437 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C05 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 1.362 1.420 -0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" C05 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 1.362 1.420 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" C04 QUS A 901 " pdb=" N14 QUS A 901 " ideal model delta sigma weight residual 1.380 1.438 -0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 13383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 18074 2.66 - 5.32: 143 5.32 - 7.98: 23 7.98 - 10.64: 1 10.64 - 13.30: 2 Bond angle restraints: 18243 Sorted by residual: angle pdb=" C03 QUS A 901 " pdb=" N14 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 112.77 126.07 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C03 QUS B 901 " pdb=" N14 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 112.77 126.06 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C LEU B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 122.06 116.38 5.68 1.86e+00 2.89e-01 9.32e+00 angle pdb=" CB MET A 802 " pdb=" CG MET A 802 " pdb=" SD MET A 802 " ideal model delta sigma weight residual 112.70 121.08 -8.38 3.00e+00 1.11e-01 7.81e+00 angle pdb=" N GLN A 360 " pdb=" CA GLN A 360 " pdb=" CB GLN A 360 " ideal model delta sigma weight residual 110.28 114.58 -4.30 1.55e+00 4.16e-01 7.68e+00 ... (remaining 18238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7195 17.93 - 35.86: 628 35.86 - 53.80: 109 53.80 - 71.73: 11 71.73 - 89.66: 8 Dihedral angle restraints: 7951 sinusoidal: 2761 harmonic: 5190 Sorted by residual: dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual 93.00 -177.69 -89.31 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 534 " pdb=" CB CYS A 534 " ideal model delta sinusoidal sigma weight residual 93.00 175.16 -82.16 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 25.10 67.90 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 7948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1204 0.033 - 0.065: 595 0.065 - 0.098: 188 0.098 - 0.131: 74 0.131 - 0.163: 6 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA THR A 742 " pdb=" N THR A 742 " pdb=" C THR A 742 " pdb=" CB THR A 742 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA THR B 742 " pdb=" N THR B 742 " pdb=" C THR B 742 " pdb=" CB THR B 742 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA VAL A 28 " pdb=" N VAL A 28 " pdb=" C VAL A 28 " pdb=" CB VAL A 28 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2064 not shown) Planarity restraints: 2358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 307 " 0.019 2.00e-02 2.50e+03 1.53e-02 5.81e+00 pdb=" CG TRP A 307 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 307 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 307 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 307 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 307 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 307 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 307 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 307 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 307 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 107 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO C 108 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 107 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D 108 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 108 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 108 " -0.027 5.00e-02 4.00e+02 ... (remaining 2355 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1735 2.75 - 3.29: 12669 3.29 - 3.83: 21169 3.83 - 4.36: 23105 4.36 - 4.90: 41560 Nonbonded interactions: 100238 Sorted by model distance: nonbonded pdb=" O SER B 116 " pdb=" OG SER B 120 " model vdw 2.217 3.040 nonbonded pdb=" O TYR A 629 " pdb=" OG1 THR A 632 " model vdw 2.219 3.040 nonbonded pdb=" O TYR B 629 " pdb=" OG1 THR B 632 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 311 " pdb=" OD1 ASP B 480 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 311 " pdb=" OD1 ASP A 480 " model vdw 2.257 3.040 ... (remaining 100233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 538 or (resid 539 and (name N or name CA or nam \ e C or name O or name CB )) or resid 540 through 827 or resid 901)) selection = (chain 'B' and (resid 25 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB )) or resid 260 through 540 or (resid 541 and (name N o \ r name CA or name C or name O or name CB )) or resid 542 through 827 or resid 90 \ 1)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 3 through 92 or (resid 93 through 94 and (name N or name C \ A or name C or name O or name CB )) or resid 95 through 125)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 32.420 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 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 : 0.003 0.073 13388 Z= 0.230 Angle : 0.624 13.304 18243 Z= 0.315 Chirality : 0.044 0.163 2067 Planarity : 0.004 0.055 2358 Dihedral : 13.359 89.659 4563 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.31 (0.21), residues: 1778 helix: 1.80 (0.20), residues: 700 sheet: -0.69 (0.31), residues: 298 loop : -0.90 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 307 HIS 0.005 0.001 HIS A 45 PHE 0.017 0.001 PHE B 456 TYR 0.016 0.001 TYR D 103 ARG 0.008 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.344 Fit side-chains REVERT: B 307 TRP cc_start: 0.6663 (p-90) cc_final: 0.5934 (p-90) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2872 time to fit residues: 71.5224 Evaluate side-chains 152 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13388 Z= 0.210 Angle : 0.582 12.732 18243 Z= 0.295 Chirality : 0.044 0.229 2067 Planarity : 0.004 0.051 2358 Dihedral : 4.668 51.313 1940 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.63 % Allowed : 6.49 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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 (0.21), residues: 1778 helix: 1.84 (0.20), residues: 712 sheet: -0.92 (0.29), residues: 324 loop : -0.87 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 307 HIS 0.004 0.001 HIS B 44 PHE 0.030 0.002 PHE A 712 TYR 0.015 0.001 TYR B 481 ARG 0.007 0.001 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 1.582 Fit side-chains REVERT: B 307 TRP cc_start: 0.6699 (p-90) cc_final: 0.6005 (p-90) REVERT: C 103 TYR cc_start: 0.7423 (m-80) cc_final: 0.6942 (m-80) outliers start: 8 outliers final: 4 residues processed: 163 average time/residue: 0.2891 time to fit residues: 66.8458 Evaluate side-chains 157 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 547 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 161 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13388 Z= 0.355 Angle : 0.635 10.297 18243 Z= 0.324 Chirality : 0.046 0.190 2067 Planarity : 0.005 0.049 2358 Dihedral : 4.893 52.734 1940 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.11 % Allowed : 9.65 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.19 (0.21), residues: 1778 helix: 1.69 (0.20), residues: 732 sheet: -1.02 (0.31), residues: 300 loop : -0.94 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 307 HIS 0.007 0.001 HIS A 44 PHE 0.031 0.002 PHE A 544 TYR 0.024 0.002 TYR A 547 ARG 0.008 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.518 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 158 average time/residue: 0.2837 time to fit residues: 64.0736 Evaluate side-chains 157 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 172 optimal weight: 0.1980 chunk 154 optimal weight: 9.9990 chunk 46 optimal weight: 0.0370 chunk 143 optimal weight: 20.0000 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13388 Z= 0.180 Angle : 0.556 11.729 18243 Z= 0.282 Chirality : 0.043 0.146 2067 Planarity : 0.004 0.049 2358 Dihedral : 4.722 56.343 1940 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.58 % Allowed : 12.50 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.32 (0.21), residues: 1778 helix: 1.81 (0.20), residues: 726 sheet: -0.93 (0.30), residues: 300 loop : -0.86 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 307 HIS 0.004 0.001 HIS A 44 PHE 0.025 0.001 PHE A 712 TYR 0.017 0.001 TYR A 547 ARG 0.009 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.553 Fit side-chains REVERT: A 307 TRP cc_start: 0.6612 (p-90) cc_final: 0.5939 (p-90) REVERT: A 360 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: B 307 TRP cc_start: 0.6582 (p-90) cc_final: 0.5903 (p-90) REVERT: B 360 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8238 (mt0) outliers start: 20 outliers final: 13 residues processed: 173 average time/residue: 0.2810 time to fit residues: 69.4995 Evaluate side-chains 170 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 0.1980 chunk 146 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13388 Z= 0.284 Angle : 0.602 11.765 18243 Z= 0.303 Chirality : 0.046 0.306 2067 Planarity : 0.004 0.049 2358 Dihedral : 4.829 56.456 1940 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.14 % Allowed : 14.32 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.28 (0.21), residues: 1778 helix: 1.80 (0.20), residues: 724 sheet: -0.92 (0.31), residues: 300 loop : -0.91 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 307 HIS 0.006 0.001 HIS A 44 PHE 0.024 0.002 PHE A 712 TYR 0.016 0.001 TYR B 542 ARG 0.007 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.502 Fit side-chains REVERT: A 307 TRP cc_start: 0.6923 (p-90) cc_final: 0.6085 (p-90) outliers start: 27 outliers final: 20 residues processed: 174 average time/residue: 0.2865 time to fit residues: 71.3986 Evaluate side-chains 170 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 547 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13388 Z= 0.328 Angle : 0.612 11.867 18243 Z= 0.312 Chirality : 0.046 0.360 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.930 57.118 1940 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.29 % Allowed : 15.11 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.19 (0.21), residues: 1778 helix: 1.71 (0.20), residues: 728 sheet: -0.92 (0.30), residues: 320 loop : -0.98 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 307 HIS 0.006 0.001 HIS A 44 PHE 0.027 0.002 PHE B 456 TYR 0.019 0.002 TYR A 547 ARG 0.009 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.405 Fit side-chains REVERT: A 360 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: B 360 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: B 414 MET cc_start: 0.8016 (tmm) cc_final: 0.7728 (tmm) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.2807 time to fit residues: 72.1758 Evaluate side-chains 177 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 107 optimal weight: 0.0570 chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13388 Z= 0.210 Angle : 0.578 12.154 18243 Z= 0.291 Chirality : 0.045 0.369 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.845 58.365 1940 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.14 % Allowed : 16.30 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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 (0.21), residues: 1778 helix: 1.75 (0.20), residues: 724 sheet: -0.85 (0.30), residues: 320 loop : -0.95 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 307 HIS 0.004 0.001 HIS A 44 PHE 0.021 0.001 PHE A 712 TYR 0.017 0.001 TYR A 542 ARG 0.009 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.441 Fit side-chains REVERT: B 414 MET cc_start: 0.7967 (tmm) cc_final: 0.7760 (tmm) REVERT: B 510 VAL cc_start: 0.7914 (p) cc_final: 0.7598 (m) outliers start: 27 outliers final: 24 residues processed: 173 average time/residue: 0.2821 time to fit residues: 69.4296 Evaluate side-chains 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13388 Z= 0.339 Angle : 0.626 11.691 18243 Z= 0.317 Chirality : 0.046 0.369 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.959 57.683 1940 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.77 % Allowed : 16.06 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.19 (0.21), residues: 1778 helix: 1.68 (0.20), residues: 732 sheet: -0.92 (0.30), residues: 320 loop : -0.96 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 307 HIS 0.006 0.001 HIS A 44 PHE 0.029 0.002 PHE B 456 TYR 0.018 0.002 TYR B 481 ARG 0.009 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.542 Fit side-chains outliers start: 35 outliers final: 30 residues processed: 177 average time/residue: 0.2835 time to fit residues: 72.3118 Evaluate side-chains 179 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 164 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 144 optimal weight: 0.0570 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 169 optimal weight: 0.0050 overall best weight: 0.5312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13388 Z= 0.186 Angle : 0.582 12.439 18243 Z= 0.291 Chirality : 0.045 0.384 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.833 59.302 1940 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.22 % Allowed : 17.01 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.27 (0.21), residues: 1778 helix: 1.74 (0.20), residues: 724 sheet: -0.83 (0.30), residues: 320 loop : -0.91 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 307 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE A 712 TYR 0.015 0.001 TYR A 481 ARG 0.010 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.537 Fit side-chains REVERT: B 510 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7597 (m) outliers start: 28 outliers final: 23 residues processed: 177 average time/residue: 0.2846 time to fit residues: 72.2503 Evaluate side-chains 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 14 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13388 Z= 0.258 Angle : 0.609 12.230 18243 Z= 0.306 Chirality : 0.046 0.381 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.884 59.306 1940 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.14 % Allowed : 17.33 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.23 (0.21), residues: 1778 helix: 1.71 (0.20), residues: 724 sheet: -0.89 (0.31), residues: 298 loop : -0.92 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 307 HIS 0.005 0.001 HIS A 44 PHE 0.023 0.002 PHE B 456 TYR 0.016 0.001 TYR B 481 ARG 0.010 0.001 ARG B 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.558 Fit side-chains REVERT: B 510 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7669 (m) outliers start: 27 outliers final: 26 residues processed: 176 average time/residue: 0.2862 time to fit residues: 72.1643 Evaluate side-chains 179 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.3980 chunk 130 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.145063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.120312 restraints weight = 30819.044| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.81 r_work: 0.3720 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13388 Z= 0.282 Angle : 0.622 12.995 18243 Z= 0.312 Chirality : 0.047 0.410 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.917 59.197 1940 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.45 % Allowed : 17.17 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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 (0.21), residues: 1778 helix: 1.68 (0.20), residues: 726 sheet: -0.89 (0.31), residues: 298 loop : -0.94 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 307 HIS 0.005 0.001 HIS A 44 PHE 0.025 0.002 PHE B 456 TYR 0.017 0.001 TYR B 481 ARG 0.010 0.001 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2725.27 seconds wall clock time: 50 minutes 34.43 seconds (3034.43 seconds total)