Starting phenix.real_space_refine on Mon Sep 14 15:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z9c_14570/09_2026/7z9c_14570.cif" } resolution = 3.06 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= 0.028 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: 7 Type Number sf(0) Gaussians P 64 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 9823 2.51 5 N 2835 2.21 5 O 3184 1.98 5 H 15371 0.53 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31337 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8213 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8213 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 450 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 448 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 561 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'BWH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.58, per 1000 atoms: 0.18 Number of scatterers: 31337 At special positions: 0 Unit cell: (126.42, 139.32, 133.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 2 11.99 O 3184 8.00 N 2835 7.00 C 9823 6.00 H 15371 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 995.2 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 23 sheets defined 51.2% alpha, 10.4% beta 12 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'A' and resid 13 through 30 removed outlier: 3.631A pdb=" N VAL A 30 " --> pdb=" O MET A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.815A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.836A pdb=" N LEU A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 226 through 236 removed outlier: 4.219A pdb=" N GLU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.623A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 387 removed outlier: 3.625A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 413 removed outlier: 3.960A pdb=" N ASN A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.612A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 420 through 425' Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.652A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.565A pdb=" N GLU A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.555A pdb=" N GLY B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 464 removed outlier: 3.717A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 475 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.790A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.189A pdb=" N ALA B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 597 removed outlier: 3.641A pdb=" N MET B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.613A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.584A pdb=" N ASP B 619 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 639 removed outlier: 4.027A pdb=" N TRP B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.581A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.581A pdb=" N ARG B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 removed outlier: 3.780A pdb=" N ALA B 722 " --> pdb=" O SER B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.749A pdb=" N ALA B 773 " --> pdb=" O ASP B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 removed outlier: 4.030A pdb=" N ARG B 788 " --> pdb=" O ALA B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 801 Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.995A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.876A pdb=" N LEU C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.595A pdb=" N GLU C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 removed outlier: 3.607A pdb=" N GLU C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.738A pdb=" N ASN C 319 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.665A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.771A pdb=" N HIS C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 412 Processing helix chain 'C' and resid 420 through 428 removed outlier: 3.527A pdb=" N LEU C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 427 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 493 removed outlier: 4.010A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 514 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.583A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 464 Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.590A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.719A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 610 removed outlier: 4.019A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 620 Processing helix chain 'D' and resid 625 through 640 removed outlier: 3.899A pdb=" N LYS D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 684 through 697 removed outlier: 3.643A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 731 removed outlier: 3.532A pdb=" N ARG D 731 " --> pdb=" O VAL D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 745 removed outlier: 3.590A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 769 through 782 removed outlier: 3.606A pdb=" N ALA D 773 " --> pdb=" O ASP D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 795 removed outlier: 3.969A pdb=" N ARG D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 801 removed outlier: 3.791A pdb=" N ASN D 801 " --> pdb=" O LEU D 797 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.169A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 removed outlier: 4.602A pdb=" N TYR A 241 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.703A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 292 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU A 306 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.622A pdb=" N TYR A 449 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 442 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 542 through 546 removed outlier: 4.042A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 653 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.698A pdb=" N THR C 9 " --> pdb=" O ARG D 764 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR D 766 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 11 " --> pdb=" O THR D 766 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB7, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 333 removed outlier: 4.022A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 246 through 249 removed outlier: 6.938A pdb=" N VAL C 304 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU C 292 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU C 306 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AC2, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AC3, first strand: chain 'D' and resid 542 through 546 removed outlier: 4.165A pdb=" N GLN D 542 " --> pdb=" O LYS D 539 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 652 removed outlier: 4.162A pdb=" N VAL D 664 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.629A pdb=" N GLN D 714 " --> pdb=" O ILE D 707 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15363 1.03 - 1.23: 35 1.23 - 1.42: 6716 1.42 - 1.61: 9501 1.61 - 1.81: 108 Bond restraints: 31723 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.611 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C41 BWH C 901 " pdb=" O6 BWH C 901 " ideal model delta sigma weight residual 1.233 1.303 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1' DC H 24 " pdb=" N1 DC H 24 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" C3' DA F 7 " pdb=" O3' DA F 7 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.30e-02 5.92e+03 9.07e+00 ... (remaining 31718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 56892 2.14 - 4.28: 520 4.28 - 6.42: 46 6.42 - 8.56: 7 8.56 - 10.70: 2 Bond angle restraints: 57467 Sorted by residual: angle pdb=" O4' DT H 22 " pdb=" C4' DT H 22 " pdb=" C3' DT H 22 " ideal model delta sigma weight residual 106.00 103.44 2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT G 32 " pdb=" C4 DT G 32 " pdb=" O4 DT G 32 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT H 26 " pdb=" C4 DT H 26 " pdb=" O4 DT H 26 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT G 31 " pdb=" C4 DT G 31 " pdb=" O4 DT G 31 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT G 30 " pdb=" C4 DT G 30 " pdb=" O4 DT G 30 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 ... (remaining 57462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.48: 13752 26.48 - 52.96: 588 52.96 - 79.44: 117 79.44 - 105.92: 1 105.92 - 132.40: 2 Dihedral angle restraints: 14460 sinusoidal: 8486 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta harmonic sigma weight residual -180.00 -153.86 -26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ARG C 32 " pdb=" C ARG C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual 180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP A 297 " pdb=" C ASP A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 14457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1680 0.035 - 0.069: 556 0.069 - 0.104: 107 0.104 - 0.139: 126 0.139 - 0.173: 34 Chirality restraints: 2503 Sorted by residual: chirality pdb=" C17 BWH C 901 " pdb=" C18 BWH C 901 " pdb=" C20 BWH C 901 " pdb=" N1 BWH C 901 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" C3' DA F 14 " pdb=" C4' DA F 14 " pdb=" O3' DA F 14 " pdb=" C2' DA F 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 BWH C 901 " -0.122 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C16 BWH C 901 " 0.044 2.00e-02 2.50e+03 pdb=" C17 BWH C 901 " -0.164 2.00e-02 2.50e+03 pdb=" N1 BWH C 901 " 0.216 2.00e-02 2.50e+03 pdb=" O2 BWH C 901 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C35 BWH C 901 " -0.033 2.00e-02 2.50e+03 9.07e-02 2.05e+02 pdb=" C36 BWH C 901 " -0.076 2.00e-02 2.50e+03 pdb=" C37 BWH C 901 " -0.057 2.00e-02 2.50e+03 pdb=" C38 BWH C 901 " 0.010 2.00e-02 2.50e+03 pdb=" C39 BWH C 901 " 0.054 2.00e-02 2.50e+03 pdb=" C40 BWH C 901 " 0.034 2.00e-02 2.50e+03 pdb=" C41 BWH C 901 " 0.039 2.00e-02 2.50e+03 pdb=" N5 BWH C 901 " -0.087 2.00e-02 2.50e+03 pdb=" O8 BWH C 901 " -0.102 2.00e-02 2.50e+03 pdb=" O9 BWH C 901 " 0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 BWH C 901 " 0.044 2.00e-02 2.50e+03 8.28e-02 1.71e+02 pdb=" C29 BWH C 901 " 0.083 2.00e-02 2.50e+03 pdb=" C30 BWH C 901 " 0.058 2.00e-02 2.50e+03 pdb=" C31 BWH C 901 " -0.006 2.00e-02 2.50e+03 pdb=" C32 BWH C 901 " -0.031 2.00e-02 2.50e+03 pdb=" C33 BWH C 901 " -0.006 2.00e-02 2.50e+03 pdb=" C34 BWH C 901 " -0.076 2.00e-02 2.50e+03 pdb=" N4 BWH C 901 " 0.029 2.00e-02 2.50e+03 pdb=" O10 BWH C 901 " 0.101 2.00e-02 2.50e+03 pdb=" O11 BWH C 901 " -0.196 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 5722 2.31 - 2.88: 69091 2.88 - 3.45: 70865 3.45 - 4.03: 99419 4.03 - 4.60: 154492 Nonbonded interactions: 399589 Sorted by model distance: nonbonded pdb=" O GLN B 591 " pdb="HD22 ASN B 595 " model vdw 1.737 2.450 nonbonded pdb=" O HIS D 679 " pdb=" HG1 THR D 683 " model vdw 1.739 2.450 nonbonded pdb=" O LEU C 320 " pdb=" HG1 THR C 324 " model vdw 1.740 2.450 nonbonded pdb=" HH TYR D 545 " pdb=" OE2 GLU D 752 " model vdw 1.743 2.450 nonbonded pdb=" O GLN D 749 " pdb=" HG1 THR D 753 " model vdw 1.745 2.450 ... (remaining 399584 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' selection = (chain 'C' and resid 8 through 524) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.590 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 36.600 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 0.183 16354 Z= 0.345 Angle : 0.649 10.704 22380 Z= 0.405 Chirality : 0.046 0.173 2503 Planarity : 0.006 0.135 2710 Dihedral : 13.786 132.401 6392 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1824 helix: 2.30 (0.18), residues: 827 sheet: -0.47 (0.39), residues: 176 loop : -1.74 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 507 TYR 0.011 0.001 TYR C 266 PHE 0.008 0.001 PHE C 368 TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.28 (16352) covalent geometry : angle 0.64867 / 0.41 (22380) hydrogen bonds : bond 0.16055 / 10.52 ( 724) hydrogen bonds : angle 5.36977 / 3.69 ( 2043) Misc. bond : bond 0.18110 / 9.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 781 MET cc_start: 0.8788 (mmt) cc_final: 0.8287 (mmt) REVERT: C 338 HIS cc_start: 0.7471 (t-90) cc_final: 0.7246 (t-90) REVERT: D 592 LYS cc_start: 0.8644 (tppp) cc_final: 0.8392 (mmtt) REVERT: D 600 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6698 (mmm160) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3871 time to fit residues: 129.1785 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN D 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094845 restraints weight = 68319.171| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.11 r_work: 0.3012 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16354 Z= 0.173 Angle : 0.547 8.488 22380 Z= 0.316 Chirality : 0.041 0.232 2503 Planarity : 0.004 0.052 2710 Dihedral : 15.745 131.884 2740 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 0.52 % Allowed : 5.23 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1824 helix: 2.27 (0.18), residues: 848 sheet: -0.60 (0.39), residues: 174 loop : -1.92 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 489 TYR 0.010 0.001 TYR C 266 PHE 0.013 0.001 PHE B 791 TRP 0.006 0.001 TRP D 629 HIS 0.008 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (16352) covalent geometry : angle 0.54671 / 0.32 (22380) hydrogen bonds : bond 0.06969 / 4.50 ( 724) hydrogen bonds : angle 4.70099 / 3.24 ( 2043) Misc. bond : bond 0.00272 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 686 GLU cc_start: 0.7904 (tp30) cc_final: 0.7524 (tt0) REVERT: B 781 MET cc_start: 0.8879 (mmt) cc_final: 0.8440 (mmt) REVERT: D 592 LYS cc_start: 0.8731 (tppp) cc_final: 0.8304 (mmtt) REVERT: D 600 ARG cc_start: 0.7414 (mtm110) cc_final: 0.6632 (mmm160) outliers start: 8 outliers final: 5 residues processed: 152 average time/residue: 0.3708 time to fit residues: 79.0414 Evaluate side-chains 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 HIS B 631 ASN C 399 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096870 restraints weight = 68162.798| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.14 r_work: 0.3049 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16354 Z= 0.113 Angle : 0.478 6.330 22380 Z= 0.278 Chirality : 0.040 0.195 2503 Planarity : 0.004 0.055 2710 Dihedral : 15.847 136.798 2740 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 0.65 % Allowed : 5.48 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1824 helix: 2.37 (0.18), residues: 851 sheet: -0.51 (0.39), residues: 176 loop : -1.86 (0.19), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 309 TYR 0.010 0.001 TYR C 266 PHE 0.007 0.001 PHE B 791 TRP 0.008 0.001 TRP D 629 HIS 0.009 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (16352) covalent geometry : angle 0.47806 / 0.28 (22380) hydrogen bonds : bond 0.05739 / 3.74 ( 724) hydrogen bonds : angle 4.43400 / 3.07 ( 2043) Misc. bond : bond 0.00664 / 0.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 686 GLU cc_start: 0.7879 (tp30) cc_final: 0.7502 (tt0) REVERT: B 781 MET cc_start: 0.8820 (mmt) cc_final: 0.8403 (mmt) REVERT: C 338 HIS cc_start: 0.8059 (t-90) cc_final: 0.7748 (t-90) REVERT: D 480 ARG cc_start: 0.6661 (mmm160) cc_final: 0.6247 (mmt90) REVERT: D 592 LYS cc_start: 0.8727 (tppp) cc_final: 0.8279 (mmtt) REVERT: D 600 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6761 (mmm160) REVERT: D 621 SER cc_start: 0.8210 (t) cc_final: 0.7978 (m) outliers start: 10 outliers final: 7 residues processed: 152 average time/residue: 0.3530 time to fit residues: 76.3962 Evaluate side-chains 143 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain D residue 671 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 121 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 399 HIS D 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093418 restraints weight = 67976.292| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.09 r_work: 0.2989 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16354 Z= 0.199 Angle : 0.538 8.029 22380 Z= 0.309 Chirality : 0.041 0.207 2503 Planarity : 0.005 0.048 2710 Dihedral : 16.008 133.693 2740 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 0.58 % Allowed : 5.94 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1824 helix: 2.31 (0.18), residues: 836 sheet: -0.59 (0.38), residues: 176 loop : -2.00 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.011 0.001 TYR C 266 PHE 0.010 0.001 PHE B 791 TRP 0.007 0.001 TRP D 751 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (16352) covalent geometry : angle 0.53822 / 0.31 (22380) hydrogen bonds : bond 0.06998 / 4.51 ( 724) hydrogen bonds : angle 4.47910 / 3.11 ( 2043) Misc. bond : bond 0.00108 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 686 GLU cc_start: 0.7841 (tp30) cc_final: 0.7470 (tt0) REVERT: B 781 MET cc_start: 0.8863 (mmt) cc_final: 0.8475 (mmt) REVERT: D 480 ARG cc_start: 0.6644 (mmm160) cc_final: 0.6233 (mmt90) REVERT: D 592 LYS cc_start: 0.8739 (tppp) cc_final: 0.8265 (mmtt) REVERT: D 600 ARG cc_start: 0.7545 (mtm110) cc_final: 0.6766 (mmm160) REVERT: D 621 SER cc_start: 0.8273 (t) cc_final: 0.8012 (m) outliers start: 9 outliers final: 6 residues processed: 142 average time/residue: 0.3439 time to fit residues: 69.5577 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN C 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095105 restraints weight = 68253.923| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.09 r_work: 0.3018 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16354 Z= 0.170 Angle : 0.524 8.567 22380 Z= 0.300 Chirality : 0.041 0.203 2503 Planarity : 0.005 0.051 2710 Dihedral : 16.160 134.790 2740 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 0.71 % Allowed : 6.26 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1824 helix: 2.21 (0.18), residues: 849 sheet: -0.69 (0.38), residues: 180 loop : -2.08 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.012 0.001 TYR C 266 PHE 0.009 0.001 PHE B 791 TRP 0.007 0.001 TRP D 629 HIS 0.005 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16352) covalent geometry : angle 0.52435 / 0.30 (22380) hydrogen bonds : bond 0.06875 / 4.43 ( 724) hydrogen bonds : angle 4.45255 / 3.10 ( 2043) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 MET cc_start: 0.5922 (tmm) cc_final: 0.5646 (ppp) REVERT: B 686 GLU cc_start: 0.7826 (tp30) cc_final: 0.7478 (tt0) REVERT: B 781 MET cc_start: 0.8878 (mmt) cc_final: 0.8523 (mmt) REVERT: D 480 ARG cc_start: 0.6681 (mmm160) cc_final: 0.6218 (mmt90) REVERT: D 554 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: D 592 LYS cc_start: 0.8736 (tppp) cc_final: 0.8259 (mmtt) REVERT: D 600 ARG cc_start: 0.7490 (mtm110) cc_final: 0.6701 (mmm160) outliers start: 11 outliers final: 7 residues processed: 142 average time/residue: 0.3373 time to fit residues: 69.1790 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 184 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN C 399 HIS D 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094930 restraints weight = 67937.733| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.19 r_work: 0.2996 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16354 Z= 0.140 Angle : 0.501 6.917 22380 Z= 0.288 Chirality : 0.040 0.195 2503 Planarity : 0.004 0.048 2710 Dihedral : 16.203 136.032 2740 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 0.90 % Allowed : 6.58 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1824 helix: 2.27 (0.18), residues: 848 sheet: -0.69 (0.38), residues: 180 loop : -2.06 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.011 0.001 TYR C 266 PHE 0.008 0.001 PHE B 791 TRP 0.006 0.001 TRP D 629 HIS 0.006 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (16352) covalent geometry : angle 0.50129 / 0.29 (22380) hydrogen bonds : bond 0.06423 / 4.15 ( 724) hydrogen bonds : angle 4.38387 / 3.05 ( 2043) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 MET cc_start: 0.5890 (tmm) cc_final: 0.5618 (ppp) REVERT: B 686 GLU cc_start: 0.7866 (tp30) cc_final: 0.7516 (tt0) REVERT: B 687 TYR cc_start: 0.6992 (t80) cc_final: 0.6504 (t80) REVERT: B 781 MET cc_start: 0.8876 (mmt) cc_final: 0.8459 (mmt) REVERT: D 480 ARG cc_start: 0.6624 (mmm160) cc_final: 0.6219 (mmt90) REVERT: D 554 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: D 592 LYS cc_start: 0.8772 (tppp) cc_final: 0.8306 (mmtt) REVERT: D 600 ARG cc_start: 0.7544 (mtm110) cc_final: 0.6755 (mmm160) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.3298 time to fit residues: 66.0009 Evaluate side-chains 136 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 chunk 177 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 146 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN C 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096291 restraints weight = 67527.294| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.02 r_work: 0.3009 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16354 Z= 0.112 Angle : 0.474 6.128 22380 Z= 0.273 Chirality : 0.039 0.184 2503 Planarity : 0.004 0.050 2710 Dihedral : 16.213 137.108 2740 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 0.84 % Allowed : 6.77 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1824 helix: 2.38 (0.18), residues: 850 sheet: -0.63 (0.38), residues: 180 loop : -1.96 (0.19), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 667 TYR 0.010 0.001 TYR C 266 PHE 0.006 0.001 PHE B 791 TRP 0.006 0.001 TRP B 725 HIS 0.005 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (16352) covalent geometry : angle 0.47408 / 0.27 (22380) hydrogen bonds : bond 0.05665 / 3.67 ( 724) hydrogen bonds : angle 4.25336 / 2.96 ( 2043) Misc. bond : bond 0.00053 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 MET cc_start: 0.5873 (tmm) cc_final: 0.5620 (ppp) REVERT: B 686 GLU cc_start: 0.7827 (tp30) cc_final: 0.7468 (tt0) REVERT: B 781 MET cc_start: 0.8821 (mmt) cc_final: 0.8450 (mmt) REVERT: D 480 ARG cc_start: 0.6615 (mmm160) cc_final: 0.6261 (mmt90) REVERT: D 554 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: D 592 LYS cc_start: 0.8780 (tppp) cc_final: 0.8322 (mmtt) REVERT: D 600 ARG cc_start: 0.7555 (mtm110) cc_final: 0.6774 (mmm160) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.3301 time to fit residues: 67.1585 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 399 HIS D 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094017 restraints weight = 68331.813| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.18 r_work: 0.2976 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16354 Z= 0.151 Angle : 0.501 6.802 22380 Z= 0.287 Chirality : 0.040 0.215 2503 Planarity : 0.004 0.046 2710 Dihedral : 16.266 135.417 2740 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 0.71 % Allowed : 6.90 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1824 helix: 2.37 (0.18), residues: 848 sheet: -0.66 (0.38), residues: 180 loop : -2.04 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 462 TYR 0.010 0.001 TYR C 266 PHE 0.007 0.001 PHE B 791 TRP 0.006 0.001 TRP D 751 HIS 0.005 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16352) covalent geometry : angle 0.50055 / 0.29 (22380) hydrogen bonds : bond 0.06313 / 4.07 ( 724) hydrogen bonds : angle 4.29292 / 2.99 ( 2043) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 MET cc_start: 0.5860 (tmm) cc_final: 0.5631 (ppp) REVERT: B 686 GLU cc_start: 0.7809 (tp30) cc_final: 0.7462 (tt0) REVERT: B 781 MET cc_start: 0.8885 (mmt) cc_final: 0.8519 (mmt) REVERT: C 314 GLU cc_start: 0.7842 (mp0) cc_final: 0.7584 (mp0) REVERT: D 480 ARG cc_start: 0.6618 (mmm160) cc_final: 0.6252 (mmt90) REVERT: D 554 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: D 592 LYS cc_start: 0.8808 (tppp) cc_final: 0.8367 (mmtt) REVERT: D 600 ARG cc_start: 0.7619 (mtm110) cc_final: 0.6845 (mmm160) outliers start: 11 outliers final: 7 residues processed: 134 average time/residue: 0.3422 time to fit residues: 66.2691 Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN C 399 HIS D 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092152 restraints weight = 68338.951| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.13 r_work: 0.2940 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16354 Z= 0.201 Angle : 0.553 7.448 22380 Z= 0.315 Chirality : 0.042 0.210 2503 Planarity : 0.005 0.051 2710 Dihedral : 16.423 134.066 2740 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.04 % Rotamer: Outliers : 0.97 % Allowed : 6.71 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1824 helix: 2.20 (0.18), residues: 836 sheet: -0.79 (0.38), residues: 180 loop : -2.19 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 507 TYR 0.012 0.001 TYR C 266 PHE 0.010 0.001 PHE B 791 TRP 0.007 0.001 TRP D 629 HIS 0.006 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (16352) covalent geometry : angle 0.55346 / 0.31 (22380) hydrogen bonds : bond 0.07373 / 4.75 ( 724) hydrogen bonds : angle 4.44766 / 3.11 ( 2043) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 554 GLN cc_start: 0.8309 (tp40) cc_final: 0.7950 (mm110) REVERT: B 781 MET cc_start: 0.8918 (mmt) cc_final: 0.8562 (mmt) REVERT: C 314 GLU cc_start: 0.7879 (mp0) cc_final: 0.7591 (mp0) REVERT: C 401 PRO cc_start: 0.9105 (Cg_exo) cc_final: 0.8851 (Cg_endo) REVERT: D 480 ARG cc_start: 0.6613 (mmm160) cc_final: 0.6254 (mmt90) REVERT: D 554 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: D 592 LYS cc_start: 0.8811 (tppp) cc_final: 0.8370 (mmtt) REVERT: D 600 ARG cc_start: 0.7665 (mtm110) cc_final: 0.6844 (mmm160) outliers start: 15 outliers final: 10 residues processed: 143 average time/residue: 0.3200 time to fit residues: 66.9829 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN C 399 HIS D 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093676 restraints weight = 67748.192| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.04 r_work: 0.2957 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16354 Z= 0.146 Angle : 0.509 6.100 22380 Z= 0.292 Chirality : 0.040 0.197 2503 Planarity : 0.004 0.045 2710 Dihedral : 16.436 136.220 2740 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 0.90 % Allowed : 6.77 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1824 helix: 2.21 (0.18), residues: 848 sheet: -0.82 (0.38), residues: 180 loop : -2.14 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 413 TYR 0.011 0.001 TYR C 266 PHE 0.008 0.001 PHE B 791 TRP 0.007 0.001 TRP D 629 HIS 0.005 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16352) covalent geometry : angle 0.50861 / 0.29 (22380) hydrogen bonds : bond 0.06620 / 4.27 ( 724) hydrogen bonds : angle 4.38281 / 3.06 ( 2043) Misc. bond : bond 0.00014 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 554 GLN cc_start: 0.8283 (tp40) cc_final: 0.7920 (mm110) REVERT: B 781 MET cc_start: 0.8859 (mmt) cc_final: 0.8493 (mmt) REVERT: C 314 GLU cc_start: 0.7884 (mp0) cc_final: 0.7572 (mp0) REVERT: C 401 PRO cc_start: 0.9113 (Cg_exo) cc_final: 0.8853 (Cg_endo) REVERT: D 480 ARG cc_start: 0.6619 (mmm160) cc_final: 0.6251 (mmt90) REVERT: D 554 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: D 592 LYS cc_start: 0.8795 (tppp) cc_final: 0.8337 (mmtt) REVERT: D 600 ARG cc_start: 0.7640 (mtm110) cc_final: 0.6804 (mmm160) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 0.3385 time to fit residues: 67.3102 Evaluate side-chains 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 96 optimal weight: 0.7980 chunk 118 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN C 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096077 restraints weight = 68375.815| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.14 r_work: 0.3009 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16354 Z= 0.104 Angle : 0.467 5.181 22380 Z= 0.270 Chirality : 0.039 0.177 2503 Planarity : 0.004 0.050 2710 Dihedral : 16.417 138.840 2740 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 0.65 % Allowed : 6.97 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1824 helix: 2.42 (0.18), residues: 848 sheet: -0.67 (0.38), residues: 180 loop : -1.98 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 667 TYR 0.009 0.001 TYR C 266 PHE 0.006 0.001 PHE B 513 TRP 0.007 0.001 TRP B 725 HIS 0.004 0.001 HIS D 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (16352) covalent geometry : angle 0.46671 / 0.27 (22380) hydrogen bonds : bond 0.05365 / 3.49 ( 724) hydrogen bonds : angle 4.20111 / 2.93 ( 2043) Misc. bond : bond 0.00039 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8063.80 seconds wall clock time: 137 minutes 4.70 seconds (8224.70 seconds total)