Starting phenix.real_space_refine on Thu Feb 5 00:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ugq_64143/02_2026/9ugq_64143_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ugq_64143/02_2026/9ugq_64143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ugq_64143/02_2026/9ugq_64143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ugq_64143/02_2026/9ugq_64143.map" model { file = "/net/cci-nas-00/data/ceres_data/9ugq_64143/02_2026/9ugq_64143_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ugq_64143/02_2026/9ugq_64143_trim.cif" } resolution = 2.96 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= -0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 8814 2.51 5 N 2274 2.21 5 O 2503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13648 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6730 Classifications: {'peptide': 852} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 27, 'TRANS': 824} Chain breaks: 2 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 6755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 6755 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 28, 'TRANS': 836} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'GLU:plan': 17, 'ASN:plan1': 8, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 99 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.23, per 1000 atoms: 0.24 Number of scatterers: 13648 At special positions: 0 Unit cell: (115.54, 99.64, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 O 2503 8.00 N 2274 7.00 C 8814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.31 Conformation dependent library (CDL) restraints added in 550.4 milliseconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 45.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 69 through 84 removed outlier: 3.944A pdb=" N GLU A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.579A pdb=" N LYS A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 327 through 349 removed outlier: 3.547A pdb=" N LYS A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 419 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.544A pdb=" N SER A 426 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.940A pdb=" N LYS A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 438 " --> pdb=" O GLN A 434 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.725A pdb=" N ILE A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.958A pdb=" N ILE A 478 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 479 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 516 removed outlier: 3.638A pdb=" N ILE A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.945A pdb=" N LEU A 529 " --> pdb=" O TYR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 554 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.556A pdb=" N THR A 590 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 removed outlier: 5.596A pdb=" N SER A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 641 removed outlier: 3.831A pdb=" N ILE A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.805A pdb=" N ILE A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 724 removed outlier: 3.735A pdb=" N LEU A 712 " --> pdb=" O ASN A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 4.014A pdb=" N LEU A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.790A pdb=" N LYS A 777 " --> pdb=" O HIS A 773 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 802 removed outlier: 3.562A pdb=" N LEU A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 848 through 861 removed outlier: 3.503A pdb=" N ILE A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 70 through 82 removed outlier: 3.746A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 265 through 278 removed outlier: 3.912A pdb=" N LYS B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 327 through 349 removed outlier: 3.593A pdb=" N ARG B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 419 removed outlier: 3.912A pdb=" N ASP B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 446 removed outlier: 3.935A pdb=" N LYS B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 438 " --> pdb=" O GLN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 removed outlier: 3.648A pdb=" N ILE B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.629A pdb=" N LYS B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 478 " --> pdb=" O GLU B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 478' Processing helix chain 'B' and resid 490 through 516 Processing helix chain 'B' and resid 525 through 529 removed outlier: 3.762A pdb=" N LEU B 529 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 554 removed outlier: 3.673A pdb=" N ILE B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 586 through 598 removed outlier: 3.576A pdb=" N THR B 590 " --> pdb=" O GLY B 586 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 617 removed outlier: 5.711A pdb=" N SER B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 641 removed outlier: 4.161A pdb=" N ILE B 630 " --> pdb=" O GLY B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.629A pdb=" N ALA B 684 " --> pdb=" O PRO B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 691 through 706 removed outlier: 3.821A pdb=" N ILE B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 701 " --> pdb=" O TRP B 697 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 703 " --> pdb=" O PHE B 699 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 723 removed outlier: 3.689A pdb=" N LEU B 712 " --> pdb=" O ASN B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.693A pdb=" N LEU B 753 " --> pdb=" O GLY B 749 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 773 removed outlier: 3.934A pdb=" N HIS B 773 " --> pdb=" O ASN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 802 Processing helix chain 'B' and resid 808 through 821 removed outlier: 3.623A pdb=" N GLU B 815 " --> pdb=" O GLN B 811 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 818 " --> pdb=" O LYS B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 862 removed outlier: 3.861A pdb=" N ILE B 852 " --> pdb=" O GLY B 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 9 through 11 No H-bonds generated for 'chain 'E' and resid 9 through 11' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.522A pdb=" N THR A 14 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 removed outlier: 4.117A pdb=" N VAL A 87 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 229 removed outlier: 7.228A pdb=" N ASN A 236 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA A 225 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 234 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ARG A 227 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY A 232 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY A 233 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 237 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 481 Processing sheet with id=AA6, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.540A pdb=" N GLU A 727 " --> pdb=" O GLN A 735 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 735 " --> pdb=" O GLU A 727 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.637A pdb=" N THR B 14 " --> pdb=" O SER B 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.693A pdb=" N VAL B 87 " --> pdb=" O TYR B 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AB1, first strand: chain 'B' and resid 220 through 227 removed outlier: 5.167A pdb=" N ILE B 222 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR B 238 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 224 " --> pdb=" O ASN B 236 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 234 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 297 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 292 " --> pdb=" O HIS B 296 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE B 298 " --> pdb=" O TYR B 290 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR B 290 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY B 300 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AB3, first strand: chain 'B' and resid 726 through 728 removed outlier: 4.186A pdb=" N TYR B 736 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 824 through 827 585 hydrogen bonds defined for protein. 1701 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: 2.33 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4989 1.38 - 1.55: 8887 1.55 - 1.72: 21 1.72 - 1.90: 68 1.90 - 2.07: 2 Bond restraints: 13967 Sorted by residual: bond pdb=" C4 AGS A 901 " pdb=" N9 AGS A 901 " ideal model delta sigma weight residual 1.374 1.301 0.073 1.00e-02 1.00e+04 5.36e+01 bond pdb=" C4 AGS B 901 " pdb=" C5 AGS B 901 " ideal model delta sigma weight residual 1.386 1.449 -0.063 1.00e-02 1.00e+04 4.00e+01 bond pdb=" C5 AGS B 901 " pdb=" N7 AGS B 901 " ideal model delta sigma weight residual 1.387 1.325 0.062 1.00e-02 1.00e+04 3.84e+01 bond pdb=" C4 AGS B 901 " pdb=" N9 AGS B 901 " ideal model delta sigma weight residual 1.374 1.313 0.061 1.00e-02 1.00e+04 3.76e+01 bond pdb=" PG AGS A 901 " pdb=" S1G AGS A 901 " ideal model delta sigma weight residual 1.949 2.068 -0.119 2.00e-02 2.50e+03 3.53e+01 ... (remaining 13962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 18453 2.56 - 5.12: 407 5.12 - 7.68: 62 7.68 - 10.24: 19 10.24 - 12.80: 2 Bond angle restraints: 18943 Sorted by residual: angle pdb=" C4 AGS A 901 " pdb=" N9 AGS A 901 " pdb=" C8 AGS A 901 " ideal model delta sigma weight residual 105.70 110.55 -4.85 4.55e-01 4.83e+00 1.13e+02 angle pdb=" C5 AGS B 901 " pdb=" C4 AGS B 901 " pdb=" N3 AGS B 901 " ideal model delta sigma weight residual 126.80 119.20 7.60 7.41e-01 1.82e+00 1.05e+02 angle pdb=" C5 AGS A 901 " pdb=" N7 AGS A 901 " pdb=" C8 AGS A 901 " ideal model delta sigma weight residual 103.67 107.51 -3.84 4.26e-01 5.51e+00 8.14e+01 angle pdb=" C4 AGS A 901 " pdb=" C5 AGS A 901 " pdb=" N7 AGS A 901 " ideal model delta sigma weight residual 110.73 106.93 3.80 4.52e-01 4.89e+00 7.06e+01 angle pdb=" C5 AGS B 901 " pdb=" N7 AGS B 901 " pdb=" C8 AGS B 901 " ideal model delta sigma weight residual 103.67 107.20 -3.53 4.26e-01 5.51e+00 6.85e+01 ... (remaining 18938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 7902 27.46 - 54.92: 320 54.92 - 82.38: 18 82.38 - 109.84: 8 109.84 - 137.30: 2 Dihedral angle restraints: 8250 sinusoidal: 3194 harmonic: 5056 Sorted by residual: dihedral pdb=" CA VAL B 343 " pdb=" C VAL B 343 " pdb=" N GLU B 344 " pdb=" CA GLU B 344 " ideal model delta harmonic sigma weight residual 180.00 138.55 41.45 0 5.00e+00 4.00e-02 6.87e+01 dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 140.41 39.59 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA ASN B 381 " pdb=" C ASN B 381 " pdb=" N SER B 382 " pdb=" CA SER B 382 " ideal model delta harmonic sigma weight residual 180.00 148.70 31.30 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 8247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1838 0.076 - 0.152: 245 0.152 - 0.229: 14 0.229 - 0.305: 4 0.305 - 0.381: 2 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CB VAL B 779 " pdb=" CA VAL B 779 " pdb=" CG1 VAL B 779 " pdb=" CG2 VAL B 779 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE A 845 " pdb=" CA ILE A 845 " pdb=" CG1 ILE A 845 " pdb=" CG2 ILE A 845 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL B 343 " pdb=" CA VAL B 343 " pdb=" CG1 VAL B 343 " pdb=" CG2 VAL B 343 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 2100 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 580 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO B 581 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 48 " 0.051 5.00e-02 4.00e+02 7.84e-02 9.82e+00 pdb=" N PRO A 49 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 611 " -0.009 2.00e-02 2.50e+03 2.03e-02 8.27e+00 pdb=" CG TYR B 611 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 611 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 611 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 611 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 611 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 611 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 611 " 0.003 2.00e-02 2.50e+03 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3046 2.79 - 3.31: 11904 3.31 - 3.84: 23406 3.84 - 4.37: 27731 4.37 - 4.90: 47850 Nonbonded interactions: 113937 Sorted by model distance: nonbonded pdb=" OH TYR B 328 " pdb=" O LEU B 417 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR A 842 " pdb=" O THR A 847 " model vdw 2.265 3.040 nonbonded pdb=" O GLY A 534 " pdb=" OG SER A 538 " model vdw 2.299 3.040 nonbonded pdb=" O LYS B 325 " pdb=" OH TYR B 448 " model vdw 2.306 3.040 nonbonded pdb=" O SER B 780 " pdb=" OG SER B 780 " model vdw 2.312 3.040 ... (remaining 113932 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 2 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 161 or (resid 162 through 173 an \ d (name N or name CA or name C or name O or name CB )) or resid 174 or (resid 17 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 176 or (resi \ d 177 through 179 and (name N or name CA or name C or name O or name CB )) or re \ sid 180 through 239 or (resid 240 through 245 and (name N or name CA or name C o \ r name O or name CB )) or resid 246 through 322 or (resid 323 and (name N or nam \ e CA or name C or name O or name CB )) or resid 324 through 325 or (resid 326 th \ rough 327 and (name N or name CA or name C or name O or name CB )) or resid 328 \ through 388 or (resid 389 through 391 and (name N or name CA or name C or name O \ or name CB )) or resid 392 through 444 or (resid 445 and (name N or name CA or \ name C or name O or name CB )) or resid 446 through 483 or (resid 484 and (name \ N or name CA or name C or name O or name CB )) or resid 485 through 517 or (resi \ d 518 and (name N or name CA or name C or name O or name CB )) or resid 519 thro \ ugh 554 or (resid 555 through 557 and (name N or name CA or name C or name O or \ name CB )) or resid 558 or (resid 559 and (name N or name CA or name C or name O \ or name CB )) or resid 560 through 561 or (resid 562 and (name N or name CA or \ name C or name O or name CB )) or resid 563 through 565 or (resid 566 and (name \ N or name CA or name C or name O or name CB )) or resid 567 through 569 or (resi \ d 570 and (name N or name CA or name C or name O or name CB )) or resid 571 thro \ ugh 574 or (resid 575 and (name N or name CA or name C or name O or name CB )) o \ r resid 576 through 578 or (resid 579 and (name N or name CA or name C or name O \ or name CB )) or resid 580 through 598 or (resid 599 and (name N or name CA or \ name C or name O or name CB )) or resid 600 through 615 or (resid 616 and (name \ N or name CA or name C or name O or name CB )) or resid 617 through 655 or (resi \ d 656 and (name N or name CA or name C or name O or name CB )) or resid 657 thro \ ugh 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) o \ r resid 665 through 716 or (resid 717 through 718 and (name N or name CA or name \ C or name O or name CB )) or resid 719 or (resid 720 and (name N or name CA or \ name C or name O or name CB )) or resid 721 through 760 or (resid 761 through 76 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 763 through \ 764 or (resid 765 and (name N or name CA or name C or name O or name CB )) or re \ sid 766 through 803 or (resid 804 and (name N or name CA or name C or name O or \ name CB )) or resid 805 or (resid 806 through 807 and (name N or name CA or name \ C or name O or name CB )) or resid 808 through 870 or (resid 871 and (name N or \ name CA or name C or name O or name CB )) or resid 901 through 902)) selection = (chain 'B' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 7 or (resid 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 22 or (resid 23 and (name N \ or name CA or name C or name O or name CB )) or resid 24 through 163 or resid 17 \ 4 through 177 or (resid 178 through 179 and (name N or name CA or name C or name \ O or name CB )) or resid 180 through 183 or (resid 184 and (name N or name CA o \ r name C or name O or name CB )) or resid 185 through 194 or (resid 195 and (nam \ e N or name CA or name C or name O or name CB )) or resid 196 through 203 or (re \ sid 204 and (name N or name CA or name C or name O or name CB )) or resid 205 th \ rough 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) \ or resid 218 through 242 or (resid 243 through 245 and (name N or name CA or na \ me C or name O or name CB )) or resid 246 through 254 or (resid 255 and (name N \ or name CA or name C or name O or name CB )) or resid 256 through 279 or (resid \ 280 and (name N or name CA or name C or name O or name CB )) or resid 281 throug \ h 343 or (resid 344 and (name N or name CA or name C or name O or name CB )) or \ resid 345 through 367 or (resid 368 and (name N or name CA or name C or name O o \ r name CB )) or resid 369 through 385 or (resid 386 and (name N or name CA or na \ me C or name O or name CB )) or resid 387 through 600 or (resid 601 and (name N \ or name CA or name C or name O or name CB )) or resid 602 through 642 or (resid \ 643 and (name N or name CA or name C or name O or name CB )) or resid 644 throug \ h 658 or (resid 659 and (name N or name CA or name C or name O or name CB )) or \ resid 660 through 666 or (resid 667 and (name N or name CA or name C or name O o \ r name CB )) or resid 668 through 669 or (resid 670 and (name N or name CA or na \ me C or name O or name CB )) or resid 671 through 682 or (resid 683 through 684 \ and (name N or name CA or name C or name O or name CB )) or resid 685 through 70 \ 6 or (resid 707 and (name N or name CA or name C or name O or name CB )) or resi \ d 708 through 902)) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.220 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.005 0.119 13967 Z= 0.280 Angle : 0.915 12.798 18943 Z= 0.536 Chirality : 0.052 0.381 2103 Planarity : 0.006 0.122 2380 Dihedral : 14.212 137.302 5016 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.33 % Favored : 91.98 % Rotamer: Outliers : 0.21 % Allowed : 0.35 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 are not related in a simple way. whole: -2.63 (0.17), residues: 1720 helix: -1.35 (0.16), residues: 729 sheet: -0.70 (0.47), residues: 130 loop : -2.27 (0.18), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 252 TYR 0.046 0.002 TYR B 611 PHE 0.025 0.002 PHE B 763 TRP 0.029 0.002 TRP A 289 HIS 0.008 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00505 (13967) covalent geometry : angle 0.91459 (18943) hydrogen bonds : bond 0.18034 ( 585) hydrogen bonds : angle 7.06825 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 0.517 Fit side-chains REVERT: A 727 GLU cc_start: 0.6868 (pt0) cc_final: 0.6347 (mt-10) REVERT: B 8 LYS cc_start: 0.7475 (tptm) cc_final: 0.7196 (tmmt) REVERT: B 99 LEU cc_start: 0.8263 (mm) cc_final: 0.7912 (tt) REVERT: B 547 LYS cc_start: 0.7794 (tttp) cc_final: 0.7320 (tmtt) REVERT: B 551 ASP cc_start: 0.7467 (m-30) cc_final: 0.6741 (t0) REVERT: B 567 LEU cc_start: 0.7550 (mm) cc_final: 0.7166 (tp) REVERT: E 11 MET cc_start: 0.8060 (mtp) cc_final: 0.7675 (mtp) outliers start: 3 outliers final: 0 residues processed: 230 average time/residue: 0.5180 time to fit residues: 131.9056 Evaluate side-chains 169 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 236 ASN A 357 HIS B 101 ASN B 433 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.183489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151599 restraints weight = 15540.106| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.04 r_work: 0.3638 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13967 Z= 0.128 Angle : 0.570 8.297 18943 Z= 0.301 Chirality : 0.041 0.176 2103 Planarity : 0.005 0.128 2380 Dihedral : 7.929 140.899 1926 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.57 % Favored : 92.91 % Rotamer: Outliers : 1.91 % Allowed : 9.24 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -1.49 (0.19), residues: 1720 helix: 0.10 (0.19), residues: 738 sheet: -0.65 (0.46), residues: 130 loop : -2.09 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.027 0.001 TYR A 611 PHE 0.026 0.001 PHE A 202 TRP 0.012 0.001 TRP A 289 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00298 (13967) covalent geometry : angle 0.56975 (18943) hydrogen bonds : bond 0.03975 ( 585) hydrogen bonds : angle 4.88882 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.570 Fit side-chains REVERT: A 227 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7353 (ttp80) REVERT: A 252 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7366 (mtm110) REVERT: A 321 ASP cc_start: 0.7764 (m-30) cc_final: 0.7519 (t0) REVERT: A 323 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8100 (pttm) REVERT: A 337 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7466 (mmpt) REVERT: A 454 LYS cc_start: 0.7891 (tppt) cc_final: 0.7667 (tppt) REVERT: A 727 GLU cc_start: 0.7360 (pt0) cc_final: 0.6609 (mt-10) REVERT: B 8 LYS cc_start: 0.7753 (tptm) cc_final: 0.7268 (tmmt) REVERT: B 547 LYS cc_start: 0.7991 (tttp) cc_final: 0.7128 (tttm) REVERT: B 551 ASP cc_start: 0.7910 (m-30) cc_final: 0.7586 (m-30) REVERT: B 692 HIS cc_start: 0.8410 (m-70) cc_final: 0.7993 (m-70) REVERT: E 11 MET cc_start: 0.8278 (mtp) cc_final: 0.7894 (mtp) outliers start: 27 outliers final: 8 residues processed: 203 average time/residue: 0.5571 time to fit residues: 124.7943 Evaluate side-chains 169 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 785 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 43 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 415 HIS B 811 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.180413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148220 restraints weight = 15648.408| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.05 r_work: 0.3602 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13967 Z= 0.147 Angle : 0.568 7.907 18943 Z= 0.296 Chirality : 0.042 0.180 2103 Planarity : 0.005 0.125 2380 Dihedral : 7.808 136.245 1926 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.57 % Favored : 92.91 % Rotamer: Outliers : 2.75 % Allowed : 12.07 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -1.00 (0.20), residues: 1720 helix: 0.72 (0.19), residues: 738 sheet: -0.67 (0.45), residues: 132 loop : -2.00 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 161 TYR 0.020 0.001 TYR B 624 PHE 0.034 0.001 PHE A 202 TRP 0.008 0.001 TRP A 289 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00354 (13967) covalent geometry : angle 0.56764 (18943) hydrogen bonds : bond 0.03798 ( 585) hydrogen bonds : angle 4.60136 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.533 Fit side-chains REVERT: A 192 ILE cc_start: 0.7283 (mt) cc_final: 0.6958 (tt) REVERT: A 321 ASP cc_start: 0.7765 (m-30) cc_final: 0.7504 (t0) REVERT: A 376 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: A 727 GLU cc_start: 0.7364 (pt0) cc_final: 0.6593 (mt-10) REVERT: B 8 LYS cc_start: 0.7929 (tptm) cc_final: 0.7443 (tmmt) REVERT: B 475 GLU cc_start: 0.8088 (tp30) cc_final: 0.7862 (tp30) REVERT: B 514 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7469 (ttp-170) REVERT: B 547 LYS cc_start: 0.7957 (tttp) cc_final: 0.7079 (tttm) REVERT: B 551 ASP cc_start: 0.7827 (m-30) cc_final: 0.7506 (m-30) REVERT: B 692 HIS cc_start: 0.8367 (m-70) cc_final: 0.8074 (m-70) REVERT: E 11 MET cc_start: 0.8265 (mtp) cc_final: 0.7866 (mtp) outliers start: 39 outliers final: 18 residues processed: 204 average time/residue: 0.5104 time to fit residues: 116.2997 Evaluate side-chains 179 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 825 CYS Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN B 101 ASN B 735 GLN B 811 GLN E 9 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.175031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142458 restraints weight = 15656.901| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.02 r_work: 0.3511 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13967 Z= 0.228 Angle : 0.634 9.451 18943 Z= 0.328 Chirality : 0.045 0.186 2103 Planarity : 0.005 0.121 2380 Dihedral : 7.914 135.341 1926 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.03 % Favored : 92.44 % Rotamer: Outliers : 4.09 % Allowed : 12.00 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -0.91 (0.20), residues: 1720 helix: 0.82 (0.19), residues: 747 sheet: -0.90 (0.44), residues: 139 loop : -1.94 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 252 TYR 0.030 0.002 TYR A 611 PHE 0.036 0.002 PHE A 202 TRP 0.010 0.002 TRP A 44 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00558 (13967) covalent geometry : angle 0.63438 (18943) hydrogen bonds : bond 0.04159 ( 585) hydrogen bonds : angle 4.62148 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 0.519 Fit side-chains REVERT: A 37 GLU cc_start: 0.7984 (tt0) cc_final: 0.7718 (tt0) REVERT: A 252 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7409 (mtm110) REVERT: A 321 ASP cc_start: 0.7777 (m-30) cc_final: 0.7531 (t0) REVERT: A 376 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: A 644 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5869 (pt) REVERT: A 668 PHE cc_start: 0.7548 (m-10) cc_final: 0.7291 (m-10) REVERT: A 727 GLU cc_start: 0.7362 (pt0) cc_final: 0.6680 (mt-10) REVERT: A 732 ASP cc_start: 0.7292 (m-30) cc_final: 0.6848 (m-30) REVERT: B 8 LYS cc_start: 0.7955 (tptm) cc_final: 0.7517 (tmmt) REVERT: B 223 GLU cc_start: 0.7925 (mp0) cc_final: 0.7626 (mp0) REVERT: B 315 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8145 (mptt) REVERT: B 361 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8734 (mp) REVERT: B 383 LYS cc_start: 0.7856 (tppt) cc_final: 0.7467 (mmmm) REVERT: B 475 GLU cc_start: 0.8154 (tp30) cc_final: 0.7887 (tp30) REVERT: B 514 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7562 (ttp-170) REVERT: B 547 LYS cc_start: 0.8013 (tttp) cc_final: 0.7207 (tttm) REVERT: B 551 ASP cc_start: 0.7816 (m-30) cc_final: 0.7470 (m-30) REVERT: B 692 HIS cc_start: 0.8408 (m-70) cc_final: 0.8093 (m-70) REVERT: B 736 TYR cc_start: 0.6574 (t80) cc_final: 0.6302 (t80) REVERT: B 793 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7496 (tmt) REVERT: E 1 MET cc_start: 0.6801 (mpp) cc_final: 0.6549 (ptp) REVERT: E 11 MET cc_start: 0.8227 (mtp) cc_final: 0.7979 (mtp) outliers start: 58 outliers final: 29 residues processed: 219 average time/residue: 0.5211 time to fit residues: 127.4621 Evaluate side-chains 193 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 825 CYS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 65 optimal weight: 9.9990 chunk 95 optimal weight: 0.0980 chunk 170 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 116 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 811 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146510 restraints weight = 15818.274| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.03 r_work: 0.3580 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13967 Z= 0.117 Angle : 0.559 11.737 18943 Z= 0.291 Chirality : 0.041 0.215 2103 Planarity : 0.004 0.119 2380 Dihedral : 7.727 133.939 1926 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.22 % Favored : 93.26 % Rotamer: Outliers : 3.60 % Allowed : 13.76 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -0.53 (0.20), residues: 1720 helix: 1.27 (0.20), residues: 739 sheet: -0.75 (0.44), residues: 139 loop : -1.85 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 161 TYR 0.013 0.001 TYR B 624 PHE 0.039 0.001 PHE A 202 TRP 0.008 0.001 TRP A 289 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00278 (13967) covalent geometry : angle 0.55881 (18943) hydrogen bonds : bond 0.03451 ( 585) hydrogen bonds : angle 4.43154 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.550 Fit side-chains REVERT: A 37 GLU cc_start: 0.7604 (tt0) cc_final: 0.7349 (tt0) REVERT: A 120 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7873 (mm) REVERT: A 376 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7523 (mt0) REVERT: A 606 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7348 (mp) REVERT: A 727 GLU cc_start: 0.7438 (pt0) cc_final: 0.6650 (mt-10) REVERT: A 732 ASP cc_start: 0.7361 (m-30) cc_final: 0.6962 (m-30) REVERT: B 8 LYS cc_start: 0.7881 (tptm) cc_final: 0.7420 (tmmt) REVERT: B 146 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7837 (ttt90) REVERT: B 223 GLU cc_start: 0.7857 (mp0) cc_final: 0.7654 (mp0) REVERT: B 315 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8005 (mtpm) REVERT: B 361 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 383 LYS cc_start: 0.7813 (tppt) cc_final: 0.7335 (mmmm) REVERT: B 475 GLU cc_start: 0.8153 (tp30) cc_final: 0.7890 (tp30) REVERT: B 514 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7417 (ttp-170) REVERT: B 547 LYS cc_start: 0.7876 (tttp) cc_final: 0.7011 (tttm) REVERT: B 551 ASP cc_start: 0.7842 (m-30) cc_final: 0.7432 (m-30) REVERT: B 692 HIS cc_start: 0.8313 (m-70) cc_final: 0.8059 (m-70) REVERT: B 727 GLU cc_start: 0.7507 (pp20) cc_final: 0.7085 (pp20) REVERT: B 736 TYR cc_start: 0.6453 (t80) cc_final: 0.6186 (t80) REVERT: B 821 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: E 1 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6544 (ptp) outliers start: 51 outliers final: 20 residues processed: 202 average time/residue: 0.4902 time to fit residues: 111.0063 Evaluate side-chains 183 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 825 CYS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 157 optimal weight: 4.9990 chunk 53 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 791 ASN B 811 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143469 restraints weight = 15665.509| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.04 r_work: 0.3548 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13967 Z= 0.181 Angle : 0.599 12.026 18943 Z= 0.308 Chirality : 0.043 0.202 2103 Planarity : 0.005 0.118 2380 Dihedral : 7.751 134.088 1926 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.86 % Favored : 92.62 % Rotamer: Outliers : 3.60 % Allowed : 15.10 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -0.55 (0.20), residues: 1720 helix: 1.22 (0.19), residues: 745 sheet: -0.68 (0.45), residues: 139 loop : -1.87 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 161 TYR 0.028 0.002 TYR A 611 PHE 0.040 0.002 PHE A 202 TRP 0.006 0.001 TRP A 44 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00445 (13967) covalent geometry : angle 0.59863 (18943) hydrogen bonds : bond 0.03755 ( 585) hydrogen bonds : angle 4.43546 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 120 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 376 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: A 606 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7365 (mp) REVERT: A 727 GLU cc_start: 0.7436 (pt0) cc_final: 0.6668 (mt-10) REVERT: A 732 ASP cc_start: 0.7365 (m-30) cc_final: 0.7000 (m-30) REVERT: B 8 LYS cc_start: 0.7918 (tptm) cc_final: 0.7463 (tmmt) REVERT: B 223 GLU cc_start: 0.7890 (mp0) cc_final: 0.7675 (mp0) REVERT: B 315 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8067 (mptt) REVERT: B 361 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8721 (mp) REVERT: B 383 LYS cc_start: 0.7877 (tppt) cc_final: 0.7381 (mmmm) REVERT: B 475 GLU cc_start: 0.8177 (tp30) cc_final: 0.7940 (tp30) REVERT: B 514 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7520 (ttp-170) REVERT: B 547 LYS cc_start: 0.7958 (tttp) cc_final: 0.7085 (tttm) REVERT: B 551 ASP cc_start: 0.7803 (m-30) cc_final: 0.7386 (m-30) REVERT: B 692 HIS cc_start: 0.8292 (m-70) cc_final: 0.8075 (m-70) REVERT: B 727 GLU cc_start: 0.7486 (pp20) cc_final: 0.7088 (pp20) REVERT: B 736 TYR cc_start: 0.6615 (t80) cc_final: 0.6398 (t80) REVERT: B 793 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7463 (tmt) REVERT: B 821 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: E 1 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6629 (ptp) outliers start: 51 outliers final: 23 residues processed: 193 average time/residue: 0.5135 time to fit residues: 110.5573 Evaluate side-chains 181 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 825 CYS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 823 TYR Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN B 811 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.175591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143089 restraints weight = 15743.622| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.04 r_work: 0.3518 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13967 Z= 0.185 Angle : 0.605 12.355 18943 Z= 0.312 Chirality : 0.043 0.193 2103 Planarity : 0.005 0.117 2380 Dihedral : 7.775 133.770 1926 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.86 % Favored : 92.62 % Rotamer: Outliers : 3.60 % Allowed : 15.88 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -0.52 (0.20), residues: 1720 helix: 1.27 (0.19), residues: 743 sheet: -0.62 (0.45), residues: 139 loop : -1.88 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 520 TYR 0.015 0.002 TYR A 328 PHE 0.039 0.002 PHE A 202 TRP 0.011 0.001 TRP A 312 HIS 0.004 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00458 (13967) covalent geometry : angle 0.60490 (18943) hydrogen bonds : bond 0.03764 ( 585) hydrogen bonds : angle 4.43670 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 120 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7935 (mm) REVERT: A 295 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: A 376 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: A 606 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7531 (mp) REVERT: A 727 GLU cc_start: 0.7336 (pt0) cc_final: 0.6669 (mt-10) REVERT: A 732 ASP cc_start: 0.7402 (m-30) cc_final: 0.7061 (m-30) REVERT: B 8 LYS cc_start: 0.7946 (tptm) cc_final: 0.7484 (tmmt) REVERT: B 223 GLU cc_start: 0.7930 (mp0) cc_final: 0.7691 (mp0) REVERT: B 315 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8145 (mptt) REVERT: B 361 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 383 LYS cc_start: 0.7878 (tppt) cc_final: 0.7356 (mmmm) REVERT: B 475 GLU cc_start: 0.8207 (tp30) cc_final: 0.7969 (tp30) REVERT: B 547 LYS cc_start: 0.7983 (tttp) cc_final: 0.7127 (tttm) REVERT: B 551 ASP cc_start: 0.7863 (m-30) cc_final: 0.7458 (m-30) REVERT: B 662 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6101 (mp) REVERT: B 692 HIS cc_start: 0.8314 (m-70) cc_final: 0.8097 (m-70) REVERT: B 727 GLU cc_start: 0.7535 (pp20) cc_final: 0.7118 (pp20) REVERT: B 736 TYR cc_start: 0.6630 (t80) cc_final: 0.6419 (t80) REVERT: B 821 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: E 1 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6679 (ptp) outliers start: 51 outliers final: 27 residues processed: 191 average time/residue: 0.4813 time to fit residues: 103.1038 Evaluate side-chains 183 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 825 CYS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 823 TYR Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 52 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN B 811 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145514 restraints weight = 15604.381| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.02 r_work: 0.3570 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13967 Z= 0.130 Angle : 0.572 11.817 18943 Z= 0.296 Chirality : 0.042 0.200 2103 Planarity : 0.004 0.114 2380 Dihedral : 7.664 132.897 1926 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.74 % Favored : 92.73 % Rotamer: Outliers : 3.25 % Allowed : 16.44 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -0.34 (0.20), residues: 1720 helix: 1.47 (0.20), residues: 743 sheet: -0.52 (0.45), residues: 139 loop : -1.84 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.029 0.001 TYR A 611 PHE 0.042 0.001 PHE A 202 TRP 0.010 0.001 TRP A 312 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00315 (13967) covalent geometry : angle 0.57184 (18943) hydrogen bonds : bond 0.03416 ( 585) hydrogen bonds : angle 4.35888 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.477 Fit side-chains REVERT: A 120 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7931 (mm) REVERT: A 295 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: A 376 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: A 727 GLU cc_start: 0.7377 (pt0) cc_final: 0.6640 (mt-10) REVERT: A 732 ASP cc_start: 0.7485 (m-30) cc_final: 0.7115 (m-30) REVERT: A 766 ASN cc_start: 0.8272 (m-40) cc_final: 0.7644 (t0) REVERT: B 8 LYS cc_start: 0.7900 (tptm) cc_final: 0.7438 (tmmt) REVERT: B 128 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7715 (mttm) REVERT: B 146 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7841 (ttt90) REVERT: B 223 GLU cc_start: 0.7894 (mp0) cc_final: 0.7661 (mp0) REVERT: B 315 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8020 (mtpm) REVERT: B 361 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8734 (mp) REVERT: B 514 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7499 (ttp-170) REVERT: B 547 LYS cc_start: 0.7963 (tttp) cc_final: 0.7121 (tttm) REVERT: B 551 ASP cc_start: 0.7835 (m-30) cc_final: 0.7507 (m-30) REVERT: B 662 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6280 (mt) REVERT: B 692 HIS cc_start: 0.8304 (m-70) cc_final: 0.8086 (m-70) REVERT: B 727 GLU cc_start: 0.7541 (pp20) cc_final: 0.7136 (pp20) REVERT: B 736 TYR cc_start: 0.6585 (t80) cc_final: 0.6313 (t80) REVERT: B 821 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: E 1 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6544 (ptp) outliers start: 46 outliers final: 22 residues processed: 187 average time/residue: 0.5213 time to fit residues: 108.9052 Evaluate side-chains 180 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN B 811 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144344 restraints weight = 15729.390| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.03 r_work: 0.3535 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13967 Z= 0.155 Angle : 0.601 13.126 18943 Z= 0.307 Chirality : 0.042 0.220 2103 Planarity : 0.005 0.113 2380 Dihedral : 7.666 133.349 1926 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.57 % Favored : 92.91 % Rotamer: Outliers : 3.03 % Allowed : 17.01 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -0.33 (0.20), residues: 1720 helix: 1.47 (0.20), residues: 743 sheet: -0.48 (0.45), residues: 139 loop : -1.83 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 161 TYR 0.017 0.001 TYR B 624 PHE 0.043 0.002 PHE A 202 TRP 0.010 0.001 TRP A 289 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00381 (13967) covalent geometry : angle 0.60117 (18943) hydrogen bonds : bond 0.03554 ( 585) hydrogen bonds : angle 4.35088 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 120 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 295 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: A 376 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: A 454 LYS cc_start: 0.7878 (tppt) cc_final: 0.7312 (ptmt) REVERT: A 611 TYR cc_start: 0.8251 (t80) cc_final: 0.8022 (t80) REVERT: A 727 GLU cc_start: 0.7390 (pt0) cc_final: 0.6652 (mt-10) REVERT: A 732 ASP cc_start: 0.7510 (m-30) cc_final: 0.7146 (m-30) REVERT: A 766 ASN cc_start: 0.8264 (m-40) cc_final: 0.7627 (t0) REVERT: B 8 LYS cc_start: 0.7847 (tptm) cc_final: 0.7405 (tmmt) REVERT: B 223 GLU cc_start: 0.7920 (mp0) cc_final: 0.7684 (mp0) REVERT: B 252 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8152 (ptm-80) REVERT: B 315 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8061 (mtpm) REVERT: B 361 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8744 (mp) REVERT: B 383 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7283 (mmmm) REVERT: B 514 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7538 (ttp-170) REVERT: B 547 LYS cc_start: 0.7973 (tttp) cc_final: 0.7144 (tttm) REVERT: B 551 ASP cc_start: 0.7823 (m-30) cc_final: 0.7485 (m-30) REVERT: B 662 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6418 (mt) REVERT: B 692 HIS cc_start: 0.8319 (m-70) cc_final: 0.8102 (m-70) REVERT: B 727 GLU cc_start: 0.7545 (pp20) cc_final: 0.7119 (pp20) REVERT: B 736 TYR cc_start: 0.6591 (t80) cc_final: 0.6360 (t80) REVERT: B 821 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: E 1 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6573 (ptp) outliers start: 43 outliers final: 27 residues processed: 185 average time/residue: 0.5390 time to fit residues: 110.5003 Evaluate side-chains 185 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 823 TYR Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 131 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 26 optimal weight: 0.0470 chunk 3 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN B 811 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.179167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147289 restraints weight = 15606.685| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.04 r_work: 0.3570 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13967 Z= 0.114 Angle : 0.576 12.965 18943 Z= 0.296 Chirality : 0.041 0.193 2103 Planarity : 0.005 0.112 2380 Dihedral : 7.545 132.464 1926 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.34 % Favored : 93.20 % Rotamer: Outliers : 2.54 % Allowed : 17.57 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -0.17 (0.21), residues: 1720 helix: 1.63 (0.20), residues: 743 sheet: -0.35 (0.45), residues: 139 loop : -1.78 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.026 0.001 TYR B 611 PHE 0.044 0.001 PHE A 202 TRP 0.011 0.001 TRP A 289 HIS 0.002 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00276 (13967) covalent geometry : angle 0.57612 (18943) hydrogen bonds : bond 0.03217 ( 585) hydrogen bonds : angle 4.30090 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 120 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7896 (mm) REVERT: A 376 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 445 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7278 (tt0) REVERT: A 454 LYS cc_start: 0.7945 (tppt) cc_final: 0.7296 (ptmt) REVERT: A 727 GLU cc_start: 0.7377 (pt0) cc_final: 0.6617 (mt-10) REVERT: A 732 ASP cc_start: 0.7504 (m-30) cc_final: 0.7158 (m-30) REVERT: A 766 ASN cc_start: 0.8283 (m-40) cc_final: 0.7661 (t0) REVERT: B 8 LYS cc_start: 0.7783 (tptm) cc_final: 0.7347 (tmmt) REVERT: B 146 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7816 (ttt90) REVERT: B 223 GLU cc_start: 0.7911 (mp0) cc_final: 0.7687 (mp0) REVERT: B 252 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8171 (ptm-80) REVERT: B 315 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8071 (mtpm) REVERT: B 383 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7313 (mmmm) REVERT: B 514 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7466 (ttp-170) REVERT: B 547 LYS cc_start: 0.7898 (tttp) cc_final: 0.7031 (tttm) REVERT: B 551 ASP cc_start: 0.7712 (m-30) cc_final: 0.7408 (m-30) REVERT: B 662 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6430 (mt) REVERT: B 727 GLU cc_start: 0.7481 (pp20) cc_final: 0.7066 (pp20) REVERT: B 821 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: E 1 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6386 (ptp) outliers start: 36 outliers final: 19 residues processed: 186 average time/residue: 0.5422 time to fit residues: 112.1345 Evaluate side-chains 179 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 823 TYR Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 152 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 62 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A 801 ASN B 811 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.175868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143349 restraints weight = 15755.118| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.05 r_work: 0.3549 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13967 Z= 0.178 Angle : 0.626 12.551 18943 Z= 0.319 Chirality : 0.043 0.232 2103 Planarity : 0.005 0.112 2380 Dihedral : 7.627 133.061 1926 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.09 % Favored : 92.44 % Rotamer: Outliers : 2.26 % Allowed : 18.49 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -0.27 (0.20), residues: 1720 helix: 1.48 (0.20), residues: 746 sheet: -0.40 (0.45), residues: 139 loop : -1.78 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 520 TYR 0.032 0.002 TYR A 611 PHE 0.042 0.002 PHE A 202 TRP 0.008 0.001 TRP B 206 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00439 (13967) covalent geometry : angle 0.62618 (18943) hydrogen bonds : bond 0.03663 ( 585) hydrogen bonds : angle 4.37338 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4639.98 seconds wall clock time: 80 minutes 5.68 seconds (4805.68 seconds total)