Starting phenix.real_space_refine on Sun Aug 24 00:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nra_49727/08_2025/9nra_49727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nra_49727/08_2025/9nra_49727.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nra_49727/08_2025/9nra_49727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nra_49727/08_2025/9nra_49727.map" model { file = "/net/cci-nas-00/data/ceres_data/9nra_49727/08_2025/9nra_49727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nra_49727/08_2025/9nra_49727.cif" } 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= 0.079 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 10066 2.51 5 N 2522 2.21 5 O 2905 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 18 residue(s): 0.02s 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: 15598 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: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2880 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 249 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: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2952 Classifications: {'peptide': 405} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 13, 'TRANS': 391} 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: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2907 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 189 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: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1333 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 173} 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: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1325 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 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: 3.46, per 1000 atoms: 0.22 Number of scatterers: 15598 At special positions: 0 Unit cell: (105.28, 122.2, 129.72, 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 2905 8.00 N 2522 7.00 C 10066 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=2.03 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: 1.02 Conformation dependent library (CDL) restraints added in 480.4 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4034 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 20 sheets defined 66.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.883A pdb=" N GLU A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.566A 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 485 removed outlier: 3.517A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.602A pdb=" N PHE A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 541 removed outlier: 3.522A pdb=" N MET A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 591 through 626 removed outlier: 3.993A pdb=" N VAL A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.859A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.785A 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 701 through 710 removed outlier: 3.531A pdb=" N GLN A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 removed outlier: 3.542A pdb=" N GLY A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.698A 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 464 through 471 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 515 through 521 removed outlier: 3.677A pdb=" N PHE B 519 " --> pdb=" O GLY B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 599 through 628 removed outlier: 4.171A pdb=" N VAL B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 628 " --> pdb=" O ALA B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 645 removed outlier: 3.960A 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: 3.649A pdb=" N GLU B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.845A 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 759 through 772 removed outlier: 4.139A pdb=" N LYS B 772 " --> pdb=" O TRP B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 793 removed outlier: 3.696A pdb=" N ASN B 793 " --> pdb=" O SER B 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 794 through 820 Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.888A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 411' Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.572A pdb=" N GLY C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 removed outlier: 3.782A 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 582 Processing helix chain 'C' and resid 591 through 625 Processing helix chain 'C' and resid 632 through 639 removed outlier: 3.999A pdb=" N THR C 639 " --> pdb=" O LEU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 673 removed outlier: 4.068A pdb=" N ALA C 673 " --> pdb=" O TYR C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 739 through 753 Processing helix chain 'C' and resid 753 through 765 removed outlier: 3.645A pdb=" N ASP C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 815 removed outlier: 3.695A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 439 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 524 through 546 removed outlier: 3.515A pdb=" N TRP D 528 " --> pdb=" O ALA D 524 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 587 removed outlier: 3.599A pdb=" N MET D 587 " --> pdb=" O LEU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 629 Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.860A pdb=" N ARG D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 679 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: 3.744A pdb=" N LYS D 697 " --> pdb=" O ALA D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.795A pdb=" N GLN D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 759 Processing helix chain 'D' and resid 760 through 770 Processing helix chain 'D' and resid 794 through 819 Processing helix chain 'E' and resid 4 through 34 removed outlier: 3.842A pdb=" N UNK E 8 " --> pdb=" O UNK E 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N UNK E 34 " --> pdb=" O UNK E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 82 Processing helix chain 'E' and resid 84 through 110 removed outlier: 4.038A pdb=" N UNK E 88 " --> pdb=" O UNK E 84 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N UNK E 90 " --> pdb=" O UNK E 86 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N UNK E 91 " --> pdb=" O UNK E 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N UNK E 98 " --> pdb=" O UNK E 94 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N UNK E 105 " --> pdb=" O UNK E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 157 Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.522A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) 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 161 removed outlier: 3.708A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 208 removed outlier: 3.620A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 33 removed outlier: 4.263A pdb=" N UNK G 8 " --> pdb=" O UNK G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 84 removed outlier: 3.565A pdb=" N UNK G 70 " --> pdb=" O UNK G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 109 removed outlier: 3.947A pdb=" N UNK G 96 " --> pdb=" O UNK G 92 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N UNK G 97 " --> pdb=" O UNK G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 159 removed outlier: 3.634A pdb=" N UNK G 159 " --> pdb=" O UNK G 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 29 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 105 through 128 Processing helix chain 'H' and resid 132 through 161 Processing helix chain 'H' and resid 178 through 208 removed outlier: 4.329A pdb=" N ALA H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS H 206 " --> pdb=" O ILE H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 439 removed outlier: 4.043A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.766A pdb=" N MET A 403 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 486 through 487 removed outlier: 4.025A pdb=" N ASP A 486 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 732 " --> pdb=" O ASP A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 498 through 501 removed outlier: 4.425A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 719 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 500 " --> pdb=" O MET A 717 " (cutoff:3.500A) removed outlier: 3.875A 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 455 through 456 removed outlier: 4.004A pdb=" N ASP B 456 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 461 " --> pdb=" O ASP B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 492 through 493 removed outlier: 4.328A pdb=" N ASP B 492 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR B 738 " --> pdb=" O ASP B 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 499 through 500 removed outlier: 3.521A pdb=" N LYS B 732 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 502 through 505 removed outlier: 3.894A pdb=" N LEU B 705 " --> pdb=" O GLY B 650 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 391 through 394 Processing sheet with id=AB1, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB2, first strand: chain 'C' and resid 486 through 487 removed outlier: 4.074A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 732 " --> pdb=" O ASP C 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB4, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.344A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 400 through 401 Processing sheet with id=AB6, first strand: chain 'D' and resid 454 through 455 Processing sheet with id=AB7, first strand: chain 'D' and resid 477 through 482 removed outlier: 7.550A pdb=" N ALA D 479 " --> pdb=" O ALA D 737 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA D 737 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 684 through 685 removed outlier: 8.668A pdb=" N THR D 685 " --> pdb=" O TYR D 649 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR D 651 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 705 " --> pdb=" O GLY D 650 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU D 652 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU D 707 " --> pdb=" O LEU D 652 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 34 through 38 removed outlier: 4.354A pdb=" N LEU F 34 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER F 61 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER F 36 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 34 through 35 removed outlier: 4.044A pdb=" N SER H 175 " --> pdb=" O TYR H 35 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 59 through 60 989 hydrogen bonds defined for protein. 2949 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: 2.03 Time building geometry restraints manager: 1.37 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: 4953 1.35 - 1.48: 4275 1.48 - 1.62: 6540 1.62 - 1.76: 1 1.76 - 1.90: 147 Bond restraints: 15916 Sorted by residual: bond pdb=" CA VAL C 472 " pdb=" CB VAL C 472 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.05e-02 9.07e+03 3.50e+00 bond pdb=" CB MET C 581 " pdb=" CG MET C 581 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.33e+00 bond pdb=" SD MET C 581 " pdb=" CE MET C 581 " ideal model delta sigma weight residual 1.791 1.751 0.040 2.50e-02 1.60e+03 2.61e+00 bond pdb=" CB LYS A 757 " pdb=" CG LYS A 757 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" CB LYS B 740 " pdb=" CG LYS B 740 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 ... (remaining 15911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 21489 3.38 - 6.75: 212 6.75 - 10.13: 32 10.13 - 13.51: 10 13.51 - 16.88: 2 Bond angle restraints: 21745 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 103.51 110.07 -6.56 9.60e-01 1.09e+00 4.67e+01 angle pdb=" N PRO D 747 " pdb=" CA PRO D 747 " pdb=" CB PRO D 747 " ideal model delta sigma weight residual 103.23 110.04 -6.81 1.07e+00 8.73e-01 4.05e+01 angle pdb=" N PRO B 747 " pdb=" CA PRO B 747 " pdb=" CB PRO B 747 " ideal model delta sigma weight residual 103.23 109.95 -6.72 1.07e+00 8.73e-01 3.94e+01 angle pdb=" N PRO B 777 " pdb=" CA PRO B 777 " pdb=" CB PRO B 777 " ideal model delta sigma weight residual 103.33 110.23 -6.90 1.10e+00 8.26e-01 3.93e+01 angle pdb=" N VAL D 668 " pdb=" CA VAL D 668 " pdb=" C VAL D 668 " ideal model delta sigma weight residual 111.81 106.72 5.09 8.60e-01 1.35e+00 3.50e+01 ... (remaining 21740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8481 18.00 - 35.99: 591 35.99 - 53.99: 109 53.99 - 71.98: 14 71.98 - 89.98: 11 Dihedral angle restraints: 9206 sinusoidal: 2910 harmonic: 6296 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 93.00 149.17 -56.17 1 1.00e+01 1.00e-02 4.26e+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 93.00 145.62 -52.62 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA PHE A 491 " pdb=" C PHE A 491 " pdb=" N MET A 492 " pdb=" CA MET A 492 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2065 0.056 - 0.113: 433 0.113 - 0.169: 62 0.169 - 0.226: 10 0.226 - 0.282: 3 Chirality restraints: 2573 Sorted by residual: chirality pdb=" CB ILE B 478 " pdb=" CA ILE B 478 " pdb=" CG1 ILE B 478 " pdb=" CG2 ILE B 478 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB THR D 722 " pdb=" CA THR D 722 " pdb=" OG1 THR D 722 " pdb=" CG2 THR D 722 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+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 1.52e+00 ... (remaining 2570 not shown) Planarity restraints: 2721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 141 " -0.015 2.00e-02 2.50e+03 2.31e-02 9.32e+00 pdb=" CG PHE H 141 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE H 141 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE H 141 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE H 141 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 141 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 174 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C TYR H 174 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR H 174 " 0.019 2.00e-02 2.50e+03 pdb=" N SER H 175 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 588 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.83e+00 pdb=" N PRO C 589 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 589 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 589 " -0.038 5.00e-02 4.00e+02 ... (remaining 2718 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 434 2.71 - 3.26: 15799 3.26 - 3.80: 25484 3.80 - 4.35: 28490 4.35 - 4.90: 47356 Nonbonded interactions: 117563 Sorted by model distance: nonbonded pdb=" O PHE A 580 " pdb=" OG1 THR A 605 " model vdw 2.160 3.040 nonbonded pdb=" O PHE C 580 " pdb=" OG1 THR C 605 " model vdw 2.216 3.040 nonbonded pdb=" O VAL A 677 " pdb=" OH TYR A 696 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU B 707 " pdb=" FAG ZK1 B 901 " model vdw 2.231 2.990 nonbonded pdb=" O ILE F 26 " pdb=" OG1 THR F 30 " model vdw 2.249 3.040 ... (remaining 117558 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 17 \ 0 or resid 172 through 208)) 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 165 or (resid 166 through 171 and (name N or name CA or name C or name O or \ name CB )) or resid 172 through 179 or (resid 180 and (name N or name CA or name \ C or name O or name CB )) or resid 181 through 208)) } 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: 0.640 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.460 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 0.004 0.055 15924 Z= 0.182 Angle : 0.890 16.883 21761 Z= 0.452 Chirality : 0.047 0.282 2573 Planarity : 0.005 0.070 2721 Dihedral : 13.302 89.976 5148 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.74 (0.18), residues: 1932 helix: -0.09 (0.16), residues: 1037 sheet: -1.46 (0.63), residues: 70 loop : -2.54 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 630 TYR 0.021 0.001 TYR H 156 PHE 0.052 0.002 PHE H 141 TRP 0.044 0.002 TRP C 602 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00358 (15916) covalent geometry : angle 0.88784 (21745) SS BOND : bond 0.00215 ( 8) SS BOND : angle 2.21082 ( 16) hydrogen bonds : bond 0.11400 ( 989) hydrogen bonds : angle 5.70756 ( 2949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 LEU cc_start: 0.8664 (tt) cc_final: 0.8273 (mt) REVERT: A 582 GLN cc_start: 0.8616 (mp10) cc_final: 0.8120 (mp10) REVERT: A 666 MET cc_start: 0.9086 (pmm) cc_final: 0.8832 (pmm) REVERT: A 686 MET cc_start: 0.7892 (tmm) cc_final: 0.7570 (tmm) REVERT: A 703 THR cc_start: 0.7989 (p) cc_final: 0.7769 (p) REVERT: B 401 THR cc_start: 0.6553 (t) cc_final: 0.6259 (t) REVERT: B 421 ASP cc_start: 0.7073 (m-30) cc_final: 0.6507 (p0) REVERT: B 729 LEU cc_start: 0.8875 (mt) cc_final: 0.8338 (mp) REVERT: B 730 ASP cc_start: 0.7633 (t70) cc_final: 0.7121 (m-30) REVERT: C 401 TYR cc_start: 0.5993 (m-10) cc_final: 0.5583 (m-10) REVERT: C 457 ASN cc_start: 0.7503 (p0) cc_final: 0.7260 (p0) REVERT: C 523 MET cc_start: 0.7972 (ppp) cc_final: 0.7173 (mmp) REVERT: C 663 PHE cc_start: 0.8119 (m-10) cc_final: 0.7610 (m-10) REVERT: C 666 MET cc_start: 0.8232 (ptt) cc_final: 0.7627 (tpt) REVERT: C 799 LEU cc_start: 0.7741 (mm) cc_final: 0.7484 (mm) REVERT: D 437 HIS cc_start: 0.8177 (t-90) cc_final: 0.7654 (t-90) REVERT: D 505 MET cc_start: 0.8068 (tmm) cc_final: 0.7725 (tmm) REVERT: D 587 MET cc_start: 0.6762 (mpp) cc_final: 0.6421 (mpp) REVERT: D 749 ASN cc_start: 0.8328 (t0) cc_final: 0.8000 (t0) REVERT: D 765 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8370 (tptm) REVERT: D 771 ASP cc_start: 0.5917 (m-30) cc_final: 0.5667 (m-30) REVERT: F 21 PHE cc_start: 0.9003 (t80) cc_final: 0.8730 (t80) REVERT: F 141 PHE cc_start: 0.6831 (m-80) cc_final: 0.6625 (m-80) REVERT: F 163 ASP cc_start: 0.7122 (p0) cc_final: 0.6695 (p0) REVERT: H 114 LEU cc_start: 0.8742 (tp) cc_final: 0.8354 (tp) REVERT: H 174 TYR cc_start: 0.4273 (p90) cc_final: 0.3863 (p90) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.0951 time to fit residues: 52.1478 Evaluate side-chains 287 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 4.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 787 ASN D 588 GLN H 60 HIS H 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.135726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107953 restraints weight = 46905.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109909 restraints weight = 31939.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.109410 restraints weight = 24395.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.109803 restraints weight = 24773.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110680 restraints weight = 22451.710| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15924 Z= 0.237 Angle : 0.723 9.826 21761 Z= 0.375 Chirality : 0.043 0.227 2573 Planarity : 0.005 0.052 2721 Dihedral : 5.255 76.553 2392 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.07 % Allowed : 7.65 % Favored : 92.28 % 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: -1.25 (0.18), residues: 1932 helix: 0.37 (0.16), residues: 1060 sheet: -1.20 (0.65), residues: 65 loop : -2.50 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 711 TYR 0.023 0.002 TYR D 426 PHE 0.033 0.002 PHE A 570 TRP 0.033 0.003 TRP A 574 HIS 0.005 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00517 (15916) covalent geometry : angle 0.72237 (21745) SS BOND : bond 0.00388 ( 8) SS BOND : angle 0.93333 ( 16) hydrogen bonds : bond 0.04572 ( 989) hydrogen bonds : angle 4.67234 ( 2949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.409 Fit side-chains REVERT: A 523 MET cc_start: 0.7274 (mmm) cc_final: 0.6849 (mmm) REVERT: A 576 SER cc_start: 0.8961 (m) cc_final: 0.8370 (p) REVERT: A 582 GLN cc_start: 0.8998 (mp10) cc_final: 0.8641 (mp10) REVERT: A 602 TRP cc_start: 0.8280 (m-10) cc_final: 0.7479 (m-10) REVERT: A 666 MET cc_start: 0.8587 (pmm) cc_final: 0.7542 (pmm) REVERT: A 670 MET cc_start: 0.8752 (pmm) cc_final: 0.8499 (pmm) REVERT: A 686 MET cc_start: 0.7971 (tmm) cc_final: 0.7647 (tmm) REVERT: A 701 GLU cc_start: 0.8824 (mp0) cc_final: 0.8375 (mp0) REVERT: A 703 THR cc_start: 0.8392 (p) cc_final: 0.8190 (p) REVERT: A 756 ASP cc_start: 0.9182 (m-30) cc_final: 0.8959 (m-30) REVERT: B 505 MET cc_start: 0.8164 (tmm) cc_final: 0.7871 (tmm) REVERT: B 519 PHE cc_start: 0.6715 (t80) cc_final: 0.6416 (t80) REVERT: B 529 MET cc_start: 0.8161 (pmm) cc_final: 0.7813 (pmm) REVERT: B 675 TYR cc_start: 0.8736 (t80) cc_final: 0.8512 (t80) REVERT: B 767 LYS cc_start: 0.8575 (tmmt) cc_final: 0.8290 (ttpp) REVERT: C 459 MET cc_start: 0.8637 (mmt) cc_final: 0.7645 (mmt) REVERT: C 494 LEU cc_start: 0.8623 (tt) cc_final: 0.8399 (tt) REVERT: C 515 ASP cc_start: 0.8185 (t70) cc_final: 0.7972 (p0) REVERT: C 523 MET cc_start: 0.8509 (ppp) cc_final: 0.7751 (mmp) REVERT: C 637 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8482 (mmtm) REVERT: C 666 MET cc_start: 0.8441 (ptt) cc_final: 0.7821 (tpt) REVERT: D 505 MET cc_start: 0.8181 (tmm) cc_final: 0.7642 (tmm) REVERT: D 533 PHE cc_start: 0.8428 (m-10) cc_final: 0.7785 (t80) REVERT: D 587 MET cc_start: 0.6410 (mpp) cc_final: 0.5757 (mpp) REVERT: D 607 TRP cc_start: 0.8046 (t-100) cc_final: 0.7841 (t-100) REVERT: D 621 ASN cc_start: 0.8945 (t0) cc_final: 0.8239 (t0) REVERT: F 141 PHE cc_start: 0.7113 (m-80) cc_final: 0.6912 (m-80) REVERT: F 163 ASP cc_start: 0.6478 (p0) cc_final: 0.5917 (p0) REVERT: F 182 PHE cc_start: 0.7710 (m-10) cc_final: 0.7163 (m-10) REVERT: H 164 PRO cc_start: 0.6488 (Cg_endo) cc_final: 0.6268 (Cg_exo) REVERT: H 181 TYR cc_start: 0.5864 (m-80) cc_final: 0.5563 (m-80) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.0859 time to fit residues: 43.0767 Evaluate side-chains 263 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 9 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.138513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108856 restraints weight = 46663.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110857 restraints weight = 35801.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111066 restraints weight = 25170.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112791 restraints weight = 23615.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112751 restraints weight = 21135.297| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15924 Z= 0.129 Angle : 0.580 9.944 21761 Z= 0.296 Chirality : 0.039 0.151 2573 Planarity : 0.004 0.042 2721 Dihedral : 4.878 80.615 2392 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % 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: -0.72 (0.19), residues: 1932 helix: 0.86 (0.16), residues: 1063 sheet: -1.23 (0.70), residues: 57 loop : -2.33 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.016 0.001 TYR A 698 PHE 0.024 0.002 PHE F 141 TRP 0.023 0.002 TRP D 768 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00285 (15916) covalent geometry : angle 0.57961 (21745) SS BOND : bond 0.00259 ( 8) SS BOND : angle 0.73516 ( 16) hydrogen bonds : bond 0.03815 ( 989) hydrogen bonds : angle 4.25850 ( 2949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.5860 (mmm) cc_final: 0.5543 (mmm) REVERT: A 523 MET cc_start: 0.6603 (mmm) cc_final: 0.6229 (mmm) REVERT: A 576 SER cc_start: 0.9017 (m) cc_final: 0.8547 (p) REVERT: A 582 GLN cc_start: 0.8975 (mp10) cc_final: 0.8453 (mp10) REVERT: A 602 TRP cc_start: 0.8143 (m-10) cc_final: 0.7882 (m-10) REVERT: A 666 MET cc_start: 0.9083 (pmm) cc_final: 0.8641 (pmm) REVERT: A 703 THR cc_start: 0.8083 (p) cc_final: 0.7865 (p) REVERT: B 505 MET cc_start: 0.7859 (tmm) cc_final: 0.7568 (tmm) REVERT: B 622 LEU cc_start: 0.8765 (tt) cc_final: 0.8415 (tt) REVERT: B 675 TYR cc_start: 0.8706 (t80) cc_final: 0.8478 (t80) REVERT: C 392 ILE cc_start: 0.8374 (pt) cc_final: 0.8038 (mp) REVERT: C 494 LEU cc_start: 0.8560 (tt) cc_final: 0.8236 (tp) REVERT: C 523 MET cc_start: 0.8315 (ppp) cc_final: 0.7692 (mmp) REVERT: C 527 PHE cc_start: 0.8363 (m-80) cc_final: 0.7306 (m-80) REVERT: C 595 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.7665 (mtt-85) REVERT: C 637 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8553 (mmtm) REVERT: C 663 PHE cc_start: 0.8864 (m-10) cc_final: 0.8132 (m-10) REVERT: C 666 MET cc_start: 0.8597 (ptt) cc_final: 0.7716 (tpt) REVERT: C 686 MET cc_start: 0.8780 (tmm) cc_final: 0.8439 (tmm) REVERT: D 417 PHE cc_start: 0.7534 (t80) cc_final: 0.7179 (t80) REVERT: D 505 MET cc_start: 0.8105 (tmm) cc_final: 0.7673 (tmm) REVERT: D 533 PHE cc_start: 0.8468 (m-10) cc_final: 0.7737 (t80) REVERT: D 587 MET cc_start: 0.5995 (mpp) cc_final: 0.5271 (mpp) REVERT: D 622 LEU cc_start: 0.8845 (tt) cc_final: 0.8605 (tt) REVERT: D 749 ASN cc_start: 0.8625 (t0) cc_final: 0.8352 (t0) REVERT: F 141 PHE cc_start: 0.7135 (m-80) cc_final: 0.6766 (m-80) REVERT: F 163 ASP cc_start: 0.6803 (p0) cc_final: 0.6516 (p0) REVERT: F 182 PHE cc_start: 0.8000 (m-10) cc_final: 0.7792 (m-10) REVERT: F 200 MET cc_start: 0.9287 (ppp) cc_final: 0.9055 (ppp) REVERT: H 55 GLU cc_start: 0.7136 (tt0) cc_final: 0.6742 (tp30) REVERT: H 164 PRO cc_start: 0.6399 (Cg_endo) cc_final: 0.6179 (Cg_exo) REVERT: H 180 PHE cc_start: 0.7741 (m-10) cc_final: 0.6446 (t80) REVERT: H 181 TYR cc_start: 0.6274 (m-80) cc_final: 0.5476 (m-80) outliers start: 2 outliers final: 0 residues processed: 321 average time/residue: 0.0847 time to fit residues: 43.0991 Evaluate side-chains 262 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 161 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 115 optimal weight: 0.3980 chunk 145 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4045 r_free = 0.4045 target = 0.137244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108888 restraints weight = 46275.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111239 restraints weight = 30846.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112050 restraints weight = 21611.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.112502 restraints weight = 20595.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.112596 restraints weight = 18540.330| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15924 Z= 0.138 Angle : 0.584 10.715 21761 Z= 0.297 Chirality : 0.038 0.170 2573 Planarity : 0.003 0.039 2721 Dihedral : 4.866 82.267 2392 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: -0.54 (0.19), residues: 1932 helix: 1.02 (0.16), residues: 1066 sheet: -1.23 (0.70), residues: 57 loop : -2.28 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 711 TYR 0.021 0.001 TYR B 618 PHE 0.024 0.001 PHE H 142 TRP 0.022 0.001 TRP D 768 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00313 (15916) covalent geometry : angle 0.58350 (21745) SS BOND : bond 0.00491 ( 8) SS BOND : angle 0.91303 ( 16) hydrogen bonds : bond 0.03606 ( 989) hydrogen bonds : angle 4.14694 ( 2949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.6372 (mmm) cc_final: 0.6112 (mmm) REVERT: A 582 GLN cc_start: 0.9083 (mp10) cc_final: 0.8263 (mp10) REVERT: A 666 MET cc_start: 0.9177 (pmm) cc_final: 0.8433 (pmm) REVERT: A 686 MET cc_start: 0.7663 (tmm) cc_final: 0.7364 (tmm) REVERT: A 698 TYR cc_start: 0.6419 (t80) cc_final: 0.6182 (t80) REVERT: A 703 THR cc_start: 0.8026 (p) cc_final: 0.7819 (p) REVERT: A 803 MET cc_start: 0.8134 (tmm) cc_final: 0.7917 (tmm) REVERT: B 414 HIS cc_start: 0.7114 (t70) cc_final: 0.6912 (t70) REVERT: C 392 ILE cc_start: 0.8301 (pt) cc_final: 0.7880 (mp) REVERT: C 494 LEU cc_start: 0.8551 (tt) cc_final: 0.8300 (tp) REVERT: C 523 MET cc_start: 0.8353 (ppp) cc_final: 0.7703 (mmp) REVERT: C 666 MET cc_start: 0.8619 (ptt) cc_final: 0.7830 (tpt) REVERT: C 804 LEU cc_start: 0.9180 (mm) cc_final: 0.8783 (mm) REVERT: D 417 PHE cc_start: 0.7610 (t80) cc_final: 0.7302 (t80) REVERT: D 505 MET cc_start: 0.8167 (tmm) cc_final: 0.7557 (tmm) REVERT: D 533 PHE cc_start: 0.8457 (m-10) cc_final: 0.7796 (t80) REVERT: D 587 MET cc_start: 0.5901 (mpp) cc_final: 0.5409 (mpp) REVERT: D 715 GLU cc_start: 0.8665 (pt0) cc_final: 0.8283 (pt0) REVERT: F 141 PHE cc_start: 0.7139 (m-10) cc_final: 0.6866 (m-80) REVERT: F 163 ASP cc_start: 0.6631 (p0) cc_final: 0.6348 (p0) REVERT: F 182 PHE cc_start: 0.8028 (m-10) cc_final: 0.7815 (m-10) REVERT: F 200 MET cc_start: 0.9197 (ppp) cc_final: 0.8965 (ppp) REVERT: H 18 PHE cc_start: 0.8762 (m-80) cc_final: 0.8226 (m-10) REVERT: H 55 GLU cc_start: 0.7174 (tt0) cc_final: 0.6593 (tp30) REVERT: H 164 PRO cc_start: 0.6266 (Cg_endo) cc_final: 0.6037 (Cg_exo) REVERT: H 180 PHE cc_start: 0.7880 (m-10) cc_final: 0.6436 (t80) REVERT: H 181 TYR cc_start: 0.6423 (m-80) cc_final: 0.5534 (m-80) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.0869 time to fit residues: 42.5074 Evaluate side-chains 255 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 168 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.133111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105213 restraints weight = 46760.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.106861 restraints weight = 30188.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106849 restraints weight = 23380.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.107231 restraints weight = 22311.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107646 restraints weight = 20609.225| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15924 Z= 0.194 Angle : 0.648 13.632 21761 Z= 0.333 Chirality : 0.040 0.176 2573 Planarity : 0.004 0.039 2721 Dihedral : 5.213 84.466 2392 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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: -0.64 (0.19), residues: 1932 helix: 0.97 (0.16), residues: 1066 sheet: -1.32 (0.68), residues: 57 loop : -2.36 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 711 TYR 0.019 0.002 TYR H 156 PHE 0.025 0.002 PHE F 142 TRP 0.034 0.002 TRP A 602 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00429 (15916) covalent geometry : angle 0.64735 (21745) SS BOND : bond 0.00313 ( 8) SS BOND : angle 1.06368 ( 16) hydrogen bonds : bond 0.03924 ( 989) hydrogen bonds : angle 4.23570 ( 2949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.6387 (mmm) cc_final: 0.6129 (mmm) REVERT: A 582 GLN cc_start: 0.8859 (mp10) cc_final: 0.7976 (mp10) REVERT: A 602 TRP cc_start: 0.8194 (m-10) cc_final: 0.7601 (m-10) REVERT: A 666 MET cc_start: 0.9096 (pmm) cc_final: 0.8727 (pmm) REVERT: A 686 MET cc_start: 0.8406 (tmm) cc_final: 0.8076 (tmm) REVERT: A 717 MET cc_start: 0.8365 (ppp) cc_final: 0.7790 (tmm) REVERT: B 414 HIS cc_start: 0.7523 (t70) cc_final: 0.7307 (t70) REVERT: B 505 MET cc_start: 0.7993 (tmm) cc_final: 0.7675 (tmm) REVERT: B 588 GLN cc_start: 0.8354 (tt0) cc_final: 0.8135 (tt0) REVERT: B 675 TYR cc_start: 0.8881 (t80) cc_final: 0.8555 (t80) REVERT: C 459 MET cc_start: 0.8770 (mmt) cc_final: 0.7820 (mmt) REVERT: C 523 MET cc_start: 0.8405 (ppp) cc_final: 0.7686 (mmp) REVERT: C 580 PHE cc_start: 0.6578 (t80) cc_final: 0.5932 (t80) REVERT: C 582 GLN cc_start: 0.8679 (mp10) cc_final: 0.8330 (mp10) REVERT: C 666 MET cc_start: 0.8663 (ptt) cc_final: 0.7974 (tpt) REVERT: C 669 TYR cc_start: 0.8960 (t80) cc_final: 0.8656 (t80) REVERT: C 785 LEU cc_start: 0.9261 (tp) cc_final: 0.9028 (tp) REVERT: D 417 PHE cc_start: 0.7508 (t80) cc_final: 0.6803 (t80) REVERT: D 505 MET cc_start: 0.8176 (tmm) cc_final: 0.7127 (tmm) REVERT: D 533 PHE cc_start: 0.8491 (m-10) cc_final: 0.7745 (t80) REVERT: D 587 MET cc_start: 0.6078 (mpp) cc_final: 0.5438 (mpp) REVERT: D 607 TRP cc_start: 0.8115 (t-100) cc_final: 0.7749 (t-100) REVERT: F 163 ASP cc_start: 0.6783 (p0) cc_final: 0.6493 (p0) REVERT: F 200 MET cc_start: 0.9269 (ppp) cc_final: 0.8987 (ppp) REVERT: H 18 PHE cc_start: 0.8843 (m-80) cc_final: 0.8154 (m-10) REVERT: H 37 ARG cc_start: 0.5693 (ptt-90) cc_final: 0.5193 (ptp-170) REVERT: H 55 GLU cc_start: 0.7169 (tt0) cc_final: 0.6643 (tp30) REVERT: H 164 PRO cc_start: 0.6503 (Cg_endo) cc_final: 0.6294 (Cg_exo) REVERT: H 180 PHE cc_start: 0.7894 (m-10) cc_final: 0.6699 (t80) REVERT: H 181 TYR cc_start: 0.6438 (m-80) cc_final: 0.5646 (m-80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.0896 time to fit residues: 41.7949 Evaluate side-chains 248 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 50 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.134396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.106214 restraints weight = 45994.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107612 restraints weight = 32321.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108929 restraints weight = 23232.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109209 restraints weight = 21591.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.109349 restraints weight = 19053.245| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15924 Z= 0.140 Angle : 0.606 11.783 21761 Z= 0.306 Chirality : 0.039 0.249 2573 Planarity : 0.004 0.056 2721 Dihedral : 5.090 87.173 2392 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -0.47 (0.19), residues: 1932 helix: 1.12 (0.16), residues: 1068 sheet: -0.97 (0.66), residues: 62 loop : -2.35 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 455 TYR 0.014 0.001 TYR D 713 PHE 0.027 0.001 PHE F 142 TRP 0.026 0.002 TRP B 769 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00317 (15916) covalent geometry : angle 0.60503 (21745) SS BOND : bond 0.00238 ( 8) SS BOND : angle 1.40475 ( 16) hydrogen bonds : bond 0.03556 ( 989) hydrogen bonds : angle 4.08143 ( 2949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 SER cc_start: 0.9044 (m) cc_final: 0.8547 (p) REVERT: A 581 MET cc_start: 0.8704 (ppp) cc_final: 0.7863 (ppp) REVERT: A 582 GLN cc_start: 0.8791 (mp10) cc_final: 0.8112 (mp10) REVERT: A 666 MET cc_start: 0.9035 (pmm) cc_final: 0.8622 (pmm) REVERT: A 686 MET cc_start: 0.8319 (tmm) cc_final: 0.8051 (tmm) REVERT: A 717 MET cc_start: 0.8354 (ppp) cc_final: 0.7764 (tmm) REVERT: A 803 MET cc_start: 0.8508 (tmm) cc_final: 0.8296 (tmm) REVERT: B 414 HIS cc_start: 0.7504 (t70) cc_final: 0.7273 (t70) REVERT: B 529 MET cc_start: 0.7974 (pmm) cc_final: 0.7755 (pmm) REVERT: B 588 GLN cc_start: 0.8881 (tt0) cc_final: 0.8591 (tt0) REVERT: B 631 MET cc_start: 0.7857 (ttt) cc_final: 0.7620 (ttt) REVERT: C 523 MET cc_start: 0.8405 (ppp) cc_final: 0.7606 (mmt) REVERT: C 580 PHE cc_start: 0.6527 (t80) cc_final: 0.5845 (t80) REVERT: C 582 GLN cc_start: 0.8802 (mp10) cc_final: 0.8537 (mp10) REVERT: C 666 MET cc_start: 0.8527 (ptt) cc_final: 0.7909 (tpt) REVERT: C 669 TYR cc_start: 0.8868 (t80) cc_final: 0.8620 (t80) REVERT: C 751 GLU cc_start: 0.7138 (pt0) cc_final: 0.6929 (pt0) REVERT: D 417 PHE cc_start: 0.7401 (t80) cc_final: 0.6874 (t80) REVERT: D 505 MET cc_start: 0.8069 (tmm) cc_final: 0.7460 (tmm) REVERT: D 533 PHE cc_start: 0.8435 (m-10) cc_final: 0.7723 (t80) REVERT: D 587 MET cc_start: 0.5995 (mpp) cc_final: 0.5591 (mpp) REVERT: D 607 TRP cc_start: 0.8099 (t-100) cc_final: 0.7774 (t-100) REVERT: D 749 ASN cc_start: 0.8621 (t0) cc_final: 0.8394 (t0) REVERT: F 163 ASP cc_start: 0.6804 (p0) cc_final: 0.6474 (p0) REVERT: F 200 MET cc_start: 0.9208 (ppp) cc_final: 0.8979 (ppp) REVERT: H 18 PHE cc_start: 0.8867 (m-80) cc_final: 0.8127 (m-10) REVERT: H 37 ARG cc_start: 0.5727 (ptt-90) cc_final: 0.5223 (ptp-170) REVERT: H 55 GLU cc_start: 0.7374 (tt0) cc_final: 0.6563 (tp30) REVERT: H 128 TYR cc_start: 0.6571 (m-80) cc_final: 0.6241 (m-10) REVERT: H 176 TYR cc_start: 0.4474 (m-80) cc_final: 0.3601 (m-80) REVERT: H 180 PHE cc_start: 0.7496 (m-10) cc_final: 0.6446 (t80) REVERT: H 181 TYR cc_start: 0.6697 (m-80) cc_final: 0.6478 (m-80) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.0945 time to fit residues: 45.4698 Evaluate side-chains 250 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 146 optimal weight: 0.7980 chunk 89 optimal weight: 0.0040 chunk 113 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 589 GLN B 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.135681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106787 restraints weight = 46134.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108786 restraints weight = 31908.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.109836 restraints weight = 25378.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.110291 restraints weight = 22973.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110417 restraints weight = 18896.499| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15924 Z= 0.124 Angle : 0.602 12.064 21761 Z= 0.300 Chirality : 0.039 0.209 2573 Planarity : 0.004 0.063 2721 Dihedral : 4.964 87.883 2392 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.07 % Allowed : 1.43 % Favored : 98.50 % 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: -0.36 (0.19), residues: 1932 helix: 1.22 (0.16), residues: 1069 sheet: -0.89 (0.68), residues: 62 loop : -2.33 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 711 TYR 0.014 0.001 TYR H 156 PHE 0.017 0.001 PHE C 575 TRP 0.023 0.001 TRP A 602 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00279 (15916) covalent geometry : angle 0.60119 (21745) SS BOND : bond 0.00221 ( 8) SS BOND : angle 1.01385 ( 16) hydrogen bonds : bond 0.03385 ( 989) hydrogen bonds : angle 4.01806 ( 2949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.8873 (pmm) cc_final: 0.8533 (pmm) REVERT: A 686 MET cc_start: 0.8087 (tmm) cc_final: 0.7771 (tmm) REVERT: A 703 THR cc_start: 0.8281 (p) cc_final: 0.8072 (p) REVERT: A 803 MET cc_start: 0.8551 (tmm) cc_final: 0.8309 (tmm) REVERT: B 414 HIS cc_start: 0.7528 (t70) cc_final: 0.7278 (t70) REVERT: B 588 GLN cc_start: 0.8855 (tt0) cc_final: 0.8530 (tt0) REVERT: B 622 LEU cc_start: 0.9065 (tt) cc_final: 0.8839 (tt) REVERT: B 631 MET cc_start: 0.7828 (ttt) cc_final: 0.7567 (ttt) REVERT: C 514 LEU cc_start: 0.8677 (pt) cc_final: 0.8440 (pt) REVERT: C 523 MET cc_start: 0.7997 (ppp) cc_final: 0.7749 (mmp) REVERT: C 663 PHE cc_start: 0.8745 (m-10) cc_final: 0.8060 (m-10) REVERT: C 666 MET cc_start: 0.8632 (ptt) cc_final: 0.7900 (tpt) REVERT: C 669 TYR cc_start: 0.8781 (t80) cc_final: 0.8449 (t80) REVERT: C 717 MET cc_start: 0.8138 (ppp) cc_final: 0.7495 (ppp) REVERT: C 751 GLU cc_start: 0.7284 (pt0) cc_final: 0.6846 (pt0) REVERT: C 807 LEU cc_start: 0.9195 (mm) cc_final: 0.8848 (pp) REVERT: C 808 ILE cc_start: 0.9386 (tt) cc_final: 0.9022 (tt) REVERT: D 505 MET cc_start: 0.8076 (tmm) cc_final: 0.7526 (tmm) REVERT: D 533 PHE cc_start: 0.8433 (m-10) cc_final: 0.7761 (t80) REVERT: D 587 MET cc_start: 0.5742 (mpp) cc_final: 0.5326 (mpp) REVERT: D 749 ASN cc_start: 0.8618 (t0) cc_final: 0.8363 (t0) REVERT: F 70 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6709 (tm-30) REVERT: F 150 ILE cc_start: 0.8853 (mm) cc_final: 0.8554 (mm) REVERT: F 163 ASP cc_start: 0.6759 (p0) cc_final: 0.6440 (p0) REVERT: F 200 MET cc_start: 0.9305 (ppp) cc_final: 0.9059 (ppp) REVERT: H 18 PHE cc_start: 0.8833 (m-80) cc_final: 0.8482 (t80) REVERT: H 37 ARG cc_start: 0.5534 (ptt-90) cc_final: 0.4986 (ptp-170) REVERT: H 55 GLU cc_start: 0.7373 (tt0) cc_final: 0.6634 (tp30) REVERT: H 128 TYR cc_start: 0.6632 (m-80) cc_final: 0.6381 (m-10) REVERT: H 176 TYR cc_start: 0.4420 (m-80) cc_final: 0.3184 (m-80) REVERT: H 180 PHE cc_start: 0.7724 (m-10) cc_final: 0.6577 (t80) REVERT: H 181 TYR cc_start: 0.6476 (m-80) cc_final: 0.6201 (m-80) outliers start: 1 outliers final: 1 residues processed: 301 average time/residue: 0.0912 time to fit residues: 43.0410 Evaluate side-chains 248 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 151 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 201 optimal weight: 0.0270 chunk 182 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.135365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.106606 restraints weight = 45868.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108362 restraints weight = 31739.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.108625 restraints weight = 24904.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108922 restraints weight = 23320.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.109205 restraints weight = 21680.522| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15924 Z= 0.124 Angle : 0.602 12.654 21761 Z= 0.300 Chirality : 0.039 0.203 2573 Planarity : 0.003 0.046 2721 Dihedral : 4.827 66.765 2392 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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: -0.30 (0.19), residues: 1932 helix: 1.28 (0.16), residues: 1071 sheet: -0.39 (0.71), residues: 52 loop : -2.36 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 65 TYR 0.010 0.001 TYR D 452 PHE 0.035 0.001 PHE F 187 TRP 0.023 0.001 TRP A 602 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00278 (15916) covalent geometry : angle 0.60171 (21745) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.96329 ( 16) hydrogen bonds : bond 0.03300 ( 989) hydrogen bonds : angle 3.95858 ( 2949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.9009 (pmm) cc_final: 0.8533 (pmm) REVERT: A 686 MET cc_start: 0.8158 (tmm) cc_final: 0.7863 (tmm) REVERT: A 703 THR cc_start: 0.8303 (p) cc_final: 0.8097 (p) REVERT: A 785 LEU cc_start: 0.8912 (mm) cc_final: 0.8469 (tp) REVERT: A 803 MET cc_start: 0.8617 (tmm) cc_final: 0.8349 (tmm) REVERT: B 414 HIS cc_start: 0.7703 (t70) cc_final: 0.7444 (t70) REVERT: B 505 MET cc_start: 0.7759 (tmm) cc_final: 0.7488 (tmm) REVERT: B 545 VAL cc_start: 0.9377 (t) cc_final: 0.9158 (t) REVERT: B 588 GLN cc_start: 0.8850 (tt0) cc_final: 0.8553 (tt0) REVERT: B 622 LEU cc_start: 0.8893 (tt) cc_final: 0.8686 (tt) REVERT: B 631 MET cc_start: 0.7876 (ttt) cc_final: 0.7523 (ttt) REVERT: B 675 TYR cc_start: 0.8796 (t80) cc_final: 0.8492 (t80) REVERT: C 514 LEU cc_start: 0.8598 (pt) cc_final: 0.8364 (pt) REVERT: C 663 PHE cc_start: 0.8767 (m-10) cc_final: 0.8101 (m-10) REVERT: C 666 MET cc_start: 0.8675 (ptt) cc_final: 0.7937 (tpt) REVERT: C 669 TYR cc_start: 0.8887 (t80) cc_final: 0.8490 (t80) REVERT: C 686 MET cc_start: 0.8355 (tmm) cc_final: 0.8098 (tmm) REVERT: C 751 GLU cc_start: 0.7365 (pt0) cc_final: 0.7038 (pt0) REVERT: C 807 LEU cc_start: 0.9141 (mm) cc_final: 0.8783 (pp) REVERT: C 808 ILE cc_start: 0.9371 (tt) cc_final: 0.8997 (tt) REVERT: D 505 MET cc_start: 0.8139 (tmm) cc_final: 0.7230 (tmm) REVERT: D 533 PHE cc_start: 0.8413 (m-10) cc_final: 0.7748 (t80) REVERT: D 587 MET cc_start: 0.5713 (mpp) cc_final: 0.5429 (mpp) REVERT: D 675 TYR cc_start: 0.8663 (t80) cc_final: 0.8277 (t80) REVERT: D 749 ASN cc_start: 0.8652 (t0) cc_final: 0.8394 (t0) REVERT: F 70 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6700 (tm-30) REVERT: F 163 ASP cc_start: 0.6864 (p0) cc_final: 0.6553 (p0) REVERT: F 200 MET cc_start: 0.9283 (ppp) cc_final: 0.9040 (ppp) REVERT: H 18 PHE cc_start: 0.8794 (m-80) cc_final: 0.8495 (t80) REVERT: H 21 PHE cc_start: 0.8665 (t80) cc_final: 0.8402 (t80) REVERT: H 37 ARG cc_start: 0.5547 (ptt-90) cc_final: 0.4937 (ptp-170) REVERT: H 55 GLU cc_start: 0.7365 (tt0) cc_final: 0.6620 (tp30) REVERT: H 64 TRP cc_start: 0.8138 (m100) cc_final: 0.7835 (m-10) REVERT: H 128 TYR cc_start: 0.6410 (m-80) cc_final: 0.6189 (m-10) REVERT: H 164 PRO cc_start: 0.5914 (Cg_endo) cc_final: 0.5642 (Cg_exo) REVERT: H 176 TYR cc_start: 0.4294 (m-80) cc_final: 0.3288 (m-80) REVERT: H 180 PHE cc_start: 0.7706 (m-10) cc_final: 0.6383 (t80) REVERT: H 181 TYR cc_start: 0.6462 (m-80) cc_final: 0.6203 (m-80) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.0880 time to fit residues: 41.8540 Evaluate side-chains 250 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 36 optimal weight: 0.0030 chunk 208 optimal weight: 0.0770 chunk 115 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 211 optimal weight: 0.0010 chunk 18 optimal weight: 0.1980 chunk 197 optimal weight: 10.0000 chunk 144 optimal weight: 0.0000 chunk 35 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.0558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 716 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.137850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.109738 restraints weight = 45267.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.111903 restraints weight = 30153.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.112710 restraints weight = 20703.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.113261 restraints weight = 19859.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113330 restraints weight = 17822.878| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15924 Z= 0.116 Angle : 0.608 12.186 21761 Z= 0.299 Chirality : 0.039 0.189 2573 Planarity : 0.003 0.044 2721 Dihedral : 4.511 53.496 2392 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % 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: -0.27 (0.19), residues: 1932 helix: 1.35 (0.16), residues: 1065 sheet: -0.41 (0.70), residues: 54 loop : -2.37 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 455 TYR 0.014 0.001 TYR C 764 PHE 0.036 0.001 PHE F 187 TRP 0.019 0.001 TRP A 602 HIS 0.004 0.000 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00245 (15916) covalent geometry : angle 0.60724 (21745) SS BOND : bond 0.00146 ( 8) SS BOND : angle 0.98037 ( 16) hydrogen bonds : bond 0.03136 ( 989) hydrogen bonds : angle 3.86197 ( 2949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8300 (tm-30) REVERT: A 538 LEU cc_start: 0.8918 (tt) cc_final: 0.8386 (mt) REVERT: A 666 MET cc_start: 0.8973 (pmm) cc_final: 0.8508 (pmm) REVERT: A 686 MET cc_start: 0.8111 (tmm) cc_final: 0.7796 (tmm) REVERT: A 703 THR cc_start: 0.8104 (p) cc_final: 0.7890 (p) REVERT: A 785 LEU cc_start: 0.8801 (mm) cc_final: 0.8383 (tp) REVERT: A 803 MET cc_start: 0.8426 (tmm) cc_final: 0.8154 (tmm) REVERT: B 414 HIS cc_start: 0.7390 (t70) cc_final: 0.7140 (t70) REVERT: B 505 MET cc_start: 0.6768 (tmm) cc_final: 0.6473 (tmm) REVERT: B 588 GLN cc_start: 0.8654 (tt0) cc_final: 0.8409 (tt0) REVERT: B 622 LEU cc_start: 0.8869 (tt) cc_final: 0.8445 (tt) REVERT: B 631 MET cc_start: 0.7888 (ttt) cc_final: 0.7538 (ttt) REVERT: B 730 ASP cc_start: 0.8751 (t0) cc_final: 0.8222 (m-30) REVERT: C 523 MET cc_start: 0.6366 (mmp) cc_final: 0.5289 (tpp) REVERT: C 663 PHE cc_start: 0.8626 (m-10) cc_final: 0.7950 (m-10) REVERT: C 666 MET cc_start: 0.8563 (ptt) cc_final: 0.7695 (tpt) REVERT: C 686 MET cc_start: 0.8596 (tmm) cc_final: 0.8385 (tmm) REVERT: C 703 THR cc_start: 0.7478 (p) cc_final: 0.7263 (p) REVERT: C 751 GLU cc_start: 0.7416 (pt0) cc_final: 0.7084 (pt0) REVERT: D 498 MET cc_start: 0.7898 (ttp) cc_final: 0.7662 (ttm) REVERT: D 505 MET cc_start: 0.8018 (tmm) cc_final: 0.7135 (tmm) REVERT: D 533 PHE cc_start: 0.8482 (m-10) cc_final: 0.7792 (t80) REVERT: D 675 TYR cc_start: 0.8499 (t80) cc_final: 0.8166 (t80) REVERT: D 709 THR cc_start: 0.8475 (m) cc_final: 0.8231 (m) REVERT: D 766 ASN cc_start: 0.8626 (t0) cc_final: 0.7621 (t0) REVERT: D 770 TYR cc_start: 0.7472 (m-80) cc_final: 0.7146 (m-80) REVERT: F 70 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6421 (tm-30) REVERT: F 150 ILE cc_start: 0.8793 (mm) cc_final: 0.8553 (mm) REVERT: F 200 MET cc_start: 0.9265 (ppp) cc_final: 0.9017 (ppp) REVERT: H 18 PHE cc_start: 0.8749 (m-80) cc_final: 0.8470 (t80) REVERT: H 21 PHE cc_start: 0.8635 (t80) cc_final: 0.8322 (t80) REVERT: H 55 GLU cc_start: 0.7378 (tt0) cc_final: 0.6574 (tp30) REVERT: H 64 TRP cc_start: 0.7971 (m100) cc_final: 0.7710 (m-10) REVERT: H 176 TYR cc_start: 0.4313 (m-80) cc_final: 0.3376 (m-80) REVERT: H 180 PHE cc_start: 0.7637 (m-10) cc_final: 0.6580 (t80) REVERT: H 181 TYR cc_start: 0.6543 (m-80) cc_final: 0.6309 (m-80) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.0952 time to fit residues: 46.9482 Evaluate side-chains 247 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 146 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.135226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105878 restraints weight = 45123.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108262 restraints weight = 29237.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109867 restraints weight = 21899.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110792 restraints weight = 18111.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111521 restraints weight = 16119.992| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15924 Z= 0.127 Angle : 0.624 12.812 21761 Z= 0.308 Chirality : 0.039 0.212 2573 Planarity : 0.003 0.043 2721 Dihedral : 4.509 54.354 2392 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.21 (0.19), residues: 1932 helix: 1.43 (0.16), residues: 1064 sheet: -0.97 (0.68), residues: 62 loop : -2.35 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 131 TYR 0.010 0.001 TYR A 643 PHE 0.033 0.001 PHE F 142 TRP 0.018 0.001 TRP D 528 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00289 (15916) covalent geometry : angle 0.62356 (21745) SS BOND : bond 0.00204 ( 8) SS BOND : angle 0.85126 ( 16) hydrogen bonds : bond 0.03188 ( 989) hydrogen bonds : angle 3.85808 ( 2949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 538 LEU cc_start: 0.8892 (tt) cc_final: 0.8338 (mt) REVERT: A 602 TRP cc_start: 0.8322 (m-10) cc_final: 0.7886 (m-90) REVERT: A 666 MET cc_start: 0.9007 (pmm) cc_final: 0.8590 (pmm) REVERT: A 686 MET cc_start: 0.7993 (tmm) cc_final: 0.7686 (tmm) REVERT: A 703 THR cc_start: 0.8282 (p) cc_final: 0.8071 (p) REVERT: A 785 LEU cc_start: 0.8807 (mm) cc_final: 0.8238 (tp) REVERT: A 803 MET cc_start: 0.8232 (tmm) cc_final: 0.7989 (tmm) REVERT: B 505 MET cc_start: 0.7651 (tmm) cc_final: 0.7393 (tmm) REVERT: B 588 GLN cc_start: 0.8796 (tt0) cc_final: 0.8591 (tt0) REVERT: B 631 MET cc_start: 0.7855 (ttt) cc_final: 0.7466 (ttt) REVERT: B 730 ASP cc_start: 0.8802 (t0) cc_final: 0.8178 (m-30) REVERT: C 514 LEU cc_start: 0.8527 (pt) cc_final: 0.8290 (pt) REVERT: C 523 MET cc_start: 0.6145 (mmp) cc_final: 0.5596 (ppp) REVERT: C 663 PHE cc_start: 0.8587 (m-10) cc_final: 0.7813 (m-10) REVERT: C 666 MET cc_start: 0.8512 (ptt) cc_final: 0.7763 (tpt) REVERT: C 751 GLU cc_start: 0.7389 (pt0) cc_final: 0.7045 (pt0) REVERT: D 498 MET cc_start: 0.7874 (ttp) cc_final: 0.7670 (ttm) REVERT: D 505 MET cc_start: 0.8118 (tmm) cc_final: 0.7172 (tmm) REVERT: D 529 MET cc_start: 0.7670 (ptp) cc_final: 0.7067 (ptt) REVERT: D 533 PHE cc_start: 0.8430 (m-10) cc_final: 0.7728 (t80) REVERT: D 587 MET cc_start: 0.5689 (mpp) cc_final: 0.5139 (mpp) REVERT: D 672 MET cc_start: 0.7336 (tpt) cc_final: 0.6955 (tpt) REVERT: D 675 TYR cc_start: 0.8364 (t80) cc_final: 0.8150 (t80) REVERT: D 709 THR cc_start: 0.8506 (m) cc_final: 0.8242 (m) REVERT: D 766 ASN cc_start: 0.8642 (t0) cc_final: 0.7631 (t0) REVERT: F 70 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6626 (tm-30) REVERT: F 192 MET cc_start: 0.8057 (tpt) cc_final: 0.7751 (tpp) REVERT: F 200 MET cc_start: 0.9269 (ppp) cc_final: 0.9004 (ppp) REVERT: H 18 PHE cc_start: 0.8759 (m-80) cc_final: 0.8464 (t80) REVERT: H 21 PHE cc_start: 0.8616 (t80) cc_final: 0.8295 (t80) REVERT: H 37 ARG cc_start: 0.6480 (ptt-90) cc_final: 0.6031 (ptp-170) REVERT: H 55 GLU cc_start: 0.7336 (tt0) cc_final: 0.6466 (tp30) REVERT: H 64 TRP cc_start: 0.7941 (m100) cc_final: 0.7696 (m-10) REVERT: H 176 TYR cc_start: 0.4392 (m-80) cc_final: 0.3533 (m-80) REVERT: H 180 PHE cc_start: 0.7652 (m-10) cc_final: 0.6449 (t80) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.0829 time to fit residues: 40.0028 Evaluate side-chains 242 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 182 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.129692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.101211 restraints weight = 46428.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.102313 restraints weight = 33790.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103163 restraints weight = 25422.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103794 restraints weight = 22047.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.103864 restraints weight = 20133.127| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15924 Z= 0.222 Angle : 0.726 13.543 21761 Z= 0.372 Chirality : 0.042 0.369 2573 Planarity : 0.004 0.064 2721 Dihedral : 5.154 59.635 2392 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.59 (0.19), residues: 1932 helix: 1.12 (0.16), residues: 1058 sheet: -1.64 (0.69), residues: 58 loop : -2.45 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 65 TYR 0.021 0.002 TYR D 452 PHE 0.042 0.002 PHE F 182 TRP 0.019 0.002 TRP D 528 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00490 (15916) covalent geometry : angle 0.72622 (21745) SS BOND : bond 0.00377 ( 8) SS BOND : angle 1.02574 ( 16) hydrogen bonds : bond 0.03906 ( 989) hydrogen bonds : angle 4.21536 ( 2949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.71 seconds wall clock time: 37 minutes 2.17 seconds (2222.17 seconds total)