Starting phenix.real_space_refine on Sun Aug 24 00:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nr7_49724/08_2025/9nr7_49724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nr7_49724/08_2025/9nr7_49724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nr7_49724/08_2025/9nr7_49724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nr7_49724/08_2025/9nr7_49724.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nr7_49724/08_2025/9nr7_49724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nr7_49724/08_2025/9nr7_49724.map" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 89 5.16 5 C 10038 2.51 5 N 2511 2.21 5 O 2899 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15553 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2942 Classifications: {'peptide': 405} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 11, 'TYR:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 142 Chain: "B" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2881 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 10, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2941 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 5, 'PHE:plan': 3, 'GLU:plan': 10, 'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 128 Chain: "D" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2908 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 7, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "E" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 583 Classifications: {'peptide': 117} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 115} Link IDs: {'TRANS': 116} Chain breaks: 2 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "F" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1325 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 568 Classifications: {'peptide': 114} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 112} Link IDs: {'TRANS': 113} Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 Chain: "H" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1297 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.70, per 1000 atoms: 0.24 Number of scatterers: 15553 At special positions: 0 Unit cell: (118.44, 133.48, 133.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 89 16.00 P 4 15.00 F 12 9.00 O 2899 8.00 N 2511 7.00 C 10038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 775 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 720 " - pdb=" SG CYS D 775 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 386.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4022 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 20 sheets defined 66.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.901A pdb=" N VAL A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.543A pdb=" N ASP A 515 " --> pdb=" O SER A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 543 Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.883A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 626 removed outlier: 4.090A pdb=" N ARG A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.159A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 removed outlier: 4.076A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.549A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 439 Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.738A pdb=" N GLU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 525 through 548 removed outlier: 4.113A pdb=" N MET B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 599 through 628 removed outlier: 4.241A pdb=" N VAL B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 628 " --> pdb=" O ALA B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 645 removed outlier: 4.000A pdb=" N THR B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 666 through 678 removed outlier: 3.528A pdb=" N GLU B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 671 " --> pdb=" O ALA B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 698 Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'B' and resid 744 through 758 Processing helix chain 'B' and resid 758 through 771 removed outlier: 4.580A pdb=" N ASP B 762 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 819 removed outlier: 4.978A pdb=" N GLY B 796 " --> pdb=" O SER B 792 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL B 797 " --> pdb=" O ASN B 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.665A pdb=" N GLY C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 509 through 514 removed outlier: 3.737A pdb=" N LEU C 514 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 543 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 625 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 712 Processing helix chain 'C' and resid 739 through 753 removed outlier: 3.546A pdb=" N ASN C 743 " --> pdb=" O ARG C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 765 removed outlier: 3.589A pdb=" N ASP C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 814 Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 426 through 439 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.617A pdb=" N ASP D 521 " --> pdb=" O SER D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 546 Processing helix chain 'D' and resid 576 through 586 Processing helix chain 'D' and resid 597 through 629 Processing helix chain 'D' and resid 638 through 644 Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.826A pdb=" N ARG D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 679 removed outlier: 4.086A pdb=" N MET D 672 " --> pdb=" O VAL D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 682 No H-bonds generated for 'chain 'D' and resid 680 through 682' Processing helix chain 'D' and resid 687 through 697 removed outlier: 3.657A pdb=" N LYS D 697 " --> pdb=" O ALA D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 Processing helix chain 'D' and resid 744 through 759 Processing helix chain 'D' and resid 760 through 770 Processing helix chain 'D' and resid 791 through 819 removed outlier: 4.528A pdb=" N GLY D 796 " --> pdb=" O SER D 792 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL D 797 " --> pdb=" O ASN D 793 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE D 798 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 799 " --> pdb=" O ALA D 795 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 800 " --> pdb=" O GLY D 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 34 Processing helix chain 'E' and resid 59 through 81 Processing helix chain 'E' and resid 84 through 110 removed outlier: 6.498A pdb=" N UNK E 90 " --> pdb=" O UNK E 86 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N UNK E 91 " --> pdb=" O UNK E 87 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N UNK E 97 " --> pdb=" O UNK E 93 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N UNK E 98 " --> pdb=" O UNK E 94 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N UNK E 109 " --> pdb=" O UNK E 105 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N UNK E 110 " --> pdb=" O UNK E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 157 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 128 Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.943A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 207 removed outlier: 3.897A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 32 removed outlier: 3.961A pdb=" N UNK G 8 " --> pdb=" O UNK G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 84 removed outlier: 3.786A pdb=" N UNK G 84 " --> pdb=" O UNK G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 109 removed outlier: 3.801A pdb=" N UNK G 93 " --> pdb=" O UNK G 89 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N UNK G 96 " --> pdb=" O UNK G 92 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N UNK G 97 " --> pdb=" O UNK G 93 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N UNK G 109 " --> pdb=" O UNK G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 158 removed outlier: 3.502A pdb=" N UNK G 158 " --> pdb=" O UNK G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 30 removed outlier: 3.952A pdb=" N THR H 30 " --> pdb=" O ILE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 105 through 128 Processing helix chain 'H' and resid 133 through 162 Processing helix chain 'H' and resid 179 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 440 removed outlier: 3.847A pdb=" N THR A 395 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 394 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.966A pdb=" N ASP A 486 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 732 " --> pdb=" O ASP A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 497 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 501 removed outlier: 4.100A pdb=" N ILE A 500 " --> pdb=" O MET A 717 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 717 " --> pdb=" O ILE A 500 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 400 removed outlier: 3.917A pdb=" N THR B 400 " --> pdb=" O ILE B 476 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 456 removed outlier: 3.615A pdb=" N ASN B 463 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 492 through 493 removed outlier: 4.088A pdb=" N ASP B 492 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 738 " --> pdb=" O ASP B 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 649 through 650 removed outlier: 3.579A pdb=" N GLY B 650 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 649 through 650 removed outlier: 3.579A pdb=" N GLY B 650 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 498 " --> pdb=" O TYR B 734 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 732 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 391 through 394 Processing sheet with id=AB3, first strand: chain 'C' and resid 402 through 404 Processing sheet with id=AB4, first strand: chain 'C' and resid 486 through 487 removed outlier: 4.341A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 732 " --> pdb=" O ASP C 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 698 through 701 removed outlier: 3.803A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 398 through 401 Processing sheet with id=AB7, first strand: chain 'D' and resid 408 through 410 removed outlier: 3.882A pdb=" N MET D 409 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 424 " --> pdb=" O MET D 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.615A pdb=" N ALA D 454 " --> pdb=" O ASN D 463 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 463 " --> pdb=" O ALA D 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 492 through 493 Processing sheet with id=AC1, first strand: chain 'D' and resid 684 through 685 removed outlier: 8.747A pdb=" N THR D 685 " --> pdb=" O TYR D 649 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR D 651 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU D 652 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N GLU D 707 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 498 " --> pdb=" O TYR D 734 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE D 502 " --> pdb=" O ASP D 730 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP D 730 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE D 504 " --> pdb=" O ASN D 728 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASN D 728 " --> pdb=" O ILE D 504 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 34 through 38 removed outlier: 4.002A pdb=" N LEU F 34 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER F 61 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER F 36 " --> pdb=" O THR F 59 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2943 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4940 1.35 - 1.49: 4258 1.49 - 1.62: 6525 1.62 - 1.76: 0 1.76 - 1.90: 148 Bond restraints: 15871 Sorted by residual: bond pdb=" C GLU B 680 " pdb=" N PRO B 681 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.50e+00 bond pdb=" C ASP C 515 " pdb=" N PRO C 516 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.75e+00 bond pdb=" CG1 ILE C 607 " pdb=" CD1 ILE C 607 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.74e+00 bond pdb=" CB GLN B 588 " pdb=" CG GLN B 588 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" C GLU A 674 " pdb=" N PRO A 675 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.47e+00 ... (remaining 15866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 21407 3.06 - 6.12: 224 6.12 - 9.18: 49 9.18 - 12.24: 4 12.24 - 15.30: 1 Bond angle restraints: 21685 Sorted by residual: angle pdb=" N PRO D 777 " pdb=" CA PRO D 777 " pdb=" CB PRO D 777 " ideal model delta sigma weight residual 103.51 110.08 -6.57 9.60e-01 1.09e+00 4.68e+01 angle pdb=" N PRO B 747 " pdb=" CA PRO B 747 " pdb=" CB PRO B 747 " ideal model delta sigma weight residual 103.23 109.99 -6.76 1.07e+00 8.73e-01 4.00e+01 angle pdb=" N PRO B 777 " pdb=" CA PRO B 777 " pdb=" CB PRO B 777 " ideal model delta sigma weight residual 103.33 110.27 -6.94 1.10e+00 8.26e-01 3.98e+01 angle pdb=" N PRO D 747 " pdb=" CA PRO D 747 " pdb=" CB PRO D 747 " ideal model delta sigma weight residual 103.23 109.94 -6.71 1.07e+00 8.73e-01 3.93e+01 angle pdb=" C ALA C 408 " pdb=" CA ALA C 408 " pdb=" CB ALA C 408 " ideal model delta sigma weight residual 116.54 110.77 5.77 1.15e+00 7.56e-01 2.52e+01 ... (remaining 21680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 8269 15.43 - 30.86: 680 30.86 - 46.29: 180 46.29 - 61.72: 35 61.72 - 77.16: 12 Dihedral angle restraints: 9176 sinusoidal: 2898 harmonic: 6278 Sorted by residual: dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 170.16 -77.16 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -150.82 64.82 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CA SER H 179 " pdb=" C SER H 179 " pdb=" N PHE H 180 " pdb=" CA PHE H 180 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 9173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2065 0.055 - 0.110: 425 0.110 - 0.164: 65 0.164 - 0.219: 5 0.219 - 0.274: 6 Chirality restraints: 2566 Sorted by residual: chirality pdb=" CB VAL H 57 " pdb=" CA VAL H 57 " pdb=" CG1 VAL H 57 " pdb=" CG2 VAL H 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PRO D 777 " pdb=" N PRO D 777 " pdb=" C PRO D 777 " pdb=" CB PRO D 777 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB THR C 453 " pdb=" CA THR C 453 " pdb=" OG1 THR C 453 " pdb=" CG2 THR C 453 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2563 not shown) Planarity restraints: 2713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 405 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 406 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 406 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 406 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 805 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.14e+00 pdb=" C VAL A 805 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL A 805 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 806 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 796 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ILE A 796 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE A 796 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 797 " -0.011 2.00e-02 2.50e+03 ... (remaining 2710 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2682 2.76 - 3.30: 15408 3.30 - 3.83: 26220 3.83 - 4.37: 26573 4.37 - 4.90: 46237 Nonbonded interactions: 117120 Sorted by model distance: nonbonded pdb=" O PHE C 580 " pdb=" OG1 THR C 605 " model vdw 2.228 3.040 nonbonded pdb=" O PHE C 810 " pdb=" OG SER C 814 " model vdw 2.266 3.040 nonbonded pdb=" NE2 GLN C 710 " pdb=" O TRP C 763 " model vdw 2.296 3.120 nonbonded pdb=" O ALA H 100 " pdb=" OG SER H 104 " model vdw 2.323 3.040 nonbonded pdb=" O MET A 581 " pdb=" NE2 GLN A 583 " model vdw 2.337 3.120 ... (remaining 117115 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 393 through 396 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 400 through 402 or (resid 403 and (name N \ or name CA or name C or name O or name CB )) or (resid 405 through 407 and (name \ N or name CA or name C or name O or name CB )) or (resid 411 through 414 and (n \ ame N or name CA or name C or name O or name CB )) or resid 415 or resid 417 thr \ ough 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid \ 436 or resid 440 through 441 or resid 443 through 449 or (resid 450 and (name N \ or name CA or name C or name O or name CB )) or resid 452 through 454 or resid \ 456 through 466 or resid 468 or resid 471 or resid 473 through 493 or (resid 494 \ and (name N or name CA or name C or name O or name CB )) or resid 495 through 5 \ 05 or (resid 506 through 507 and (name N or name CA or name C or name O or name \ CB )) or resid 508 through 510 or (resid 511 and (name N or name CA or name C or \ name O or name CB )) or resid 512 through 514 or (resid 515 and (name N or name \ CA or name C or name O or name CB )) or resid 516 through 541 or (resid 566 thr \ ough 567 and (name N or name CA or name C or name O or name CB )) or resid 568 t \ hrough 594 or (resid 595 and (name N or name CA or name C or name O or name CB ) \ ) or resid 596 through 624 or (resid 625 and (name N or name CA or name C or nam \ e O or name CB )) or resid 626 through 632 or (resid 633 and (name N or name CA \ or name C or name O or name CB )) or resid 634 or (resid 635 through 638 and (na \ me N or name CA or name C or name O or name CB )) or resid 639 through 642 or (r \ esid 643 and (name N or name CA or name C or name O or name CB )) or resid 644 t \ hrough 646 or resid 649 through 654 or (resid 655 through 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 662 or resid 664 thr \ ough 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) \ or resid 672 through 677 or (resid 678 and (name N or name CA or name C or name \ O or name CB )) or resid 680 through 682 or resid 684 through 685 or (resid 688 \ and (name N or name CA or name C or name O or name CB )) or resid 689 or (resid \ 690 through 691 and (name N or name CA or name C or name O or name CB )) or resi \ d 692 through 695 or resid 697 or resid 699 through 700 or (resid 701 and (name \ N or name CA or name C or name O or name CB )) or resid 702 through 707 or resid \ 709 through 716 or (resid 717 through 718 and (name N or name CA or name C or n \ ame O or name CB )) or resid 719 through 729 or resid 731 through 733 or (resid \ 734 and (name N or name CA or name C or name O or name CB )) or resid 735 throug \ h 736 or resid 738 through 739 or (resid 741 and (name N or name CA or name C or \ name O or name CB )) or resid 742 through 747 or (resid 748 and (name N or name \ CA or name C or name O or name CB )) or resid 749 or (resid 751 and (name N or \ name CA or name C or name O or name CB )) or resid 753 or resid 755 through 760 \ or (resid 761 and (name N or name CA or name C or name O or name CB )) or resid \ 762 through 770 or resid 776 through 780 or (resid 781 through 782 and (name N o \ r name CA or name C or name O or name CB )) or resid 783 through 795 or resid 79 \ 7 through 808 or (resid 809 and (name N or name CA or name C or name O or name C \ B )) or resid 810 through 812 or (resid 813 and (name N or name CA or name C or \ name O or name CB )) or resid 901)) selection = (chain 'B' and (resid 399 through 402 or resid 404 or resid 406 through 409 or ( \ resid 411 through 413 and (name N or name CA or name C or name O or name CB )) o \ r resid 417 through 421 or (resid 423 and (name N or name CA or name C or name O \ or name CB )) or resid 424 through 428 or resid 430 through 431 or resid 433 th \ rough 437 or resid 439 or resid 442 or resid 446 through 447 or resid 449 throug \ h 456 or (resid 458 and (name N or name CA or name C or name O or name CB )) or \ resid 459 through 460 or resid 462 through 472 or resid 474 or resid 477 or resi \ d 479 through 499 or (resid 500 and (name N or name CA or name C or name O or na \ me CB )) or resid 501 through 509 or (resid 510 through 513 and (name N or name \ CA or name C or name O or name CB )) or resid 514 through 516 or (resid 517 and \ (name N or name CA or name C or name O or name CB )) or resid 518 through 547 or \ resid 572 through 628 or (resid 629 and (name N or name CA or name C or name O \ or name CB )) or resid 630 or (resid 631 and (name N or name CA or name C or nam \ e O or name CB )) or resid 632 through 643 or (resid 644 and (name N or name CA \ or name C or name O or name CB )) or resid 645 through 648 or (resid 649 and (na \ me N or name CA or name C or name O or name CB )) or resid 650 through 652 or re \ sid 655 through 668 or (resid 670 through 671 and (name N or name CA or name C o \ r name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or nam \ e CA or name C or name O or name CB )) or resid 678 through 683 or (resid 684 an \ d (name N or name CA or name C or name O or name CB )) or resid 686 through 688 \ or resid 690 through 691 or resid 694 through 701 or resid 703 or resid 705 thro \ ugh 706 or (resid 707 and (name N or name CA or name C or name O or name CB )) o \ r resid 708 through 713 or resid 715 through 722 or (resid 723 through 724 and ( \ name N or name CA or name C or name O or name CB )) or resid 725 through 735 or \ resid 737 through 739 or (resid 740 and (name N or name CA or name C or name O o \ r name CB )) or resid 741 through 742 or resid 744 through 745 or resid 747 thro \ ugh 755 or resid 757 or resid 759 or resid 761 through 765 or (resid 766 through \ 767 and (name N or name CA or name C or name O or name CB )) or resid 768 throu \ gh 776 or resid 782 through 785 or (resid 786 through 788 and (name N or name CA \ or name C or name O or name CB )) or resid 789 through 801 or resid 803 through \ 814 or (resid 815 and (name N or name CA or name C or name O or name CB )) or r \ esid 816 through 819 or resid 901)) selection = (chain 'C' and (resid 393 through 396 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 400 through 402 or (resid 403 and (name N \ or name CA or name C or name O or name CB )) or (resid 405 through 407 and (name \ N or name CA or name C or name O or name CB )) or resid 411 through 415 or (res \ id 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thr \ ough 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid \ 436 or resid 440 through 441 or resid 443 through 448 or (resid 449 through 450 \ and (name N or name CA or name C or name O or name CB )) or (resid 452 and (nam \ e N or name CA or name C or name O or name CB )) or resid 453 through 454 or res \ id 456 through 458 or (resid 459 and (name N or name CA or name C or name O or n \ ame CB )) or resid 460 through 466 or resid 468 or resid 471 or resid 473 throug \ h 493 or (resid 494 and (name N or name CA or name C or name O or name CB )) or \ resid 495 through 505 or (resid 506 through 507 and (name N or name CA or name C \ or name O or name CB )) or resid 508 through 514 or (resid 515 and (name N or n \ ame CA or name C or name O or name CB )) or resid 516 through 541 or (resid 566 \ through 567 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 8 through 594 or (resid 595 and (name N or name CA or name C or name O or name C \ B )) or resid 596 through 624 or (resid 625 and (name N or name CA or name C or \ name O or name CB )) or resid 626 through 629 or (resid 630 and (name N or name \ CA or name C or name O or name CB )) or resid 631 through 632 or (resid 633 and \ (name N or name CA or name C or name O or name CB )) or resid 634 or (resid 635 \ through 638 and (name N or name CA or name C or name O or name CB )) or resid 63 \ 9 through 646 or resid 649 through 654 or (resid 655 through 657 and (name N or \ name CA or name C or name O or name CB )) or resid 658 through 662 or resid 664 \ through 670 or resid 672 through 678 or resid 680 through 682 or resid 684 throu \ gh 685 or (resid 688 and (name N or name CA or name C or name O or name CB )) or \ resid 689 or (resid 690 through 691 and (name N or name CA or name C or name O \ or name CB )) or resid 692 through 695 or resid 697 or resid 699 through 707 or \ resid 709 through 716 or (resid 717 through 718 and (name N or name CA or name C \ or name O or name CB )) or resid 719 through 729 or resid 731 through 736 or re \ sid 738 through 739 or (resid 741 and (name N or name CA or name C or name O or \ name CB )) or resid 742 through 747 or (resid 748 and (name N or name CA or name \ C or name O or name CB )) or resid 749 or (resid 751 and (name N or name CA or \ name C or name O or name CB )) or resid 753 or resid 755 through 760 or (resid 7 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 762 through \ 770 or resid 776 through 795 or resid 797 through 812 or (resid 813 and (name N \ or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'D' and (resid 399 through 402 or (resid 404 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 through 408 or (resid 409 and (name N \ or name CA or name C or name O or name CB )) or (resid 411 through 413 and (name \ N or name CA or name C or name O or name CB )) or (resid 417 through 418 and (n \ ame N or name CA or name C or name O or name CB )) or resid 419 or (resid 420 an \ d (name N or name CA or name C or name O or name CB )) or resid 421 or (resid 42 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 424 through \ 428 or resid 430 through 431 or resid 433 through 437 or resid 439 or resid 442 \ or resid 446 through 447 or resid 449 through 454 or (resid 455 through 456 and \ (name N or name CA or name C or name O or name CB )) or (resid 458 and (name N o \ r name CA or name C or name O or name CB )) or resid 459 through 460 or resid 46 \ 2 through 464 or (resid 465 and (name N or name CA or name C or name O or name C \ B )) or resid 466 through 472 or resid 474 or resid 477 or resid 479 through 509 \ or (resid 510 through 513 and (name N or name CA or name C or name O or name CB \ )) or resid 514 through 516 or (resid 517 and (name N or name CA or name C or n \ ame O or name CB )) or resid 518 through 547 or (resid 572 through 573 and (name \ N or name CA or name C or name O or name CB )) or resid 574 through 628 or (res \ id 629 and (name N or name CA or name C or name O or name CB )) or resid 630 thr \ ough 640 or (resid 641 through 644 and (name N or name CA or name C or name O or \ name CB )) or resid 645 or (resid 646 and (name N or name CA or name C or name \ O or name CB )) or resid 647 through 648 or (resid 649 and (name N or name CA or \ name C or name O or name CB )) or resid 650 through 652 or resid 655 through 66 \ 0 or (resid 661 through 663 and (name N or name CA or name C or name O or name C \ B )) or resid 664 through 668 or (resid 670 through 671 and (name N or name CA o \ r name C or name O or name CB )) or resid 672 through 675 or (resid 676 and (nam \ e N or name CA or name C or name O or name CB )) or resid 678 through 683 or (re \ sid 684 and (name N or name CA or name C or name O or name CB )) or resid 686 th \ rough 688 or resid 690 through 691 or (resid 694 and (name N or name CA or name \ C or name O or name CB )) or resid 695 or (resid 696 through 697 and (name N or \ name CA or name C or name O or name CB )) or resid 698 through 701 or resid 703 \ or resid 705 through 706 or (resid 707 and (name N or name CA or name C or name \ O or name CB )) or resid 708 through 713 or resid 715 through 723 or (resid 724 \ and (name N or name CA or name C or name O or name CB )) or resid 725 through 73 \ 5 or resid 737 through 739 or (resid 740 and (name N or name CA or name C or nam \ e O or name CB )) or resid 741 through 742 or resid 744 through 745 or resid 747 \ through 753 or (resid 754 and (name N or name CA or name C or name O or name CB \ )) or resid 755 or resid 757 or resid 759 or resid 761 through 765 or (resid 76 \ 6 through 767 and (name N or name CA or name C or name O or name CB )) or resid \ 768 through 776 or resid 782 through 785 or (resid 786 through 788 and (name N o \ r name CA or name C or name O or name CB )) or resid 789 through 801 or resid 80 \ 3 through 814 or (resid 815 and (name N or name CA or name C or name O or name C \ B )) or resid 816 through 901)) } ncs_group { reference = (chain 'E' and (resid 5 through 76 or (resid 77 and (name N or name CA or name C \ or name O )) or resid 78 through 92 or (resid 93 and (name N or name CA or name \ C or name O )) or resid 94 through 160)) selection = (chain 'G' and (resid 2 through 74 or (resid 75 through 76 and (name N or name C \ A or name C or name O )) or resid 77 through 90 or (resid 91 through 92 and (nam \ e N or name CA or name C or name O )) or resid 93 through 160)) } ncs_group { reference = (chain 'F' and ((resid 6 and (name N or name CA or name C or name O or name CB ) \ ) or resid 7 through 96 or (resid 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 101 or (resid 102 through 103 and (name N or n \ ame CA or name C or name O or name CB )) or resid 104 through 126 or (resid 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 through 16 \ 5 or resid 174 through 207)) selection = (chain 'H' and (resid 6 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 81 or resid 93 through 116 or (resi \ d 117 and (name N or name CA or name C or name O or name CB )) or resid 118 thro \ ugh 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) o \ r resid 181 through 207)) } 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 group one per residue 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: 0.820 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.270 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15879 Z= 0.167 Angle : 0.824 15.302 21701 Z= 0.418 Chirality : 0.046 0.274 2566 Planarity : 0.005 0.055 2713 Dihedral : 12.991 75.143 5130 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.18), residues: 1926 helix: 0.04 (0.16), residues: 1019 sheet: 0.31 (0.72), residues: 55 loop : -2.48 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.015 0.001 TYR F 156 PHE 0.032 0.001 PHE B 533 TRP 0.026 0.002 TRP A 602 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00319 (15871) covalent geometry : angle 0.82360 (21685) SS BOND : bond 0.00287 ( 8) SS BOND : angle 1.50630 ( 16) hydrogen bonds : bond 0.12762 ( 990) hydrogen bonds : angle 5.94874 ( 2943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.514 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 643 TYR cc_start: 0.4823 (p90) cc_final: 0.4481 (p90) REVERT: A 670 MET cc_start: 0.8227 (pmm) cc_final: 0.7825 (pmm) REVERT: A 761 LYS cc_start: 0.7613 (ptmm) cc_final: 0.7171 (pttt) REVERT: A 810 PHE cc_start: 0.8420 (t80) cc_final: 0.8044 (t80) REVERT: C 536 LEU cc_start: 0.8387 (tt) cc_final: 0.7519 (pp) REVERT: C 704 MET cc_start: 0.5565 (ttt) cc_final: 0.5297 (ttm) REVERT: C 807 LEU cc_start: 0.9169 (mt) cc_final: 0.8917 (mt) REVERT: D 541 VAL cc_start: 0.9059 (t) cc_final: 0.8638 (m) REVERT: H 141 PHE cc_start: 0.6555 (m-80) cc_final: 0.6124 (m-80) REVERT: H 200 MET cc_start: 0.6856 (ppp) cc_final: 0.6449 (ppp) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.1003 time to fit residues: 49.7486 Evaluate side-chains 244 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.160064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.134434 restraints weight = 44074.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131726 restraints weight = 39413.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.132474 restraints weight = 36029.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.132706 restraints weight = 31866.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.132904 restraints weight = 30095.912| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15879 Z= 0.182 Angle : 0.635 7.768 21701 Z= 0.326 Chirality : 0.040 0.142 2566 Planarity : 0.005 0.052 2713 Dihedral : 4.814 57.397 2385 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.07 % Allowed : 7.09 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.19), residues: 1926 helix: 0.64 (0.16), residues: 1045 sheet: -0.91 (0.59), residues: 84 loop : -2.35 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 481 TYR 0.015 0.002 TYR C 519 PHE 0.025 0.002 PHE A 567 TRP 0.016 0.002 TRP D 607 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00400 (15871) covalent geometry : angle 0.63459 (21685) SS BOND : bond 0.00184 ( 8) SS BOND : angle 0.71563 ( 16) hydrogen bonds : bond 0.03811 ( 990) hydrogen bonds : angle 4.39596 ( 2943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.487 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 498 ILE cc_start: 0.8159 (tp) cc_final: 0.7912 (tt) REVERT: A 515 ASP cc_start: 0.7873 (m-30) cc_final: 0.7588 (m-30) REVERT: A 686 MET cc_start: 0.6630 (tmm) cc_final: 0.6287 (tmm) REVERT: A 706 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7834 (mm-30) REVERT: A 761 LYS cc_start: 0.7674 (ptmm) cc_final: 0.7401 (ptpt) REVERT: A 799 LEU cc_start: 0.7449 (mt) cc_final: 0.7058 (mt) REVERT: A 803 MET cc_start: 0.7741 (mmm) cc_final: 0.7414 (mmm) REVERT: A 810 PHE cc_start: 0.7935 (t80) cc_final: 0.7611 (t80) REVERT: B 428 VAL cc_start: 0.9158 (m) cc_final: 0.8812 (p) REVERT: B 723 MET cc_start: 0.8332 (ttm) cc_final: 0.7123 (ttp) REVERT: B 767 LYS cc_start: 0.7362 (tmmt) cc_final: 0.7106 (pptt) REVERT: B 771 ASP cc_start: 0.8237 (m-30) cc_final: 0.8029 (m-30) REVERT: C 523 MET cc_start: 0.8808 (tmm) cc_final: 0.8236 (tmm) REVERT: D 428 VAL cc_start: 0.8484 (m) cc_final: 0.8263 (p) REVERT: D 533 PHE cc_start: 0.7651 (t80) cc_final: 0.7437 (t80) REVERT: D 607 TRP cc_start: 0.7878 (t-100) cc_final: 0.7675 (t-100) REVERT: D 672 MET cc_start: 0.8025 (tpp) cc_final: 0.7455 (tpp) REVERT: F 58 MET cc_start: 0.7371 (tpt) cc_final: 0.6330 (tpt) REVERT: F 143 VAL cc_start: 0.5563 (t) cc_final: 0.5068 (m) REVERT: F 147 LEU cc_start: 0.9499 (mm) cc_final: 0.9232 (mm) REVERT: H 143 VAL cc_start: 0.5492 (m) cc_final: 0.5285 (m) REVERT: H 188 ILE cc_start: 0.8334 (mm) cc_final: 0.8019 (mm) REVERT: H 200 MET cc_start: 0.6485 (ppp) cc_final: 0.5845 (ppp) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.0981 time to fit residues: 47.2349 Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 104 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN B 621 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 ASN H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.150776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.124154 restraints weight = 44397.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121988 restraints weight = 41200.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.122387 restraints weight = 36883.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.122653 restraints weight = 32948.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.122868 restraints weight = 30554.037| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 15879 Z= 0.300 Angle : 0.792 9.250 21701 Z= 0.414 Chirality : 0.045 0.235 2566 Planarity : 0.005 0.063 2713 Dihedral : 5.662 59.928 2385 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.21 % Allowed : 7.59 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.19), residues: 1926 helix: 0.21 (0.16), residues: 1043 sheet: -1.36 (0.51), residues: 112 loop : -2.56 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 624 TYR 0.030 0.003 TYR A 698 PHE 0.031 0.003 PHE D 798 TRP 0.050 0.004 TRP D 768 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00659 (15871) covalent geometry : angle 0.79202 (21685) SS BOND : bond 0.01093 ( 8) SS BOND : angle 1.08477 ( 16) hydrogen bonds : bond 0.04868 ( 990) hydrogen bonds : angle 4.82560 ( 2943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 281 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.8502 (ppp) cc_final: 0.8015 (ppp) REVERT: A 498 ILE cc_start: 0.8713 (tp) cc_final: 0.8425 (tt) REVERT: A 514 LEU cc_start: 0.6984 (mt) cc_final: 0.6597 (mt) REVERT: A 519 TYR cc_start: 0.6447 (p90) cc_final: 0.5900 (p90) REVERT: A 523 MET cc_start: 0.9256 (tmm) cc_final: 0.8770 (tmm) REVERT: A 542 PHE cc_start: 0.6917 (t80) cc_final: 0.6637 (t80) REVERT: B 428 VAL cc_start: 0.9243 (m) cc_final: 0.9006 (p) REVERT: B 535 TYR cc_start: 0.8301 (t80) cc_final: 0.7494 (t80) REVERT: B 588 GLN cc_start: 0.7158 (pp30) cc_final: 0.6720 (tt0) REVERT: B 625 PHE cc_start: 0.8524 (t80) cc_final: 0.8284 (t80) REVERT: B 767 LYS cc_start: 0.7333 (tmmt) cc_final: 0.6962 (tmmt) REVERT: B 816 PHE cc_start: 0.4765 (t80) cc_final: 0.4464 (t80) REVERT: C 492 MET cc_start: 0.8489 (ptm) cc_final: 0.7959 (ptp) REVERT: C 523 MET cc_start: 0.9319 (tmm) cc_final: 0.8610 (tmm) REVERT: D 672 MET cc_start: 0.7053 (tpp) cc_final: 0.6276 (tpp) REVERT: D 766 ASN cc_start: 0.8397 (t0) cc_final: 0.7982 (t0) REVERT: F 143 VAL cc_start: 0.5933 (t) cc_final: 0.5428 (m) REVERT: F 147 LEU cc_start: 0.9403 (mm) cc_final: 0.8999 (mm) REVERT: H 181 TYR cc_start: 0.6502 (t80) cc_final: 0.6087 (t80) outliers start: 3 outliers final: 2 residues processed: 284 average time/residue: 0.1032 time to fit residues: 45.7912 Evaluate side-chains 226 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 207 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.154183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126802 restraints weight = 43574.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124508 restraints weight = 41631.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.125549 restraints weight = 34801.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.126189 restraints weight = 28083.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.126396 restraints weight = 26117.339| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15879 Z= 0.153 Angle : 0.610 9.016 21701 Z= 0.312 Chirality : 0.039 0.183 2566 Planarity : 0.004 0.068 2713 Dihedral : 5.081 58.449 2385 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.19), residues: 1926 helix: 0.67 (0.16), residues: 1034 sheet: -1.35 (0.53), residues: 103 loop : -2.50 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 624 TYR 0.020 0.001 TYR C 519 PHE 0.029 0.002 PHE F 21 TRP 0.027 0.002 TRP A 667 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00340 (15871) covalent geometry : angle 0.60985 (21685) SS BOND : bond 0.00924 ( 8) SS BOND : angle 0.95705 ( 16) hydrogen bonds : bond 0.03655 ( 990) hydrogen bonds : angle 4.35632 ( 2943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.500 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 492 MET cc_start: 0.9336 (ppp) cc_final: 0.8748 (ppp) REVERT: A 498 ILE cc_start: 0.8879 (tp) cc_final: 0.8569 (tt) REVERT: A 514 LEU cc_start: 0.6868 (mt) cc_final: 0.6466 (mt) REVERT: A 519 TYR cc_start: 0.6405 (p90) cc_final: 0.5889 (p90) REVERT: A 523 MET cc_start: 0.9328 (tmm) cc_final: 0.8784 (tmm) REVERT: A 542 PHE cc_start: 0.7091 (t80) cc_final: 0.6734 (t80) REVERT: A 724 ASP cc_start: 0.8571 (p0) cc_final: 0.7708 (p0) REVERT: A 761 LYS cc_start: 0.8514 (ptpt) cc_final: 0.7640 (pttt) REVERT: B 428 VAL cc_start: 0.9092 (m) cc_final: 0.8814 (p) REVERT: B 535 TYR cc_start: 0.8204 (t80) cc_final: 0.7432 (t80) REVERT: B 587 MET cc_start: 0.7214 (mmm) cc_final: 0.6268 (mmm) REVERT: B 607 TRP cc_start: 0.7750 (t-100) cc_final: 0.6960 (t-100) REVERT: C 483 GLU cc_start: 0.6671 (pm20) cc_final: 0.5246 (pt0) REVERT: C 492 MET cc_start: 0.8498 (ptm) cc_final: 0.7962 (ptp) REVERT: C 523 MET cc_start: 0.9125 (tmm) cc_final: 0.8437 (tmm) REVERT: D 529 MET cc_start: 0.5256 (mmt) cc_final: 0.4943 (mmt) REVERT: D 533 PHE cc_start: 0.7416 (t80) cc_final: 0.7172 (t80) REVERT: D 535 TYR cc_start: 0.8178 (t80) cc_final: 0.7772 (t80) REVERT: D 672 MET cc_start: 0.7358 (tpp) cc_final: 0.6889 (tpp) REVERT: D 715 GLU cc_start: 0.8808 (pt0) cc_final: 0.8511 (tt0) REVERT: D 766 ASN cc_start: 0.8512 (t0) cc_final: 0.8102 (t0) REVERT: D 816 PHE cc_start: 0.6531 (t80) cc_final: 0.6264 (t80) REVERT: F 143 VAL cc_start: 0.5765 (t) cc_final: 0.5451 (t) REVERT: F 147 LEU cc_start: 0.9305 (mm) cc_final: 0.8904 (mm) REVERT: H 181 TYR cc_start: 0.6242 (t80) cc_final: 0.5856 (t80) REVERT: H 188 ILE cc_start: 0.8386 (mm) cc_final: 0.7848 (mm) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.0958 time to fit residues: 44.0714 Evaluate side-chains 226 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 195 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 ASN H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.151160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123426 restraints weight = 44225.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.121756 restraints weight = 38023.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.122207 restraints weight = 32466.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.122551 restraints weight = 28560.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122775 restraints weight = 26355.428| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15879 Z= 0.210 Angle : 0.681 9.646 21701 Z= 0.350 Chirality : 0.041 0.167 2566 Planarity : 0.004 0.050 2713 Dihedral : 5.163 56.009 2385 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.19), residues: 1926 helix: 0.53 (0.16), residues: 1038 sheet: -1.20 (0.58), residues: 87 loop : -2.61 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 624 TYR 0.021 0.002 TYR A 698 PHE 0.074 0.002 PHE C 527 TRP 0.036 0.002 TRP D 768 HIS 0.004 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00471 (15871) covalent geometry : angle 0.68031 (21685) SS BOND : bond 0.00430 ( 8) SS BOND : angle 1.38442 ( 16) hydrogen bonds : bond 0.03999 ( 990) hydrogen bonds : angle 4.50214 ( 2943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.6585 (p90) cc_final: 0.6090 (p90) REVERT: A 523 MET cc_start: 0.9238 (tmm) cc_final: 0.8678 (tmm) REVERT: A 666 MET cc_start: 0.9088 (pmm) cc_final: 0.8791 (pmm) REVERT: A 761 LYS cc_start: 0.8554 (ptpt) cc_final: 0.7517 (pttt) REVERT: B 428 VAL cc_start: 0.9180 (m) cc_final: 0.8960 (p) REVERT: B 505 MET cc_start: 0.8397 (ppp) cc_final: 0.7319 (ppp) REVERT: B 535 TYR cc_start: 0.8303 (t80) cc_final: 0.7709 (t80) REVERT: B 587 MET cc_start: 0.7583 (mmm) cc_final: 0.6799 (mmm) REVERT: B 607 TRP cc_start: 0.8071 (t-100) cc_final: 0.7033 (t-100) REVERT: B 768 TRP cc_start: 0.5988 (t60) cc_final: 0.5572 (t60) REVERT: B 771 ASP cc_start: 0.8253 (m-30) cc_final: 0.7793 (m-30) REVERT: C 492 MET cc_start: 0.8479 (ptm) cc_final: 0.8014 (ptp) REVERT: C 519 TYR cc_start: 0.7257 (p90) cc_final: 0.7044 (p90) REVERT: C 523 MET cc_start: 0.9041 (tmm) cc_final: 0.8192 (tmm) REVERT: C 527 PHE cc_start: 0.6206 (m-80) cc_final: 0.5977 (m-80) REVERT: C 758 LEU cc_start: 0.8761 (mt) cc_final: 0.8269 (mt) REVERT: C 761 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7578 (pttt) REVERT: D 404 GLU cc_start: 0.5627 (mm-30) cc_final: 0.5325 (mm-30) REVERT: D 535 TYR cc_start: 0.8222 (t80) cc_final: 0.7794 (t80) REVERT: D 672 MET cc_start: 0.7469 (tpp) cc_final: 0.6962 (tpp) REVERT: D 715 GLU cc_start: 0.8977 (pt0) cc_final: 0.8647 (tt0) REVERT: D 766 ASN cc_start: 0.8528 (t0) cc_final: 0.8025 (t0) REVERT: D 816 PHE cc_start: 0.6631 (t80) cc_final: 0.6245 (t80) REVERT: F 147 LEU cc_start: 0.9348 (mm) cc_final: 0.8964 (mm) REVERT: F 160 ASN cc_start: 0.8604 (m110) cc_final: 0.8367 (m110) REVERT: F 191 GLU cc_start: 0.8113 (mp0) cc_final: 0.6618 (mp0) REVERT: H 117 MET cc_start: 0.6953 (mmt) cc_final: 0.6693 (mmt) REVERT: H 181 TYR cc_start: 0.6928 (t80) cc_final: 0.6352 (t80) REVERT: H 200 MET cc_start: 0.6372 (ppp) cc_final: 0.5939 (ppp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1014 time to fit residues: 44.6594 Evaluate side-chains 228 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 163 optimal weight: 40.0000 chunk 206 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.153770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124703 restraints weight = 43722.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.123985 restraints weight = 42995.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.125524 restraints weight = 31977.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126067 restraints weight = 25284.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.126318 restraints weight = 23683.782| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15879 Z= 0.147 Angle : 0.628 9.471 21701 Z= 0.318 Chirality : 0.040 0.233 2566 Planarity : 0.004 0.050 2713 Dihedral : 4.936 58.206 2385 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.19), residues: 1926 helix: 0.80 (0.16), residues: 1027 sheet: -1.31 (0.56), residues: 94 loop : -2.52 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 630 TYR 0.015 0.001 TYR A 698 PHE 0.046 0.002 PHE C 527 TRP 0.043 0.002 TRP D 608 HIS 0.003 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00329 (15871) covalent geometry : angle 0.62581 (21685) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.94394 ( 16) hydrogen bonds : bond 0.03590 ( 990) hydrogen bonds : angle 4.31182 ( 2943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.9211 (ppp) cc_final: 0.8484 (ppp) REVERT: A 498 ILE cc_start: 0.8827 (tp) cc_final: 0.8542 (tt) REVERT: A 519 TYR cc_start: 0.6347 (p90) cc_final: 0.5857 (p90) REVERT: A 523 MET cc_start: 0.9155 (tmm) cc_final: 0.8570 (tmm) REVERT: A 643 TYR cc_start: 0.6326 (p90) cc_final: 0.5937 (p90) REVERT: B 428 VAL cc_start: 0.9027 (m) cc_final: 0.8782 (p) REVERT: B 535 TYR cc_start: 0.8186 (t80) cc_final: 0.7683 (t80) REVERT: B 587 MET cc_start: 0.7369 (mmm) cc_final: 0.6862 (mmm) REVERT: B 607 TRP cc_start: 0.7880 (t-100) cc_final: 0.7016 (t-100) REVERT: B 768 TRP cc_start: 0.5798 (t60) cc_final: 0.5130 (t60) REVERT: C 523 MET cc_start: 0.9066 (tmm) cc_final: 0.8575 (tmm) REVERT: C 597 VAL cc_start: 0.7529 (t) cc_final: 0.7072 (p) REVERT: C 761 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7056 (pptt) REVERT: C 810 PHE cc_start: 0.8408 (t80) cc_final: 0.8125 (t80) REVERT: D 404 GLU cc_start: 0.5682 (mm-30) cc_final: 0.5360 (mm-30) REVERT: D 505 MET cc_start: 0.6737 (ppp) cc_final: 0.6092 (ppp) REVERT: D 535 TYR cc_start: 0.8169 (t80) cc_final: 0.7724 (t80) REVERT: D 607 TRP cc_start: 0.8595 (t-100) cc_final: 0.7788 (t-100) REVERT: D 612 LEU cc_start: 0.8621 (tt) cc_final: 0.8404 (tt) REVERT: D 672 MET cc_start: 0.7555 (tpp) cc_final: 0.7261 (tpp) REVERT: D 710 MET cc_start: 0.8003 (mmm) cc_final: 0.7690 (tmm) REVERT: D 715 GLU cc_start: 0.8851 (pt0) cc_final: 0.8581 (tt0) REVERT: D 762 ASP cc_start: 0.8298 (p0) cc_final: 0.7971 (m-30) REVERT: H 181 TYR cc_start: 0.6827 (t80) cc_final: 0.6311 (t80) REVERT: H 200 MET cc_start: 0.6279 (ppp) cc_final: 0.5843 (ppp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.0911 time to fit residues: 41.3890 Evaluate side-chains 220 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 174 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.153361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.125507 restraints weight = 43745.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.123602 restraints weight = 42348.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124604 restraints weight = 32967.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124999 restraints weight = 27782.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.125191 restraints weight = 26683.199| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15879 Z= 0.153 Angle : 0.639 10.688 21701 Z= 0.323 Chirality : 0.040 0.194 2566 Planarity : 0.004 0.054 2713 Dihedral : 4.853 56.510 2385 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.19), residues: 1926 helix: 0.81 (0.16), residues: 1035 sheet: -1.31 (0.62), residues: 76 loop : -2.54 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 624 TYR 0.019 0.001 TYR H 156 PHE 0.043 0.002 PHE C 527 TRP 0.029 0.002 TRP D 608 HIS 0.002 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00342 (15871) covalent geometry : angle 0.63785 (21685) SS BOND : bond 0.00205 ( 8) SS BOND : angle 1.28358 ( 16) hydrogen bonds : bond 0.03607 ( 990) hydrogen bonds : angle 4.27110 ( 2943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.6490 (p90) cc_final: 0.6020 (p90) REVERT: A 542 PHE cc_start: 0.7872 (t80) cc_final: 0.7557 (t80) REVERT: A 666 MET cc_start: 0.9122 (pmm) cc_final: 0.8627 (pmm) REVERT: A 761 LYS cc_start: 0.8588 (ptpt) cc_final: 0.7675 (pttt) REVERT: B 428 VAL cc_start: 0.9043 (m) cc_final: 0.8808 (p) REVERT: B 535 TYR cc_start: 0.8258 (t80) cc_final: 0.7744 (t80) REVERT: B 607 TRP cc_start: 0.7931 (t-100) cc_final: 0.6870 (t-100) REVERT: B 765 LYS cc_start: 0.8556 (tptm) cc_final: 0.8298 (tppt) REVERT: B 768 TRP cc_start: 0.5937 (t60) cc_final: 0.5240 (t60) REVERT: C 523 MET cc_start: 0.9109 (tmm) cc_final: 0.8633 (tmm) REVERT: C 597 VAL cc_start: 0.7784 (t) cc_final: 0.7246 (p) REVERT: C 761 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7023 (pptt) REVERT: C 810 PHE cc_start: 0.8415 (t80) cc_final: 0.8140 (t80) REVERT: D 404 GLU cc_start: 0.5664 (mm-30) cc_final: 0.5334 (mm-30) REVERT: D 535 TYR cc_start: 0.8076 (t80) cc_final: 0.7579 (t80) REVERT: D 612 LEU cc_start: 0.8676 (tt) cc_final: 0.8443 (tt) REVERT: D 672 MET cc_start: 0.7596 (tpp) cc_final: 0.7241 (tpp) REVERT: D 710 MET cc_start: 0.8269 (mmm) cc_final: 0.7845 (tmm) REVERT: D 715 GLU cc_start: 0.8903 (pt0) cc_final: 0.8586 (tt0) REVERT: D 799 TYR cc_start: 0.7467 (m-80) cc_final: 0.6947 (m-10) REVERT: F 173 SER cc_start: 0.5774 (t) cc_final: 0.4738 (p) REVERT: F 191 GLU cc_start: 0.7979 (mp0) cc_final: 0.6550 (mp0) REVERT: H 117 MET cc_start: 0.6986 (mmt) cc_final: 0.6766 (mmt) REVERT: H 181 TYR cc_start: 0.6403 (t80) cc_final: 0.6028 (t80) REVERT: H 200 MET cc_start: 0.6473 (ppp) cc_final: 0.6078 (ppp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.0925 time to fit residues: 41.7865 Evaluate side-chains 226 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 147 optimal weight: 0.0670 chunk 132 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 157 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 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 = 0.4271 r_free = 0.4271 target = 0.155103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127936 restraints weight = 43815.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126853 restraints weight = 38363.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.128086 restraints weight = 31375.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.128359 restraints weight = 25449.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.128554 restraints weight = 23694.096| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15879 Z= 0.126 Angle : 0.612 11.547 21701 Z= 0.309 Chirality : 0.039 0.219 2566 Planarity : 0.004 0.097 2713 Dihedral : 4.717 56.350 2385 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.19), residues: 1926 helix: 0.93 (0.16), residues: 1033 sheet: -1.34 (0.60), residues: 77 loop : -2.49 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 688 TYR 0.018 0.001 TYR H 156 PHE 0.038 0.002 PHE C 527 TRP 0.038 0.002 TRP B 769 HIS 0.002 0.000 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00277 (15871) covalent geometry : angle 0.61172 (21685) SS BOND : bond 0.00152 ( 8) SS BOND : angle 0.94954 ( 16) hydrogen bonds : bond 0.03377 ( 990) hydrogen bonds : angle 4.18085 ( 2943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.6022 (p90) cc_final: 0.5492 (p90) REVERT: A 523 MET cc_start: 0.9080 (tmm) cc_final: 0.8485 (tmm) REVERT: A 542 PHE cc_start: 0.7888 (t80) cc_final: 0.7579 (t80) REVERT: A 666 MET cc_start: 0.9123 (pmm) cc_final: 0.8696 (pmm) REVERT: A 686 MET cc_start: 0.7492 (tmm) cc_final: 0.6834 (tmm) REVERT: A 761 LYS cc_start: 0.8584 (ptpt) cc_final: 0.7632 (pttt) REVERT: A 803 MET cc_start: 0.7624 (mmm) cc_final: 0.7217 (mmm) REVERT: B 428 VAL cc_start: 0.9018 (m) cc_final: 0.8758 (p) REVERT: B 535 TYR cc_start: 0.8095 (t80) cc_final: 0.7491 (t80) REVERT: B 587 MET cc_start: 0.7637 (mmm) cc_final: 0.6851 (mmt) REVERT: B 607 TRP cc_start: 0.7809 (t-100) cc_final: 0.6738 (t-100) REVERT: B 762 ASP cc_start: 0.8237 (m-30) cc_final: 0.7640 (p0) REVERT: B 768 TRP cc_start: 0.5382 (t60) cc_final: 0.4628 (t60) REVERT: B 771 ASP cc_start: 0.7907 (m-30) cc_final: 0.7630 (m-30) REVERT: C 523 MET cc_start: 0.9045 (tmm) cc_final: 0.8552 (tmm) REVERT: C 597 VAL cc_start: 0.7617 (t) cc_final: 0.7089 (p) REVERT: C 610 SER cc_start: 0.9538 (p) cc_final: 0.9197 (t) REVERT: C 704 MET cc_start: 0.7523 (ttt) cc_final: 0.7314 (ttm) REVERT: C 724 ASP cc_start: 0.8677 (p0) cc_final: 0.8322 (p0) REVERT: C 758 LEU cc_start: 0.9006 (mt) cc_final: 0.8731 (mt) REVERT: C 761 LYS cc_start: 0.7999 (ptpt) cc_final: 0.6994 (pptt) REVERT: C 810 PHE cc_start: 0.8252 (t80) cc_final: 0.8028 (t80) REVERT: D 404 GLU cc_start: 0.5451 (mm-30) cc_final: 0.5146 (mm-30) REVERT: D 429 ASP cc_start: 0.8184 (t0) cc_final: 0.7932 (t0) REVERT: D 529 MET cc_start: 0.5602 (mmt) cc_final: 0.5231 (mmt) REVERT: D 535 TYR cc_start: 0.8059 (t80) cc_final: 0.7608 (t80) REVERT: D 672 MET cc_start: 0.7526 (tpp) cc_final: 0.7295 (tpp) REVERT: D 715 GLU cc_start: 0.8878 (pt0) cc_final: 0.8460 (tt0) REVERT: D 762 ASP cc_start: 0.8078 (p0) cc_final: 0.7870 (m-30) REVERT: D 799 TYR cc_start: 0.7903 (m-80) cc_final: 0.7486 (m-10) REVERT: F 115 LEU cc_start: 0.8198 (mm) cc_final: 0.7785 (tp) REVERT: F 173 SER cc_start: 0.5768 (t) cc_final: 0.4698 (p) REVERT: F 191 GLU cc_start: 0.7641 (mp0) cc_final: 0.6623 (mp0) REVERT: H 117 MET cc_start: 0.6929 (mmt) cc_final: 0.6709 (mmt) REVERT: H 181 TYR cc_start: 0.6344 (t80) cc_final: 0.5999 (t80) REVERT: H 200 MET cc_start: 0.6396 (ppp) cc_final: 0.5775 (ppp) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.0983 time to fit residues: 46.1240 Evaluate side-chains 232 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 139 optimal weight: 0.6980 chunk 164 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 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 644 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 = 0.4254 r_free = 0.4254 target = 0.153870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.128573 restraints weight = 44457.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.127143 restraints weight = 48578.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.128490 restraints weight = 38487.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.128829 restraints weight = 30085.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.128960 restraints weight = 28056.408| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15879 Z= 0.147 Angle : 0.637 12.351 21701 Z= 0.323 Chirality : 0.040 0.211 2566 Planarity : 0.005 0.100 2713 Dihedral : 4.733 55.257 2385 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.19), residues: 1926 helix: 0.89 (0.16), residues: 1036 sheet: -1.29 (0.61), residues: 77 loop : -2.46 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 102 TYR 0.019 0.001 TYR H 156 PHE 0.038 0.002 PHE C 527 TRP 0.049 0.002 TRP C 601 HIS 0.002 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00327 (15871) covalent geometry : angle 0.63679 (21685) SS BOND : bond 0.00168 ( 8) SS BOND : angle 0.90703 ( 16) hydrogen bonds : bond 0.03462 ( 990) hydrogen bonds : angle 4.21895 ( 2943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.9301 (ppp) cc_final: 0.8933 (ppp) REVERT: A 519 TYR cc_start: 0.6293 (p90) cc_final: 0.5855 (p90) REVERT: A 523 MET cc_start: 0.9052 (tmm) cc_final: 0.8502 (tmm) REVERT: A 542 PHE cc_start: 0.7923 (t80) cc_final: 0.7607 (t80) REVERT: A 597 VAL cc_start: 0.7985 (t) cc_final: 0.7593 (p) REVERT: A 666 MET cc_start: 0.9045 (pmm) cc_final: 0.8686 (pmm) REVERT: A 686 MET cc_start: 0.7191 (tmm) cc_final: 0.6679 (tmm) REVERT: A 761 LYS cc_start: 0.8498 (ptpt) cc_final: 0.7534 (pttt) REVERT: A 803 MET cc_start: 0.7587 (mmm) cc_final: 0.7195 (mmm) REVERT: B 428 VAL cc_start: 0.9021 (m) cc_final: 0.8740 (p) REVERT: B 607 TRP cc_start: 0.7732 (t-100) cc_final: 0.6700 (t-100) REVERT: B 768 TRP cc_start: 0.5876 (t60) cc_final: 0.5140 (t60) REVERT: B 771 ASP cc_start: 0.7893 (m-30) cc_final: 0.7600 (m-30) REVERT: B 790 SER cc_start: 0.8828 (t) cc_final: 0.8447 (t) REVERT: C 492 MET cc_start: 0.8379 (ptp) cc_final: 0.8156 (ptm) REVERT: C 515 ASP cc_start: 0.7745 (m-30) cc_final: 0.7465 (m-30) REVERT: C 523 MET cc_start: 0.9032 (tmm) cc_final: 0.8586 (tmm) REVERT: C 758 LEU cc_start: 0.8810 (mt) cc_final: 0.8602 (mt) REVERT: C 761 LYS cc_start: 0.7951 (ptpt) cc_final: 0.6902 (pptt) REVERT: D 404 GLU cc_start: 0.5229 (mm-30) cc_final: 0.4962 (mm-30) REVERT: D 535 TYR cc_start: 0.8009 (t80) cc_final: 0.7589 (t80) REVERT: D 607 TRP cc_start: 0.8413 (t-100) cc_final: 0.8070 (t-100) REVERT: D 715 GLU cc_start: 0.8964 (pt0) cc_final: 0.8492 (tt0) REVERT: D 762 ASP cc_start: 0.8061 (p0) cc_final: 0.7796 (m-30) REVERT: D 799 TYR cc_start: 0.7970 (m-80) cc_final: 0.7614 (m-10) REVERT: F 115 LEU cc_start: 0.7688 (mm) cc_final: 0.7413 (tp) REVERT: F 173 SER cc_start: 0.5826 (t) cc_final: 0.4777 (p) REVERT: F 191 GLU cc_start: 0.7702 (mp0) cc_final: 0.6553 (mp0) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.0931 time to fit residues: 42.1648 Evaluate side-chains 228 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 55 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.155784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129833 restraints weight = 44064.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127783 restraints weight = 37853.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.129037 restraints weight = 32870.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129634 restraints weight = 26358.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.129732 restraints weight = 24053.784| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15879 Z= 0.123 Angle : 0.616 12.896 21701 Z= 0.309 Chirality : 0.039 0.193 2566 Planarity : 0.004 0.092 2713 Dihedral : 4.661 57.878 2385 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.19), residues: 1926 helix: 0.98 (0.16), residues: 1042 sheet: -1.30 (0.58), residues: 77 loop : -2.51 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 688 TYR 0.020 0.001 TYR H 156 PHE 0.035 0.002 PHE C 527 TRP 0.036 0.002 TRP D 608 HIS 0.002 0.000 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00271 (15871) covalent geometry : angle 0.61616 (21685) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.82179 ( 16) hydrogen bonds : bond 0.03242 ( 990) hydrogen bonds : angle 4.11851 ( 2943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.8849 (ppp) cc_final: 0.8592 (ppp) REVERT: A 519 TYR cc_start: 0.5661 (p90) cc_final: 0.5088 (p90) REVERT: A 523 MET cc_start: 0.9222 (tmm) cc_final: 0.8863 (tmm) REVERT: A 542 PHE cc_start: 0.8002 (t80) cc_final: 0.7701 (t80) REVERT: A 597 VAL cc_start: 0.7946 (t) cc_final: 0.7707 (m) REVERT: A 666 MET cc_start: 0.9031 (pmm) cc_final: 0.8695 (pmm) REVERT: A 761 LYS cc_start: 0.8556 (ptpt) cc_final: 0.7729 (pttt) REVERT: A 803 MET cc_start: 0.7645 (mmm) cc_final: 0.7286 (mmm) REVERT: B 428 VAL cc_start: 0.8983 (m) cc_final: 0.8730 (p) REVERT: B 535 TYR cc_start: 0.7638 (t80) cc_final: 0.7268 (t80) REVERT: B 607 TRP cc_start: 0.7439 (t-100) cc_final: 0.6613 (t-100) REVERT: B 768 TRP cc_start: 0.5730 (t60) cc_final: 0.4957 (t60) REVERT: B 771 ASP cc_start: 0.7879 (m-30) cc_final: 0.7596 (m-30) REVERT: C 492 MET cc_start: 0.8310 (ptp) cc_final: 0.8058 (ptm) REVERT: C 523 MET cc_start: 0.9094 (tmm) cc_final: 0.8651 (tmm) REVERT: C 758 LEU cc_start: 0.8737 (mt) cc_final: 0.8344 (mt) REVERT: C 761 LYS cc_start: 0.7916 (ptpt) cc_final: 0.6873 (pptt) REVERT: C 810 PHE cc_start: 0.8349 (t80) cc_final: 0.8083 (t80) REVERT: D 535 TYR cc_start: 0.8043 (t80) cc_final: 0.7638 (t80) REVERT: D 607 TRP cc_start: 0.8246 (t-100) cc_final: 0.7915 (t-100) REVERT: D 715 GLU cc_start: 0.8831 (pt0) cc_final: 0.8481 (tt0) REVERT: F 173 SER cc_start: 0.7267 (t) cc_final: 0.6543 (p) REVERT: H 200 MET cc_start: 0.6721 (ppp) cc_final: 0.6028 (ppp) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1005 time to fit residues: 46.5059 Evaluate side-chains 228 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 134 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.152349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.122602 restraints weight = 43727.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121994 restraints weight = 42876.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.123502 restraints weight = 31505.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123629 restraints weight = 25187.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123818 restraints weight = 24335.179| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15879 Z= 0.162 Angle : 0.656 12.642 21701 Z= 0.332 Chirality : 0.040 0.189 2566 Planarity : 0.005 0.097 2713 Dihedral : 4.810 57.928 2385 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.19), residues: 1926 helix: 0.91 (0.16), residues: 1037 sheet: -1.40 (0.59), residues: 78 loop : -2.47 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 102 TYR 0.019 0.001 TYR H 156 PHE 0.037 0.002 PHE C 527 TRP 0.038 0.003 TRP C 601 HIS 0.002 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00361 (15871) covalent geometry : angle 0.65617 (21685) SS BOND : bond 0.00185 ( 8) SS BOND : angle 0.91765 ( 16) hydrogen bonds : bond 0.03557 ( 990) hydrogen bonds : angle 4.19689 ( 2943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.20 seconds wall clock time: 38 minutes 34.13 seconds (2314.13 seconds total)