Starting phenix.real_space_refine on Fri Mar 6 13:42:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9m_14574/03_2026/7z9m_14574_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9m_14574/03_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_14574/03_2026/7z9m_14574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9m_14574/03_2026/7z9m_14574.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9m_14574/03_2026/7z9m_14574_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9m_14574/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 5.92, per 1000 atoms: 0.19 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: 2.85 Conformation dependent library (CDL) restraints added in 905.1 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: 5.37 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: 7.43 Time building geometry restraints manager: 3.98 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=" 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 bond pdb=" O1P PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.522 1.476 0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 31719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 57059 2.26 - 4.53: 368 4.53 - 6.79: 36 6.79 - 9.06: 3 9.06 - 11.32: 2 Bond angle restraints: 57468 Sorted by residual: angle pdb=" OH PTR C 122 " pdb=" P PTR C 122 " pdb=" O2P PTR C 122 " ideal model delta sigma weight residual 99.92 111.24 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" OH PTR A 122 " pdb=" P PTR A 122 " pdb=" O2P PTR A 122 " ideal model delta sigma weight residual 99.92 109.57 -9.65 3.00e+00 1.11e-01 1.03e+01 angle pdb=" O3' DG E 7 " pdb=" C3' DG E 7 " pdb=" C2' DG E 7 " ideal model delta sigma weight residual 111.50 116.08 -4.58 1.50e+00 4.44e-01 9.33e+00 angle pdb=" O3' DA F 7 " pdb=" C3' DA F 7 " pdb=" C2' DA F 7 " ideal model delta sigma weight residual 111.50 115.81 -4.31 1.50e+00 4.44e-01 8.27e+00 angle pdb=" C ASP B 414 " pdb=" N PRO B 415 " pdb=" CA PRO B 415 " ideal model delta sigma weight residual 121.65 119.04 2.61 1.01e+00 9.80e-01 6.67e+00 ... (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: 1699 0.036 - 0.071: 595 0.071 - 0.106: 123 0.106 - 0.142: 80 0.142 - 0.177: 6 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=" CA ILE A 155 " pdb=" N ILE A 155 " pdb=" C ILE A 155 " pdb=" CB ILE A 155 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.910 Find NCS groups from input model: 0.340 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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= 0.278 Angle : 0.629 11.324 22381 Z= 0.338 Chirality : 0.041 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 covalent geometry : bond 0.00409 (16353) covalent geometry : angle 0.62881 (22381) hydrogen bonds : bond 0.17276 ( 725) hydrogen bonds : angle 5.62047 ( 2062) Misc. bond : bond 0.18113 ( 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 : 0.861 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: 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: 0.4164 time to fit residues: 127.1306 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 : 0.838 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 591 GLN B 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.126486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087315 restraints weight = 84062.266| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.16 r_work: 0.3068 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16355 Z= 0.229 Angle : 0.588 7.699 22381 Z= 0.328 Chirality : 0.043 0.153 2503 Planarity : 0.005 0.046 2710 Dihedral : 16.560 142.148 2790 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.77 % Allowed : 6.45 % Favored : 92.77 % 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 (0.19), residues: 1824 helix: 2.24 (0.17), residues: 847 sheet: -0.33 (0.39), residues: 180 loop : -1.96 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 302 TYR 0.015 0.002 TYR C 266 PHE 0.017 0.002 PHE B 719 TRP 0.006 0.001 TRP B 647 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00539 (16353) covalent geometry : angle 0.58827 (22381) hydrogen bonds : bond 0.07138 ( 725) hydrogen bonds : angle 4.78783 ( 2062) Misc. bond : bond 0.00053 ( 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 132 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.843 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: 0.8465 (mmm) cc_final: 0.8129 (mmt) REVERT: A 306 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6945 (mm-30) REVERT: B 483 TYR cc_start: 0.7737 (t80) cc_final: 0.7450 (t80) REVERT: B 581 GLU cc_start: 0.8625 (tt0) cc_final: 0.8225 (tm-30) REVERT: B 642 GLN cc_start: 0.7054 (pm20) cc_final: 0.6679 (mm-40) REVERT: D 593 MET cc_start: 0.7698 (mtt) cc_final: 0.7404 (mtt) REVERT: D 597 MET cc_start: 0.6569 (ptt) cc_final: 0.6291 (ptt) outliers start: 12 outliers final: 9 residues processed: 128 average time/residue: 0.3497 time to fit residues: 63.2905 Evaluate side-chains 112 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3878 r_free = 0.3878 target = 0.128558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088697 restraints weight = 83291.624| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.85 r_work: 0.3112 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2146 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= 0.120 Angle : 0.498 5.669 22381 Z= 0.276 Chirality : 0.039 0.142 2503 Planarity : 0.004 0.044 2710 Dihedral : 16.301 141.598 2790 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.71 % Allowed : 7.16 % Favored : 92.13 % 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: 2.45 (0.17), residues: 850 sheet: -0.19 (0.39), residues: 176 loop : -1.96 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.012 0.001 TYR C 266 PHE 0.008 0.001 PHE B 649 TRP 0.005 0.001 TRP B 629 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00261 (16353) covalent geometry : angle 0.49846 (22381) hydrogen bonds : bond 0.05513 ( 725) hydrogen bonds : angle 4.41095 ( 2062) Misc. bond : bond 0.00045 ( 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 120 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.949 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: A 26 MET cc_start: 0.8526 (mmm) cc_final: 0.8165 (mmt) REVERT: B 483 TYR cc_start: 0.7710 (t80) cc_final: 0.7432 (t80) REVERT: B 581 GLU cc_start: 0.8630 (tt0) cc_final: 0.8200 (tm-30) REVERT: B 642 GLN cc_start: 0.7128 (pm20) cc_final: 0.6760 (mm-40) REVERT: D 593 MET cc_start: 0.7768 (mtt) cc_final: 0.7477 (mtt) outliers start: 11 outliers final: 9 residues processed: 116 average time/residue: 0.3430 time to fit residues: 56.8522 Evaluate side-chains 113 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 595 ASN 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: 8.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.128170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088579 restraints weight = 80677.330| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.06 r_work: 0.3079 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16355 Z= 0.129 Angle : 0.489 6.901 22381 Z= 0.271 Chirality : 0.039 0.144 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.165 142.086 2788 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.84 % Allowed : 7.29 % Favored : 91.87 % 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: 0.67 (0.20), residues: 1824 helix: 2.60 (0.17), residues: 850 sheet: -0.33 (0.39), residues: 179 loop : -1.92 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.011 0.001 TYR C 266 PHE 0.006 0.001 PHE B 660 TRP 0.007 0.001 TRP B 647 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00292 (16353) covalent geometry : angle 0.48863 (22381) hydrogen bonds : bond 0.05215 ( 725) hydrogen bonds : angle 4.25242 ( 2062) Misc. bond : bond 0.00047 ( 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 120 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.759 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: 0.8232 (mmm) cc_final: 0.7928 (mmt) REVERT: A 306 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6605 (mm-30) REVERT: B 581 GLU cc_start: 0.8629 (tt0) cc_final: 0.8212 (tm-30) REVERT: B 667 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6072 (ptp-110) REVERT: C 516 LYS cc_start: 0.7409 (mtpp) cc_final: 0.7203 (ptmt) REVERT: D 593 MET cc_start: 0.7763 (mtt) cc_final: 0.7482 (mtm) REVERT: D 712 ARG cc_start: 0.6143 (mmm-85) cc_final: 0.5858 (tpp-160) outliers start: 13 outliers final: 7 residues processed: 117 average time/residue: 0.3430 time to fit residues: 57.3095 Evaluate side-chains 104 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 667 ARG 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 595 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.127601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088477 restraints weight = 81274.156| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.11 r_work: 0.3057 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16355 Z= 0.152 Angle : 0.510 6.821 22381 Z= 0.281 Chirality : 0.040 0.146 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.300 142.651 2788 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.90 % Allowed : 7.81 % 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: 0.58 (0.20), residues: 1824 helix: 2.51 (0.17), residues: 850 sheet: -0.40 (0.39), residues: 179 loop : -1.95 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 599 TYR 0.012 0.001 TYR C 266 PHE 0.011 0.001 PHE B 681 TRP 0.004 0.001 TRP D 725 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00353 (16353) covalent geometry : angle 0.50964 (22381) hydrogen bonds : bond 0.05559 ( 725) hydrogen bonds : angle 4.29139 ( 2062) Misc. bond : bond 0.00052 ( 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 118 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.842 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: 0.8275 (mmm) cc_final: 0.7895 (mmt) REVERT: A 306 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6630 (mm-30) REVERT: B 581 GLU cc_start: 0.8643 (tt0) cc_final: 0.8232 (tm-30) REVERT: B 667 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.6033 (ptp-110) REVERT: C 516 LYS cc_start: 0.7443 (mtpp) cc_final: 0.7227 (ptmt) REVERT: D 593 MET cc_start: 0.7906 (mtt) cc_final: 0.7655 (mtm) outliers start: 14 outliers final: 11 residues processed: 115 average time/residue: 0.3719 time to fit residues: 59.1666 Evaluate side-chains 107 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET 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 667 ARG 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 595 ASN 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: 2.9990 chunk 84 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089829 restraints weight = 80827.073| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.03 r_work: 0.3085 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16355 Z= 0.115 Angle : 0.483 5.884 22381 Z= 0.266 Chirality : 0.039 0.141 2503 Planarity : 0.004 0.042 2710 Dihedral : 16.257 142.907 2788 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 0.77 % Allowed : 8.06 % Favored : 91.16 % 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: 0.73 (0.20), residues: 1824 helix: 2.63 (0.18), residues: 851 sheet: -0.34 (0.39), residues: 179 loop : -1.87 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 600 TYR 0.010 0.001 TYR C 266 PHE 0.031 0.001 PHE B 719 TRP 0.004 0.001 TRP B 629 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00256 (16353) covalent geometry : angle 0.48327 (22381) hydrogen bonds : bond 0.04870 ( 725) hydrogen bonds : angle 4.12212 ( 2062) Misc. bond : bond 0.00040 ( 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 114 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.669 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: 0.8224 (mmm) cc_final: 0.7905 (mmt) REVERT: A 32 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7697 (mtt-85) REVERT: A 306 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6973 (mm-30) REVERT: B 581 GLU cc_start: 0.8648 (tt0) cc_final: 0.8236 (tm-30) REVERT: B 667 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6020 (ptp-110) REVERT: C 516 LYS cc_start: 0.7428 (mtpp) cc_final: 0.7213 (ptmt) REVERT: D 593 MET cc_start: 0.7891 (mtt) cc_final: 0.7675 (mtm) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 0.3393 time to fit residues: 53.9021 Evaluate side-chains 101 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 667 ARG 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 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: 0.3980 chunk 52 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 146 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087166 restraints weight = 80735.713| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.93 r_work: 0.3142 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16355 Z= 0.092 Angle : 0.458 5.787 22381 Z= 0.253 Chirality : 0.038 0.135 2503 Planarity : 0.003 0.040 2710 Dihedral : 16.158 143.351 2788 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 0.39 % Allowed : 8.65 % Favored : 90.97 % 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: 0.94 (0.20), residues: 1824 helix: 2.76 (0.18), residues: 855 sheet: -0.43 (0.37), residues: 199 loop : -1.70 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 599 TYR 0.009 0.001 TYR B 587 PHE 0.014 0.001 PHE B 681 TRP 0.004 0.001 TRP D 647 HIS 0.003 0.000 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00197 (16353) covalent geometry : angle 0.45823 (22381) hydrogen bonds : bond 0.04025 ( 725) hydrogen bonds : angle 3.92036 ( 2062) Misc. bond : bond 0.00038 ( 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 117 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8239 (mmm) cc_final: 0.7835 (mmt) REVERT: A 306 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7028 (mm-30) REVERT: B 581 GLU cc_start: 0.8624 (tt0) cc_final: 0.8209 (tm-30) REVERT: B 667 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6123 (ptp-110) outliers start: 6 outliers final: 3 residues processed: 115 average time/residue: 0.3359 time to fit residues: 55.0629 Evaluate side-chains 104 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 553 ASP 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: 0.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 172 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.130401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087269 restraints weight = 80804.485| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.92 r_work: 0.3145 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16355 Z= 0.094 Angle : 0.458 5.560 22381 Z= 0.252 Chirality : 0.038 0.136 2503 Planarity : 0.003 0.040 2710 Dihedral : 16.144 143.936 2788 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 0.39 % Allowed : 8.77 % Favored : 90.84 % 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: 1.00 (0.20), residues: 1824 helix: 2.77 (0.18), residues: 855 sheet: -0.30 (0.37), residues: 199 loop : -1.65 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 309 TYR 0.008 0.001 TYR C 149 PHE 0.028 0.001 PHE B 719 TRP 0.003 0.000 TRP B 629 HIS 0.003 0.000 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00203 (16353) covalent geometry : angle 0.45757 (22381) hydrogen bonds : bond 0.03964 ( 725) hydrogen bonds : angle 3.89635 ( 2062) Misc. bond : bond 0.00031 ( 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 109 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 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: A 26 MET cc_start: 0.8242 (mmm) cc_final: 0.7829 (mmt) REVERT: A 306 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7031 (mm-30) REVERT: B 581 GLU cc_start: 0.8634 (tt0) cc_final: 0.8219 (tm-30) REVERT: B 597 MET cc_start: 0.7380 (tpp) cc_final: 0.6699 (ptp) REVERT: B 667 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6113 (ptp-110) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.3465 time to fit residues: 52.9881 Evaluate side-chains 104 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 667 ARG 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 D residue 553 ASP 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: 6.9990 chunk 154 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086674 restraints weight = 81676.520| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.96 r_work: 0.3031 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16355 Z= 0.238 Angle : 0.579 8.915 22381 Z= 0.320 Chirality : 0.043 0.158 2503 Planarity : 0.005 0.042 2710 Dihedral : 16.541 142.743 2788 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.46 % Favored : 92.49 % Rotamer: Outliers : 0.77 % Allowed : 8.52 % Favored : 90.71 % 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: 0.49 (0.20), residues: 1824 helix: 2.41 (0.17), residues: 851 sheet: -0.40 (0.39), residues: 179 loop : -1.97 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.013 0.001 TYR C 266 PHE 0.015 0.002 PHE B 719 TRP 0.006 0.001 TRP D 725 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00579 (16353) covalent geometry : angle 0.57947 (22381) hydrogen bonds : bond 0.06408 ( 725) hydrogen bonds : angle 4.42635 ( 2062) Misc. bond : bond 0.00066 ( 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 113 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.782 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: A 26 MET cc_start: 0.8324 (mmm) cc_final: 0.7942 (mmt) REVERT: A 32 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: A 286 VAL cc_start: 0.8355 (t) cc_final: 0.7966 (p) REVERT: A 306 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7268 (tm-30) REVERT: B 581 GLU cc_start: 0.8619 (tt0) cc_final: 0.8215 (tm-30) REVERT: B 667 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6133 (ptp-110) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 0.3470 time to fit residues: 54.4782 Evaluate side-chains 107 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 667 ARG 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 595 ASN 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: 0.6980 chunk 165 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086764 restraints weight = 81769.750| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.19 r_work: 0.3018 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16355 Z= 0.218 Angle : 0.570 8.599 22381 Z= 0.314 Chirality : 0.042 0.157 2503 Planarity : 0.004 0.044 2710 Dihedral : 16.740 148.003 2788 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 0.65 % Allowed : 8.58 % Favored : 90.77 % 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: 0.19 (0.20), residues: 1824 helix: 2.18 (0.17), residues: 851 sheet: -0.56 (0.39), residues: 179 loop : -2.15 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 689 TYR 0.013 0.001 TYR C 266 PHE 0.015 0.002 PHE B 719 TRP 0.005 0.001 TRP D 725 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00521 (16353) covalent geometry : angle 0.57019 (22381) hydrogen bonds : bond 0.06439 ( 725) hydrogen bonds : angle 4.50378 ( 2062) Misc. bond : bond 0.00079 ( 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 107 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.829 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: 0.8309 (mmm) cc_final: 0.8002 (mmt) REVERT: A 32 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7675 (mtt-85) REVERT: B 581 GLU cc_start: 0.8615 (tt0) cc_final: 0.8238 (tm-30) REVERT: B 667 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6226 (ptp-110) REVERT: D 491 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7348 (m90) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.3549 time to fit residues: 53.4519 Evaluate side-chains 101 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 491 HIS 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: 8.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.125300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087335 restraints weight = 81756.155| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.14 r_work: 0.3024 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16355 Z= 0.208 Angle : 0.761 57.300 22381 Z= 0.484 Chirality : 0.042 0.546 2503 Planarity : 0.005 0.130 2710 Dihedral : 16.738 147.943 2788 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.29 % Favored : 92.65 % Rotamer: Outliers : 0.45 % Allowed : 8.84 % Favored : 90.71 % Cbeta Deviations : 0.06 % 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: 0.18 (0.20), residues: 1824 helix: 2.17 (0.17), residues: 850 sheet: -0.56 (0.39), residues: 179 loop : -2.16 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.012 0.001 TYR C 266 PHE 0.011 0.001 PHE B 719 TRP 0.005 0.001 TRP D 725 HIS 0.154 0.003 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00431 (16353) covalent geometry : angle 0.76118 (22381) hydrogen bonds : bond 0.06259 ( 725) hydrogen bonds : angle 4.48958 ( 2062) Misc. bond : bond 0.00067 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6914.70 seconds wall clock time: 117 minutes 54.57 seconds (7074.57 seconds total)