Starting phenix.real_space_refine on Mon Sep 14 15:21:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9m_14574/09_2026/7z9m_14574_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9m_14574/09_2026/7z9m_14574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z9m_14574/09_2026/7z9m_14574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9m_14574/09_2026/7z9m_14574.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9m_14574/09_2026/7z9m_14574_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9m_14574/09_2026/7z9m_14574_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 9821 2.51 5 N 2840 2.21 5 O 3181 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 11 residue(s): 0.02s 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 Unresolved non-hydrogen dihedrals: 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 Unresolved non-hydrogen dihedrals: 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: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IL1': 1} Classifications: {'undetermined': 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.70, per 1000 atoms: 0.18 Number of scatterers: 31337 At special positions: 0 Unit cell: (128.14, 139.32, 134.16, 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 3181 8.00 N 2840 7.00 C 9821 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: 3.04 Conformation dependent library (CDL) restraints added in 917.9 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: 76 helices and 23 sheets defined 51.7% alpha, 10.8% beta 7 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.846A 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: 3.891A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.891A pdb=" N LEU A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.873A 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 212 removed outlier: 3.591A pdb=" N GLU A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 removed outlier: 4.313A pdb=" N GLU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.614A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 388 removed outlier: 3.562A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 413 removed outlier: 4.033A pdb=" N ASN A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.986A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.528A pdb=" N LYS A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.581A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 514 Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.570A pdb=" N GLY B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 464 removed outlier: 3.746A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.707A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.130A pdb=" N ALA B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 597 removed outlier: 3.552A pdb=" N MET B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 601 removed outlier: 3.645A pdb=" N TYR B 601 " --> pdb=" O GLU B 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 598 through 601' Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.555A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 639 removed outlier: 4.171A pdb=" N TRP B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.663A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.794A pdb=" N ARG B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 removed outlier: 3.743A pdb=" N ALA B 722 " --> pdb=" O SER B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 734 No H-bonds generated for 'chain 'B' and resid 732 through 734' Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.632A pdb=" N ALA B 773 " --> pdb=" O ASP B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 removed outlier: 3.831A 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 82 through 92 removed outlier: 3.624A 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: 3.772A pdb=" N LEU C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.580A 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 212 removed outlier: 3.506A pdb=" N GLU C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.512A pdb=" N GLU C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.571A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.539A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.889A 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 427 removed outlier: 3.695A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.738A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.728A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (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: 3.715A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 525 " --> pdb=" O ILE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 577 through 596 Processing helix chain 'D' and resid 602 through 610 removed outlier: 3.590A pdb=" N LEU D 606 " --> pdb=" O PRO D 602 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 609 " --> pdb=" O MET D 605 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 621 removed outlier: 3.954A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 640 removed outlier: 4.277A pdb=" N ARG D 628 " --> pdb=" O GLN D 624 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.570A pdb=" N ARG D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 741 through 745 removed outlier: 3.549A pdb=" N GLU D 744 " --> pdb=" O GLY D 741 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 745' Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 784 through 795 removed outlier: 3.819A pdb=" N ARG D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.303A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.360A 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: 4.786A 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: 3.821A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 292 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.585A 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: 3.600A pdb=" N TYR A 449 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.930A 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: 4.010A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 566 through 568 removed outlier: 4.054A pdb=" N LEU B 566 " --> pdb=" O GLU B 708 " (cutoff:3.500A) 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: 3.755A pdb=" N THR C 9 " --> pdb=" O MET D 762 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.263A 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: 4.082A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 245 through 250 removed outlier: 7.123A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 307 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 336 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: 4.055A 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 Processing sheet with id=AC5, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.715A pdb=" N GLN D 714 " --> pdb=" O ILE D 707 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 4.09 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: 6727 1.42 - 1.61: 9490 1.61 - 1.81: 109 Bond restraints: 31724 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.610 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.613 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C ALA A 412 " pdb=" N ASN A 413 " ideal model delta sigma weight residual 1.327 1.392 -0.065 1.71e-02 3.42e+03 1.45e+01 bond pdb=" C1' DT F 12 " pdb=" N1 DT F 12 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" C7 IL1 A 901 " pdb=" O3 IL1 A 901 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.33e+00 ... (remaining 31719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 56985 2.26 - 4.53: 441 4.53 - 6.79: 37 6.79 - 9.06: 3 9.06 - 11.32: 2 Bond angle restraints: 57468 Sorted by residual: angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT H 20 " pdb=" C4 DT H 20 " pdb=" O4 DT H 20 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT H 17 " pdb=" C4 DT H 17 " pdb=" O4 DT H 17 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT G 32 " pdb=" C4 DT G 32 " pdb=" O4 DT G 32 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT H 26 " pdb=" C4 DT H 26 " pdb=" O4 DT H 26 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 ... (remaining 57463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 13816 27.29 - 54.57: 584 54.57 - 81.86: 103 81.86 - 109.15: 5 109.15 - 136.44: 2 Dihedral angle restraints: 14510 sinusoidal: 8536 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 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+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 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+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 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 14507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1673 0.036 - 0.071: 578 0.071 - 0.106: 104 0.106 - 0.142: 120 0.142 - 0.177: 28 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" C3' DC G 21 " pdb=" C4' DC G 21 " pdb=" O3' DC G 21 " pdb=" C2' DC G 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 IL1 A 901 " -0.246 2.00e-02 2.50e+03 1.23e-01 3.41e+02 pdb=" C29 IL1 A 901 " 0.023 2.00e-02 2.50e+03 pdb=" C30 IL1 A 901 " 0.073 2.00e-02 2.50e+03 pdb=" C31 IL1 A 901 " 0.105 2.00e-02 2.50e+03 pdb=" C32 IL1 A 901 " 0.092 2.00e-02 2.50e+03 pdb=" C33 IL1 A 901 " -0.050 2.00e-02 2.50e+03 pdb=" C34 IL1 A 901 " 0.105 2.00e-02 2.50e+03 pdb=" C35 IL1 A 901 " 0.075 2.00e-02 2.50e+03 pdb=" N8 IL1 A 901 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 IL1 A 901 " -0.123 2.00e-02 2.50e+03 1.02e-01 1.30e+02 pdb=" C23 IL1 A 901 " 0.033 2.00e-02 2.50e+03 pdb=" C24 IL1 A 901 " -0.093 2.00e-02 2.50e+03 pdb=" N6 IL1 A 901 " 0.163 2.00e-02 2.50e+03 pdb=" O6 IL1 A 901 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C IL1 A 901 " 0.016 2.00e-02 2.50e+03 5.98e-02 8.93e+01 pdb=" O IL1 A 901 " 0.076 2.00e-02 2.50e+03 pdb=" C1 IL1 A 901 " -0.011 2.00e-02 2.50e+03 pdb=" C10 IL1 A 901 " -0.048 2.00e-02 2.50e+03 pdb=" C11 IL1 A 901 " -0.027 2.00e-02 2.50e+03 pdb=" C12 IL1 A 901 " 0.011 2.00e-02 2.50e+03 pdb=" C2 IL1 A 901 " 0.009 2.00e-02 2.50e+03 pdb=" C38 IL1 A 901 " 0.004 2.00e-02 2.50e+03 pdb=" N1 IL1 A 901 " 0.099 2.00e-02 2.50e+03 pdb=" O8 IL1 A 901 " -0.128 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 4955 2.30 - 2.87: 69354 2.87 - 3.45: 71379 3.45 - 4.02: 98835 4.02 - 4.60: 154410 Nonbonded interactions: 398933 Sorted by model distance: nonbonded pdb=" O GLN D 749 " pdb=" HG1 THR D 753 " model vdw 1.722 2.450 nonbonded pdb="HD21 ASN B 569 " pdb=" O LEU B 700 " model vdw 1.725 2.450 nonbonded pdb="HH22 ARG B 516 " pdb=" OD1 ASP B 774 " model vdw 1.727 2.450 nonbonded pdb=" OD1 ASP B 622 " pdb=" HG1 THR B 653 " model vdw 1.730 2.450 nonbonded pdb="MG MG D 901 " pdb=" O HOH D1003 " model vdw 1.731 2.050 ... (remaining 398928 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 8 through 524) selection = chain 'C' } 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: 4.240 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: 0.220 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.470 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 16355 Z= 0.346 Angle : 0.665 11.324 22381 Z= 0.421 Chirality : 0.046 0.177 2503 Planarity : 0.005 0.123 2710 Dihedral : 14.233 136.435 6438 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.26 % Allowed : 3.03 % Favored : 96.71 % 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: 0.56 (0.20), residues: 1824 helix: 2.34 (0.18), residues: 831 sheet: -0.21 (0.40), residues: 180 loop : -1.71 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.013 0.001 TYR C 266 PHE 0.009 0.001 PHE D 777 TRP 0.008 0.001 TRP B 647 HIS 0.004 0.001 HIS B 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.28 (16353) covalent geometry : angle 0.66526 / 0.42 (22381) hydrogen bonds : bond 0.17276 / 11.88 ( 725) hydrogen bonds : angle 5.62047 / 4.10 ( 2062) Misc. bond : bond 0.18113 / 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 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.885 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: 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: symmetry clash REVERT: A 26 MET cc_start: 0.7865 (mmm) cc_final: 0.7600 (mmt) REVERT: A 491 ILE cc_start: 0.7944 (mt) cc_final: 0.7627 (mt) REVERT: B 483 TYR cc_start: 0.7855 (t80) cc_final: 0.7603 (t80) REVERT: B 548 ASP cc_start: 0.8060 (t0) cc_final: 0.7822 (m-30) REVERT: B 581 GLU cc_start: 0.8429 (tt0) cc_final: 0.8090 (tm-30) REVERT: B 642 GLN cc_start: 0.6727 (pm20) cc_final: 0.6436 (mm-40) REVERT: D 593 MET cc_start: 0.7049 (mtt) cc_final: 0.6755 (mtt) outliers start: 4 outliers final: 2 residues processed: 228 average time/residue: 0.4021 time to fit residues: 125.8072 Evaluate side-chains 112 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 631 ASN B 714 GLN C 484 GLN C 524 ASN D 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.087823 restraints weight = 83900.638| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.16 r_work: 0.3077 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16355 Z= 0.230 Angle : 0.602 6.465 22381 Z= 0.343 Chirality : 0.042 0.206 2503 Planarity : 0.004 0.044 2710 Dihedral : 16.431 138.382 2790 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.71 % Allowed : 6.45 % Favored : 92.84 % 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: 0.40 (0.20), residues: 1824 helix: 2.30 (0.17), residues: 841 sheet: -0.37 (0.39), residues: 180 loop : -1.93 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.013 0.001 TYR C 266 PHE 0.022 0.002 PHE B 719 TRP 0.005 0.001 TRP B 647 HIS 0.005 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (16353) covalent geometry : angle 0.60240 / 0.34 (22381) hydrogen bonds : bond 0.07393 / 4.93 ( 725) hydrogen bonds : angle 4.96482 / 3.59 ( 2062) Misc. bond : bond 0.01109 / 0.56 ( 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 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.851 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8456 (mmm) cc_final: 0.8147 (mmt) REVERT: B 483 TYR cc_start: 0.7735 (t80) cc_final: 0.7462 (t80) REVERT: B 581 GLU cc_start: 0.8620 (tt0) cc_final: 0.8222 (tm-30) REVERT: B 642 GLN cc_start: 0.7065 (pm20) cc_final: 0.6707 (mm-40) REVERT: B 714 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.6031 (tp-100) REVERT: C 301 MET cc_start: 0.8202 (ttm) cc_final: 0.7965 (ttt) REVERT: D 593 MET cc_start: 0.7655 (mtt) cc_final: 0.7385 (mtt) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 0.3578 time to fit residues: 64.4192 Evaluate side-chains 115 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 725 TRP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 726 LEU 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: 2.9990 chunk 140 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 465 GLN D 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.128426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089269 restraints weight = 83130.812| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.16 r_work: 0.3103 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16355 Z= 0.132 Angle : 0.517 5.984 22381 Z= 0.295 Chirality : 0.040 0.197 2503 Planarity : 0.004 0.044 2710 Dihedral : 16.424 140.942 2790 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.71 % Allowed : 6.84 % Favored : 92.45 % 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: 2.31 (0.17), residues: 848 sheet: -0.35 (0.39), residues: 180 loop : -1.93 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 713 TYR 0.011 0.001 TYR C 266 PHE 0.010 0.001 PHE B 649 TRP 0.018 0.001 TRP B 725 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16353) covalent geometry : angle 0.51693 / 0.29 (22381) hydrogen bonds : bond 0.06254 / 4.19 ( 725) hydrogen bonds : angle 4.66256 / 3.38 ( 2062) Misc. bond : bond 0.00341 / 0.17 ( 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 123 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.868 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8388 (mmm) cc_final: 0.8044 (mmt) REVERT: B 483 TYR cc_start: 0.7697 (t80) cc_final: 0.7405 (t80) REVERT: B 581 GLU cc_start: 0.8626 (tt0) cc_final: 0.8213 (tm-30) REVERT: B 642 GLN cc_start: 0.7053 (pm20) cc_final: 0.6690 (mm-40) REVERT: C 301 MET cc_start: 0.8180 (ttm) cc_final: 0.7906 (ttt) REVERT: D 593 MET cc_start: 0.7682 (mtt) cc_final: 0.7368 (mtt) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.3272 time to fit residues: 56.7726 Evaluate side-chains 111 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 719 PHE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 121 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 160 optimal weight: 10.0000 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 HIS A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.128715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090013 restraints weight = 82751.925| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.95 r_work: 0.3115 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16355 Z= 0.126 Angle : 0.493 6.083 22381 Z= 0.281 Chirality : 0.039 0.180 2503 Planarity : 0.004 0.065 2710 Dihedral : 16.390 140.937 2788 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.52 % Allowed : 7.16 % 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: 0.54 (0.20), residues: 1824 helix: 2.44 (0.17), residues: 842 sheet: -0.33 (0.39), residues: 179 loop : -1.90 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 712 TYR 0.010 0.001 TYR C 266 PHE 0.012 0.001 PHE D 681 TRP 0.007 0.001 TRP D 725 HIS 0.004 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (16353) covalent geometry : angle 0.49346 / 0.28 (22381) hydrogen bonds : bond 0.05570 / 3.75 ( 725) hydrogen bonds : angle 4.48110 / 3.25 ( 2062) Misc. bond : bond 0.00031 / 0.02 ( 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 115 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.097 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8367 (mmm) cc_final: 0.8008 (mmt) REVERT: A 306 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 483 TYR cc_start: 0.7697 (t80) cc_final: 0.7430 (t80) REVERT: B 581 GLU cc_start: 0.8614 (tt0) cc_final: 0.8195 (tm-30) REVERT: B 642 GLN cc_start: 0.7066 (pm20) cc_final: 0.6703 (mm-40) REVERT: C 26 MET cc_start: 0.7716 (tpp) cc_final: 0.7508 (tpp) outliers start: 8 outliers final: 8 residues processed: 112 average time/residue: 0.3278 time to fit residues: 54.0400 Evaluate side-chains 108 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.128526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089130 restraints weight = 83453.738| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.95 r_work: 0.3131 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16355 Z= 0.131 Angle : 0.489 6.326 22381 Z= 0.278 Chirality : 0.039 0.175 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.343 140.775 2788 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.65 % Allowed : 7.61 % Favored : 91.74 % 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: 0.57 (0.20), residues: 1824 helix: 2.48 (0.17), residues: 842 sheet: -0.19 (0.39), residues: 175 loop : -1.93 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 309 TYR 0.010 0.001 TYR C 266 PHE 0.007 0.001 PHE B 649 TRP 0.014 0.001 TRP D 725 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16353) covalent geometry : angle 0.48904 / 0.28 (22381) hydrogen bonds : bond 0.05544 / 3.72 ( 725) hydrogen bonds : angle 4.42383 / 3.21 ( 2062) Misc. bond : bond 0.00058 / 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 111 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.765 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8539 (mmm) cc_final: 0.8182 (mmt) REVERT: B 483 TYR cc_start: 0.7739 (t80) cc_final: 0.7482 (t80) REVERT: B 581 GLU cc_start: 0.8621 (tt0) cc_final: 0.8192 (tm-30) REVERT: B 642 GLN cc_start: 0.7109 (pm20) cc_final: 0.6750 (mm-40) REVERT: C 26 MET cc_start: 0.7868 (tpp) cc_final: 0.7638 (tpp) REVERT: D 593 MET cc_start: 0.7917 (mpp) cc_final: 0.7580 (mpp) outliers start: 10 outliers final: 9 residues processed: 108 average time/residue: 0.3226 time to fit residues: 51.1296 Evaluate side-chains 104 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 184 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 179 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.128238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089329 restraints weight = 80695.752| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.93 r_work: 0.3073 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16355 Z= 0.155 Angle : 0.506 7.024 22381 Z= 0.286 Chirality : 0.039 0.173 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.345 140.463 2788 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.65 % Allowed : 7.68 % Favored : 91.68 % 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: 0.53 (0.20), residues: 1824 helix: 2.47 (0.17), residues: 843 sheet: -0.39 (0.39), residues: 179 loop : -1.94 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 309 TYR 0.012 0.001 TYR C 266 PHE 0.007 0.001 PHE C 330 TRP 0.009 0.001 TRP D 725 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16353) covalent geometry : angle 0.50574 / 0.29 (22381) hydrogen bonds : bond 0.05738 / 3.84 ( 725) hydrogen bonds : angle 4.41909 / 3.21 ( 2062) Misc. bond : bond 0.00034 / 0.02 ( 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 110 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.837 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: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8257 (mmm) cc_final: 0.7890 (mmt) REVERT: B 483 TYR cc_start: 0.7603 (t80) cc_final: 0.7332 (t80) REVERT: B 581 GLU cc_start: 0.8629 (tt0) cc_final: 0.8214 (tm-30) REVERT: B 642 GLN cc_start: 0.7150 (pm20) cc_final: 0.6777 (mm-40) REVERT: C 26 MET cc_start: 0.7552 (tpp) cc_final: 0.7347 (tpp) REVERT: D 593 MET cc_start: 0.7916 (mpp) cc_final: 0.7570 (mpp) outliers start: 10 outliers final: 9 residues processed: 107 average time/residue: 0.3073 time to fit residues: 48.4670 Evaluate side-chains 102 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 146 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.128775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089666 restraints weight = 80964.451| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.08 r_work: 0.3080 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.002 0.021 16355 Z= 0.118 Angle : 0.481 6.741 22381 Z= 0.272 Chirality : 0.039 0.177 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.317 140.898 2788 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.65 % Allowed : 7.87 % Favored : 91.48 % 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: 0.62 (0.20), residues: 1824 helix: 2.54 (0.17), residues: 845 sheet: -0.36 (0.39), residues: 179 loop : -1.89 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 600 TYR 0.010 0.001 TYR C 266 PHE 0.010 0.001 PHE B 681 TRP 0.009 0.001 TRP D 725 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (16353) covalent geometry : angle 0.48140 / 0.27 (22381) hydrogen bonds : bond 0.05291 / 3.56 ( 725) hydrogen bonds : angle 4.30736 / 3.13 ( 2062) Misc. bond : bond 0.00056 / 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 109 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.863 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: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8233 (mmm) cc_final: 0.7849 (mmt) REVERT: B 483 TYR cc_start: 0.7568 (t80) cc_final: 0.7313 (t80) REVERT: B 581 GLU cc_start: 0.8628 (tt0) cc_final: 0.8210 (tm-30) REVERT: B 642 GLN cc_start: 0.7139 (pm20) cc_final: 0.6765 (mm-40) REVERT: D 593 MET cc_start: 0.7896 (mpp) cc_final: 0.7562 (mpp) outliers start: 10 outliers final: 8 residues processed: 105 average time/residue: 0.3150 time to fit residues: 49.0611 Evaluate side-chains 102 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 719 PHE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.129496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090305 restraints weight = 80816.694| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.00 r_work: 0.3093 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16355 Z= 0.111 Angle : 0.472 6.574 22381 Z= 0.265 Chirality : 0.039 0.174 2503 Planarity : 0.004 0.047 2710 Dihedral : 16.284 140.699 2788 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.65 % Allowed : 7.74 % Favored : 91.61 % 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: 0.74 (0.20), residues: 1824 helix: 2.64 (0.17), residues: 845 sheet: -0.53 (0.37), residues: 199 loop : -1.78 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 599 TYR 0.013 0.001 TYR B 587 PHE 0.011 0.001 PHE D 681 TRP 0.007 0.001 TRP D 725 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (16353) covalent geometry : angle 0.47171 / 0.27 (22381) hydrogen bonds : bond 0.04928 / 3.33 ( 725) hydrogen bonds : angle 4.19413 / 3.05 ( 2062) Misc. bond : bond 0.00038 / 0.02 ( 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 110 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8208 (mmm) cc_final: 0.7815 (mmt) REVERT: B 581 GLU cc_start: 0.8630 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 642 GLN cc_start: 0.7128 (pm20) cc_final: 0.6740 (mm-40) REVERT: D 593 MET cc_start: 0.7880 (mpp) cc_final: 0.7557 (mpp) outliers start: 10 outliers final: 7 residues processed: 107 average time/residue: 0.3018 time to fit residues: 48.5589 Evaluate side-chains 104 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 719 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.127524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088317 restraints weight = 80724.033| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.99 r_work: 0.3073 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16355 Z= 0.149 Angle : 0.497 6.525 22381 Z= 0.279 Chirality : 0.039 0.172 2503 Planarity : 0.004 0.050 2710 Dihedral : 16.341 140.410 2788 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.52 % Allowed : 8.13 % Favored : 91.35 % 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: 0.67 (0.20), residues: 1824 helix: 2.63 (0.18), residues: 844 sheet: -0.39 (0.39), residues: 179 loop : -1.90 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 309 TYR 0.011 0.001 TYR C 266 PHE 0.015 0.001 PHE B 681 TRP 0.006 0.001 TRP D 725 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16353) covalent geometry : angle 0.49699 / 0.28 (22381) hydrogen bonds : bond 0.05352 / 3.59 ( 725) hydrogen bonds : angle 4.25845 / 3.10 ( 2062) Misc. bond : bond 0.00038 / 0.02 ( 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 106 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.852 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: A 26 MET cc_start: 0.8256 (mmm) cc_final: 0.7881 (mmt) REVERT: A 306 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6599 (mm-30) REVERT: B 581 GLU cc_start: 0.8644 (tt0) cc_final: 0.8233 (tm-30) REVERT: D 593 MET cc_start: 0.7881 (mpp) cc_final: 0.7550 (mpp) outliers start: 8 outliers final: 8 residues processed: 105 average time/residue: 0.3286 time to fit residues: 50.6800 Evaluate side-chains 102 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 719 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088244 restraints weight = 81110.335| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.08 r_work: 0.3069 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16355 Z= 0.133 Angle : 0.492 6.893 22381 Z= 0.275 Chirality : 0.039 0.174 2503 Planarity : 0.004 0.049 2710 Dihedral : 16.390 140.714 2788 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.58 % Allowed : 7.87 % Favored : 91.55 % 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: 0.67 (0.20), residues: 1824 helix: 2.62 (0.17), residues: 844 sheet: -0.39 (0.39), residues: 179 loop : -1.90 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 480 TYR 0.014 0.001 TYR B 587 PHE 0.009 0.001 PHE B 660 TRP 0.006 0.001 TRP D 725 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16353) covalent geometry : angle 0.49203 / 0.27 (22381) hydrogen bonds : bond 0.05263 / 3.54 ( 725) hydrogen bonds : angle 4.22832 / 3.08 ( 2062) Misc. bond : bond 0.00035 / 0.02 ( 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 110 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.827 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: A 26 MET cc_start: 0.8216 (mmm) cc_final: 0.7838 (mmt) REVERT: B 581 GLU cc_start: 0.8644 (tt0) cc_final: 0.8233 (tm-30) REVERT: B 597 MET cc_start: 0.7132 (ptp) cc_final: 0.6907 (ptp) REVERT: D 593 MET cc_start: 0.7891 (mpp) cc_final: 0.7565 (mpp) outliers start: 9 outliers final: 9 residues processed: 108 average time/residue: 0.3332 time to fit residues: 52.5290 Evaluate side-chains 107 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 719 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 81 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.127730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088716 restraints weight = 81509.325| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.04 r_work: 0.3064 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16355 Z= 0.151 Angle : 0.506 6.765 22381 Z= 0.283 Chirality : 0.039 0.170 2503 Planarity : 0.004 0.050 2710 Dihedral : 16.433 140.599 2788 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 0.65 % Allowed : 8.06 % Favored : 91.29 % 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: 0.61 (0.20), residues: 1824 helix: 2.54 (0.18), residues: 850 sheet: -0.40 (0.39), residues: 179 loop : -1.94 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 309 TYR 0.011 0.001 TYR C 266 PHE 0.017 0.001 PHE B 681 TRP 0.005 0.001 TRP D 725 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16353) covalent geometry : angle 0.50617 / 0.28 (22381) hydrogen bonds : bond 0.05438 / 3.64 ( 725) hydrogen bonds : angle 4.25903 / 3.10 ( 2062) 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: 6899.53 seconds wall clock time: 117 minutes 46.48 seconds (7066.48 seconds total)