Starting phenix.real_space_refine on Sat Aug 23 15:29:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t7h_41092/08_2025/8t7h_41092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t7h_41092/08_2025/8t7h_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_41092/08_2025/8t7h_41092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t7h_41092/08_2025/8t7h_41092.map" model { file = "/net/cci-nas-00/data/ceres_data/8t7h_41092/08_2025/8t7h_41092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t7h_41092/08_2025/8t7h_41092.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 7, 'GLU:plan': 15, 'PHE:plan': 10, 'TYR:plan': 7, 'ARG:plan': 9, 'GLN:plan1': 4, 'ASN:plan1': 4, 'HIS:plan': 1} 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: {'ASP:plan': 7, 'GLU:plan': 15, 'PHE:plan': 10, 'TYR:plan': 7, 'ARG:plan': 9, 'GLN:plan1': 4, 'ASN:plan1': 4, 'HIS:plan': 1} 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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: 3.56, per 1000 atoms: 0.27 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: 1.18 Conformation dependent library (CDL) restraints added in 853.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.54 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: 2.64 Time building geometry restraints manager: 1.63 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 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 901)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.880 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- 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 13408 Z= 0.154 Angle : 0.626 13.304 18283 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 465 TYR 0.016 0.001 TYR D 103 PHE 0.017 0.001 PHE B 456 TRP 0.041 0.002 TRP A 307 HIS 0.005 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00345 (13388) covalent geometry : angle 0.62393 (18243) SS BOND : bond 0.00444 ( 20) SS BOND : angle 1.20600 ( 40) hydrogen bonds : bond 0.13211 ( 654) hydrogen bonds : angle 5.13769 ( 1842) *********************** 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 : 0.516 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: 0.1349 time to fit residues: 33.7280 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 7.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.143138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108470 restraints weight = 28980.440| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.74 r_work: 0.3575 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13408 Z= 0.127 Angle : 0.576 12.482 18283 Z= 0.292 Chirality : 0.044 0.232 2067 Planarity : 0.004 0.051 2358 Dihedral : 4.649 51.336 1940 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.47 % Allowed : 6.57 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.21), residues: 1778 helix: 1.74 (0.20), residues: 724 sheet: -0.94 (0.29), residues: 326 loop : -0.81 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 366 TYR 0.014 0.001 TYR B 481 PHE 0.031 0.002 PHE A 712 TRP 0.020 0.001 TRP A 307 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00288 (13388) covalent geometry : angle 0.57433 (18243) SS BOND : bond 0.00351 ( 20) SS BOND : angle 1.12491 ( 40) hydrogen bonds : bond 0.04154 ( 654) hydrogen bonds : angle 4.43747 ( 1842) *********************** 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 166 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.501 Fit side-chains REVERT: B 307 TRP cc_start: 0.7048 (p-90) cc_final: 0.6371 (p-90) REVERT: C 103 TYR cc_start: 0.7711 (m-80) cc_final: 0.6886 (m-80) outliers start: 6 outliers final: 4 residues processed: 161 average time/residue: 0.1419 time to fit residues: 32.2581 Evaluate side-chains 155 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 3 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 chunk 29 optimal weight: 0.0370 chunk 12 optimal weight: 0.0060 chunk 63 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.146813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.121528 restraints weight = 30757.186| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.61 r_work: 0.3771 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13408 Z= 0.101 Angle : 0.533 10.720 18283 Z= 0.270 Chirality : 0.043 0.218 2067 Planarity : 0.004 0.049 2358 Dihedral : 4.508 54.013 1940 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.87 % Allowed : 8.86 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.21), residues: 1778 helix: 1.86 (0.20), residues: 726 sheet: -0.83 (0.30), residues: 300 loop : -0.78 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 55 TYR 0.019 0.001 TYR A 547 PHE 0.034 0.001 PHE A 544 TRP 0.013 0.001 TRP A 557 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00219 (13388) covalent geometry : angle 0.53126 (18243) SS BOND : bond 0.00249 ( 20) SS BOND : angle 1.07887 ( 40) hydrogen bonds : bond 0.03674 ( 654) hydrogen bonds : angle 4.22882 ( 1842) *********************** 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 171 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.503 Fit side-chains REVERT: A 744 LEU cc_start: 0.8793 (tt) cc_final: 0.8518 (mt) REVERT: B 85 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8179 (mt) REVERT: B 307 TRP cc_start: 0.6664 (p-90) cc_final: 0.5965 (p-90) outliers start: 11 outliers final: 9 residues processed: 164 average time/residue: 0.1385 time to fit residues: 32.3657 Evaluate side-chains 159 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN 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 382 ASN 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 177 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 87 optimal weight: 0.0770 chunk 138 optimal weight: 6.9990 chunk 124 optimal weight: 0.0370 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 chunk 53 optimal weight: 0.0000 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.146579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.120776 restraints weight = 30940.243| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.73 r_work: 0.3735 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13408 Z= 0.149 Angle : 0.571 11.639 18283 Z= 0.288 Chirality : 0.044 0.172 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.616 54.799 1940 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.50 % Allowed : 9.97 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1778 helix: 1.82 (0.20), residues: 732 sheet: -0.87 (0.30), residues: 300 loop : -0.79 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 55 TYR 0.015 0.001 TYR A 547 PHE 0.026 0.002 PHE A 712 TRP 0.014 0.001 TRP B 307 HIS 0.004 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00356 (13388) covalent geometry : angle 0.56925 (18243) SS BOND : bond 0.00369 ( 20) SS BOND : angle 1.09369 ( 40) hydrogen bonds : bond 0.03977 ( 654) hydrogen bonds : angle 4.19698 ( 1842) *********************** 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 177 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6958 (p-90) cc_final: 0.6043 (p-90) REVERT: A 744 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8463 (mt) REVERT: B 85 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 307 TRP cc_start: 0.6944 (p-90) cc_final: 0.6107 (p-90) REVERT: B 360 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8363 (mt0) outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.1336 time to fit residues: 32.1246 Evaluate side-chains 163 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 382 ASN Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 744 LEU 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 510 VAL 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 107 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN ** B 157 GLN ** 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 = 0.4367 r_free = 0.4367 target = 0.146239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.121584 restraints weight = 31072.454| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.86 r_work: 0.3684 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13408 Z= 0.150 Angle : 0.579 11.965 18283 Z= 0.291 Chirality : 0.045 0.303 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.672 55.967 1940 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.50 % Allowed : 12.10 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.21), residues: 1778 helix: 1.83 (0.20), residues: 726 sheet: -0.84 (0.31), residues: 300 loop : -0.84 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 55 TYR 0.016 0.001 TYR A 547 PHE 0.025 0.002 PHE A 712 TRP 0.014 0.001 TRP A 557 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00360 (13388) covalent geometry : angle 0.57659 (18243) SS BOND : bond 0.00380 ( 20) SS BOND : angle 1.19162 ( 40) hydrogen bonds : bond 0.03942 ( 654) hydrogen bonds : angle 4.17906 ( 1842) *********************** 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 173 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6904 (p-90) cc_final: 0.6251 (p-90) REVERT: A 360 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8390 (mt0) REVERT: A 744 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 85 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8317 (mt) REVERT: B 307 TRP cc_start: 0.6920 (p-90) cc_final: 0.6371 (p-90) outliers start: 19 outliers final: 12 residues processed: 164 average time/residue: 0.1352 time to fit residues: 31.7339 Evaluate side-chains 166 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 A residue 744 LEU 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 510 VAL 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 103 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 171 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.145144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.120286 restraints weight = 30740.671| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.86 r_work: 0.3652 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13408 Z= 0.202 Angle : 0.620 11.944 18283 Z= 0.313 Chirality : 0.047 0.364 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.822 56.311 1940 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.82 % Allowed : 13.61 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.21), residues: 1778 helix: 1.71 (0.20), residues: 734 sheet: -0.86 (0.31), residues: 300 loop : -0.87 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 55 TYR 0.017 0.001 TYR A 481 PHE 0.027 0.002 PHE B 456 TRP 0.015 0.002 TRP B 307 HIS 0.007 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00495 (13388) covalent geometry : angle 0.61764 (18243) SS BOND : bond 0.00477 ( 20) SS BOND : angle 1.22006 ( 40) hydrogen bonds : bond 0.04273 ( 654) hydrogen bonds : angle 4.23758 ( 1842) *********************** 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 180 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7102 (p-90) cc_final: 0.6416 (p-90) REVERT: A 542 TYR cc_start: 0.5108 (p90) cc_final: 0.4905 (p90) REVERT: B 307 TRP cc_start: 0.7059 (p-90) cc_final: 0.6402 (p-90) outliers start: 23 outliers final: 16 residues processed: 170 average time/residue: 0.1237 time to fit residues: 30.0909 Evaluate side-chains 168 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET 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 382 ASN Chi-restraints excluded: chain A residue 731 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 510 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.146136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.119658 restraints weight = 30803.886| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.69 r_work: 0.3670 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13408 Z= 0.133 Angle : 0.579 11.792 18283 Z= 0.290 Chirality : 0.045 0.369 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.758 57.975 1940 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.74 % Allowed : 14.87 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.21), residues: 1778 helix: 1.73 (0.20), residues: 726 sheet: -0.80 (0.31), residues: 300 loop : -0.86 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 55 TYR 0.015 0.001 TYR A 481 PHE 0.022 0.002 PHE A 712 TRP 0.017 0.001 TRP A 557 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00313 (13388) covalent geometry : angle 0.57680 (18243) SS BOND : bond 0.00337 ( 20) SS BOND : angle 1.16553 ( 40) hydrogen bonds : bond 0.03845 ( 654) hydrogen bonds : angle 4.16581 ( 1842) *********************** 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: 22 poor density : 160 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6968 (p-90) cc_final: 0.6271 (p-90) REVERT: A 542 TYR cc_start: 0.5488 (p90) cc_final: 0.5277 (p90) REVERT: A 744 LEU cc_start: 0.8766 (tt) cc_final: 0.8495 (mt) REVERT: B 307 TRP cc_start: 0.6962 (p-90) cc_final: 0.6286 (p-90) REVERT: B 510 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7691 (m) outliers start: 22 outliers final: 15 residues processed: 172 average time/residue: 0.1131 time to fit residues: 28.0234 Evaluate side-chains 173 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 731 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 499 VAL Chi-restraints excluded: chain B residue 510 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 108 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 198 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.137750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.111570 restraints weight = 29526.847| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.87 r_work: 0.3566 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.125 13408 Z= 0.602 Angle : 0.979 15.410 18283 Z= 0.506 Chirality : 0.064 0.373 2067 Planarity : 0.007 0.079 2358 Dihedral : 5.822 55.595 1940 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.29 % Allowed : 16.69 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.20), residues: 1778 helix: 1.12 (0.20), residues: 732 sheet: -1.15 (0.29), residues: 320 loop : -1.51 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 68 TYR 0.034 0.003 TYR B 64 PHE 0.085 0.005 PHE B 456 TRP 0.035 0.004 TRP B 307 HIS 0.018 0.003 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.01491 (13388) covalent geometry : angle 0.97534 (18243) SS BOND : bond 0.01205 ( 20) SS BOND : angle 2.12965 ( 40) hydrogen bonds : bond 0.06415 ( 654) hydrogen bonds : angle 4.80442 ( 1842) *********************** 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 186 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 604 TYR cc_start: 0.8064 (m-80) cc_final: 0.7757 (m-80) REVERT: B 273 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8056 (p) REVERT: B 629 TYR cc_start: 0.7505 (m-10) cc_final: 0.7257 (m-10) REVERT: D 103 TYR cc_start: 0.7920 (m-80) cc_final: 0.7329 (m-80) outliers start: 29 outliers final: 24 residues processed: 179 average time/residue: 0.1315 time to fit residues: 33.6166 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 : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET 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 535 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 27 VAL 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 214 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP 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 535 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 59 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 198 GLN A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.144700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.118264 restraints weight = 31037.885| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.70 r_work: 0.3703 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13408 Z= 0.148 Angle : 0.623 11.992 18283 Z= 0.316 Chirality : 0.045 0.361 2067 Planarity : 0.004 0.049 2358 Dihedral : 5.150 56.527 1940 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.14 % Allowed : 17.56 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.20), residues: 1778 helix: 1.50 (0.20), residues: 726 sheet: -1.07 (0.29), residues: 320 loop : -1.29 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 366 TYR 0.021 0.001 TYR A 542 PHE 0.019 0.002 PHE B 456 TRP 0.019 0.002 TRP A 557 HIS 0.006 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00348 (13388) covalent geometry : angle 0.61996 (18243) SS BOND : bond 0.00440 ( 20) SS BOND : angle 1.36744 ( 40) hydrogen bonds : bond 0.04162 ( 654) hydrogen bonds : angle 4.35673 ( 1842) *********************** 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 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: B 817 MET cc_start: 0.8290 (ppp) cc_final: 0.7962 (ppp) outliers start: 27 outliers final: 18 residues processed: 174 average time/residue: 0.1291 time to fit residues: 32.3236 Evaluate side-chains 173 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 409 TYR Chi-restraints excluded: chain A residue 547 TYR 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 301 LEU Chi-restraints excluded: chain B residue 336 TRP 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 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 34 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 chunk 108 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.142527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108367 restraints weight = 29901.941| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.09 r_work: 0.3571 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13408 Z= 0.149 Angle : 0.605 11.917 18283 Z= 0.305 Chirality : 0.046 0.363 2067 Planarity : 0.004 0.048 2358 Dihedral : 4.952 57.142 1940 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.58 % Allowed : 18.12 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.21), residues: 1778 helix: 1.63 (0.20), residues: 724 sheet: -0.97 (0.30), residues: 318 loop : -1.08 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 55 TYR 0.017 0.001 TYR B 481 PHE 0.022 0.002 PHE A 456 TRP 0.019 0.002 TRP D 38 HIS 0.005 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00355 (13388) covalent geometry : angle 0.60285 (18243) SS BOND : bond 0.00398 ( 20) SS BOND : angle 1.20651 ( 40) hydrogen bonds : bond 0.04010 ( 654) hydrogen bonds : angle 4.20987 ( 1842) ********************** 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 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: B 510 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7664 (m) REVERT: B 817 MET cc_start: 0.8467 (ppp) cc_final: 0.8120 (ppp) outliers start: 20 outliers final: 15 residues processed: 170 average time/residue: 0.1423 time to fit residues: 34.5224 Evaluate side-chains 169 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 547 TYR 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 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 499 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 51 optimal weight: 0.0980 chunk 46 optimal weight: 0.0030 chunk 166 optimal weight: 10.0000 chunk 102 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 overall best weight: 0.2168 ------------------------------------------------------------------------------- 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 C 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.144304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.117579 restraints weight = 29998.562| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.87 r_work: 0.3734 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13408 Z= 0.101 Angle : 0.573 12.264 18283 Z= 0.285 Chirality : 0.044 0.363 2067 Planarity : 0.004 0.049 2358 Dihedral : 4.749 59.999 1940 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.27 % Allowed : 18.75 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.21), residues: 1778 helix: 1.79 (0.20), residues: 716 sheet: -0.86 (0.31), residues: 298 loop : -0.94 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 55 TYR 0.015 0.001 TYR A 723 PHE 0.017 0.001 PHE A 712 TRP 0.027 0.002 TRP A 557 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00220 (13388) covalent geometry : angle 0.57132 (18243) SS BOND : bond 0.00250 ( 20) SS BOND : angle 1.05077 ( 40) hydrogen bonds : bond 0.03410 ( 654) hydrogen bonds : angle 4.07926 ( 1842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.68 seconds wall clock time: 67 minutes 8.89 seconds (4028.89 seconds total)