Starting phenix.real_space_refine on Thu Jul 31 02:33:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7unk_26625/07_2025/7unk_26625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7unk_26625/07_2025/7unk_26625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7unk_26625/07_2025/7unk_26625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7unk_26625/07_2025/7unk_26625.map" model { file = "/net/cci-nas-00/data/ceres_data/7unk_26625/07_2025/7unk_26625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7unk_26625/07_2025/7unk_26625.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2586 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6968 2.51 5 N 1911 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8060 Classifications: {'peptide': 1047} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 68, 'TRANS': 978} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 990 Chain: "D" Number of atoms: 1318 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1203 Conformer: "C" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 137} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1203 Chain: "E" Number of atoms: 600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 568 Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N AASP C 81 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 81 " occ=0.50 residue: pdb=" N AGLN C 125 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 125 " occ=0.50 residue: pdb=" N ARG C 131 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 131 " occ=0.50 residue: pdb=" N ASER D 5 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 5 " occ=0.50 residue: pdb=" N ASER D 33 " occ=0.33 ... (16 atoms not shown) pdb=" OG CSER D 33 " occ=0.33 residue: pdb=" N AGLU D 56 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 56 " occ=0.50 residue: pdb=" N ASER D 80 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 80 " occ=0.50 residue: pdb=" N ALEU D 97 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU D 97 " occ=0.50 residue: pdb=" N ASER D 98 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 98 " occ=0.50 residue: pdb=" N ASER D 100 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 100 " occ=0.50 residue: pdb=" N AGLU D 124 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 124 " occ=0.50 residue: pdb=" N AGLU D 142 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 142 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 10.19, per 1000 atoms: 0.93 Number of scatterers: 10992 At special positions: 0 Unit cell: (87.57, 111.756, 140.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2057 8.00 N 1911 7.00 C 6968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 6 sheets defined 70.0% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.552A pdb=" N LEU A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 45 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.549A pdb=" N ARG A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.937A pdb=" N ALA A 73 " --> pdb=" O ARG A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 76 through 89 Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 131 through 149 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.520A pdb=" N PHE A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.581A pdb=" N LEU A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.632A pdb=" N ALA A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Proline residue: A 204 - end of helix Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.983A pdb=" N ALA A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 260 through 278 removed outlier: 3.514A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 287 through 300 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 309 through 313 removed outlier: 4.065A pdb=" N GLN A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 removed outlier: 4.199A pdb=" N PHE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 Proline residue: A 351 - end of helix Proline residue: A 355 - end of helix removed outlier: 3.526A pdb=" N ARG A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.619A pdb=" N ARG A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.302A pdb=" N LEU A 396 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.317A pdb=" N SER A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 451 through 467 Processing helix chain 'A' and resid 468 through 474 Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.864A pdb=" N LEU A 487 " --> pdb=" O CYS A 483 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 488 " --> pdb=" O MET A 484 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.744A pdb=" N GLU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 537 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 559 through 575 removed outlier: 4.096A pdb=" N GLU A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.901A pdb=" N GLY A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 removed outlier: 4.295A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 669 through 687 removed outlier: 3.736A pdb=" N ASP A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 705 removed outlier: 4.198A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER A 697 " --> pdb=" O PRO A 693 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 710 through 735 removed outlier: 3.795A pdb=" N GLY A 722 " --> pdb=" O HIS A 718 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 758 Proline residue: A 753 - end of helix Processing helix chain 'A' and resid 764 through 782 removed outlier: 3.675A pdb=" N VAL A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 770 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 791 through 805 removed outlier: 3.554A pdb=" N GLU A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.697A pdb=" N LEU A 831 " --> pdb=" O TYR A 827 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 838 " --> pdb=" O HIS A 834 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Proline residue: A 840 - end of helix removed outlier: 3.542A pdb=" N GLY A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 866 removed outlier: 3.625A pdb=" N GLY A 857 " --> pdb=" O PRO A 853 " (cutoff:3.500A) Proline residue: A 860 - end of helix Processing helix chain 'A' and resid 871 through 890 Processing helix chain 'A' and resid 891 through 894 removed outlier: 3.870A pdb=" N ALA A 894 " --> pdb=" O ALA A 891 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 896 through 908 Proline residue: A 902 - end of helix Processing helix chain 'A' and resid 912 through 930 Processing helix chain 'A' and resid 931 through 936 removed outlier: 4.430A pdb=" N GLU A 936 " --> pdb=" O PRO A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 952 removed outlier: 3.784A pdb=" N PHE A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Proline residue: A 947 - end of helix removed outlier: 3.686A pdb=" N ALA A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 971 Processing helix chain 'A' and resid 981 through 988 removed outlier: 4.215A pdb=" N ALA A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 996 No H-bonds generated for 'chain 'A' and resid 994 through 996' Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.702A pdb=" N PHE A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1033 removed outlier: 3.617A pdb=" N LEU A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A1032 " --> pdb=" O SER A1028 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1051 removed outlier: 4.100A pdb=" N LYS A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1044 " --> pdb=" O THR A1040 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1066 removed outlier: 4.088A pdb=" N GLN A1060 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A1061 " --> pdb=" O ASP A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1077 removed outlier: 3.783A pdb=" N GLU A1073 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A1077 " --> pdb=" O GLU A1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.626A pdb=" N VAL D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.800A pdb=" N ARG D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 49 through 76 removed outlier: 3.709A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.536A pdb=" N LYS E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 622 through 626 removed outlier: 3.952A pdb=" N VAL A 623 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 662 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.170A pdb=" N ARG C 83 " --> pdb=" O VAL E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 10 removed outlier: 4.042A pdb=" N GLY D 8 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 27 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.598A pdb=" N ALA D 16 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG D 137 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 136 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 116 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 138 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR D 101 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 107 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 39 " --> pdb=" O ASER D 100 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU D 38 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU D 61 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TRP D 40 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER D 59 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU D 42 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.598A pdb=" N ALA D 16 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG D 137 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 136 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 116 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 138 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 145 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL D 146 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU E 97 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 95 " --> pdb=" O ARG D 148 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1801 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: 3.61 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3718 1.34 - 1.46: 2053 1.46 - 1.58: 5343 1.58 - 1.70: 1 1.70 - 1.82: 82 Bond restraints: 11197 Sorted by residual: bond pdb=" N ASN C 108 " pdb=" CA ASN C 108 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.80e+00 bond pdb=" N LEU C 109 " pdb=" CA LEU C 109 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.76e+00 bond pdb=" N LYS C 23 " pdb=" CA LYS C 23 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.54e-02 4.22e+03 4.04e+00 bond pdb=" N ALA C 25 " pdb=" CA ALA C 25 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.38e-02 5.25e+03 3.64e+00 bond pdb=" N CYS C 110 " pdb=" CA CYS C 110 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.54e+00 ... (remaining 11192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14769 1.66 - 3.32: 334 3.32 - 4.98: 70 4.98 - 6.64: 23 6.64 - 8.30: 6 Bond angle restraints: 15202 Sorted by residual: angle pdb=" C ALA A 73 " pdb=" CA ALA A 73 " pdb=" CB ALA A 73 " ideal model delta sigma weight residual 116.63 110.44 6.19 1.16e+00 7.43e-01 2.85e+01 angle pdb=" CA ALA C 24 " pdb=" C ALA C 24 " pdb=" O ALA C 24 " ideal model delta sigma weight residual 121.84 116.75 5.09 1.16e+00 7.43e-01 1.92e+01 angle pdb=" N VAL A 652 " pdb=" CA VAL A 652 " pdb=" C VAL A 652 " ideal model delta sigma weight residual 111.77 107.39 4.38 1.04e+00 9.25e-01 1.77e+01 angle pdb=" CA THR C 22 " pdb=" C THR C 22 " pdb=" O THR C 22 " ideal model delta sigma weight residual 122.41 117.42 4.99 1.21e+00 6.83e-01 1.70e+01 angle pdb=" CA ALA C 25 " pdb=" C ALA C 25 " pdb=" O ALA C 25 " ideal model delta sigma weight residual 122.45 117.18 5.27 1.30e+00 5.92e-01 1.64e+01 ... (remaining 15197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6158 17.94 - 35.87: 632 35.87 - 53.81: 105 53.81 - 71.74: 34 71.74 - 89.68: 17 Dihedral angle restraints: 6946 sinusoidal: 2810 harmonic: 4136 Sorted by residual: dihedral pdb=" CA GLN A 52 " pdb=" C GLN A 52 " pdb=" N ILE A 53 " pdb=" CA ILE A 53 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA THR A 609 " pdb=" C THR A 609 " pdb=" N THR A 610 " pdb=" CA THR A 610 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " pdb=" OD1 ASP A 405 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1226 0.037 - 0.075: 394 0.075 - 0.112: 150 0.112 - 0.149: 7 0.149 - 0.186: 2 Chirality restraints: 1779 Sorted by residual: chirality pdb=" CA LEU C 109 " pdb=" N LEU C 109 " pdb=" C LEU C 109 " pdb=" CB LEU C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA THR A 240 " pdb=" N THR A 240 " pdb=" C THR A 240 " pdb=" CB THR A 240 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA VAL A 652 " pdb=" N VAL A 652 " pdb=" C VAL A 652 " pdb=" CB VAL A 652 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1776 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 108 " 0.027 2.00e-02 2.50e+03 5.64e-02 3.19e+01 pdb=" C ASN C 108 " -0.098 2.00e-02 2.50e+03 pdb=" O ASN C 108 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU C 109 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 109 " 0.025 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C LEU C 109 " -0.088 2.00e-02 2.50e+03 pdb=" O LEU C 109 " 0.033 2.00e-02 2.50e+03 pdb=" N CYS C 110 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 20 " 0.066 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO D 21 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO D 21 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 21 " 0.053 5.00e-02 4.00e+02 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 258 2.72 - 3.26: 11233 3.26 - 3.81: 17240 3.81 - 4.35: 20652 4.35 - 4.90: 35265 Nonbonded interactions: 84648 Sorted by model distance: nonbonded pdb=" OG SER A 917 " pdb=" OD1 ASN A 960 " model vdw 2.169 3.040 nonbonded pdb=" NZ LYS C 122 " pdb=" OG SER D 91 " model vdw 2.225 3.120 nonbonded pdb=" OG SER A 618 " pdb=" OE2 GLU A 620 " model vdw 2.250 3.040 nonbonded pdb=" O ALA A 950 " pdb=" NH2 ARG A 953 " model vdw 2.250 3.120 nonbonded pdb=" O VAL D 45 " pdb=" OG1 THR D 93 " model vdw 2.257 3.040 ... (remaining 84643 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.33 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 11197 Z= 0.147 Angle : 0.659 8.302 15202 Z= 0.352 Chirality : 0.041 0.186 1779 Planarity : 0.006 0.097 1984 Dihedral : 15.440 89.676 4256 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.75 % Allowed : 0.42 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1422 helix: 1.56 (0.18), residues: 846 sheet: 1.60 (0.80), residues: 46 loop : -0.72 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 40 HIS 0.015 0.001 HIS D 36 PHE 0.029 0.001 PHE A 56 TYR 0.009 0.001 TYR A 179 ARG 0.008 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.16654 ( 612) hydrogen bonds : angle 5.40287 ( 1801) covalent geometry : bond 0.00310 (11197) covalent geometry : angle 0.65936 (15202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 1.270 Fit side-chains REVERT: A 187 MET cc_start: 0.8459 (ttp) cc_final: 0.8142 (ttm) REVERT: A 464 ASN cc_start: 0.8513 (m-40) cc_final: 0.8167 (m-40) REVERT: A 696 GLU cc_start: 0.7560 (tt0) cc_final: 0.7325 (tt0) REVERT: C 8 ARG cc_start: 0.5465 (tpt170) cc_final: 0.4565 (tpt170) REVERT: C 22 THR cc_start: 0.7898 (p) cc_final: 0.7665 (p) REVERT: C 26 ARG cc_start: 0.5249 (OUTLIER) cc_final: 0.2533 (tpt90) REVERT: C 108 ASN cc_start: 0.8821 (t0) cc_final: 0.8619 (t0) REVERT: D 2 SER cc_start: 0.8819 (t) cc_final: 0.8562 (t) REVERT: D 101 TYR cc_start: 0.5799 (t80) cc_final: 0.5068 (t80) REVERT: D 136 VAL cc_start: 0.7331 (t) cc_final: 0.7079 (p) outliers start: 4 outliers final: 0 residues processed: 174 average time/residue: 0.2841 time to fit residues: 67.5864 Evaluate side-chains 130 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 HIS D 53 HIS E 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122176 restraints weight = 111960.538| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 8.64 r_work: 0.3140 rms_B_bonded: 6.99 restraints_weight: 2.0000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11197 Z= 0.130 Angle : 0.607 9.488 15202 Z= 0.299 Chirality : 0.041 0.177 1779 Planarity : 0.005 0.075 1984 Dihedral : 4.013 59.046 1542 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.08 % Allowed : 8.83 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.23), residues: 1422 helix: 1.66 (0.18), residues: 866 sheet: 1.59 (0.79), residues: 46 loop : -0.80 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 40 HIS 0.017 0.001 HIS D 53 PHE 0.018 0.001 PHE A 56 TYR 0.011 0.001 TYR A 179 ARG 0.007 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 612) hydrogen bonds : angle 4.20877 ( 1801) covalent geometry : bond 0.00295 (11197) covalent geometry : angle 0.60672 (15202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.111 Fit side-chains REVERT: A 187 MET cc_start: 0.9004 (ttp) cc_final: 0.8596 (ttm) REVERT: A 528 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8323 (tp30) REVERT: A 867 LYS cc_start: 0.8080 (tppt) cc_final: 0.7763 (mmmt) REVERT: C 8 ARG cc_start: 0.5908 (tpt170) cc_final: 0.5156 (tpt170) REVERT: C 26 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.2029 (tpt90) REVERT: D 1 MET cc_start: 0.7770 (ppp) cc_final: 0.7558 (ppp) REVERT: D 54 ASP cc_start: 0.9189 (p0) cc_final: 0.8924 (p0) REVERT: D 136 VAL cc_start: 0.7390 (t) cc_final: 0.7084 (p) outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 0.2713 time to fit residues: 55.9239 Evaluate side-chains 133 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 76 optimal weight: 0.0010 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.175373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121009 restraints weight = 100972.053| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 8.61 r_work: 0.3088 rms_B_bonded: 7.02 restraints_weight: 2.0000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11197 Z= 0.126 Angle : 0.566 6.763 15202 Z= 0.277 Chirality : 0.040 0.171 1779 Planarity : 0.005 0.067 1984 Dihedral : 3.908 57.325 1542 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.67 % Allowed : 10.42 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1422 helix: 1.81 (0.19), residues: 859 sheet: 1.49 (0.78), residues: 46 loop : -0.72 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 40 HIS 0.009 0.001 HIS D 53 PHE 0.016 0.001 PHE A1005 TYR 0.011 0.001 TYR A 179 ARG 0.009 0.001 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 612) hydrogen bonds : angle 4.03287 ( 1801) covalent geometry : bond 0.00298 (11197) covalent geometry : angle 0.56589 (15202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.140 Fit side-chains REVERT: A 187 MET cc_start: 0.8976 (ttp) cc_final: 0.8607 (ttm) REVERT: C 26 ARG cc_start: 0.4584 (OUTLIER) cc_final: 0.2017 (tpt90) REVERT: D 54 ASP cc_start: 0.9095 (p0) cc_final: 0.8889 (p0) REVERT: D 101 TYR cc_start: 0.5291 (t80) cc_final: 0.4831 (t80) REVERT: D 136 VAL cc_start: 0.7329 (t) cc_final: 0.7031 (p) REVERT: D 137 ARG cc_start: 0.7381 (ptt180) cc_final: 0.7179 (ptt180) outliers start: 16 outliers final: 10 residues processed: 145 average time/residue: 0.2838 time to fit residues: 56.1931 Evaluate side-chains 137 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 101 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 GLN A 760 ASN D 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.166780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111109 restraints weight = 107038.494| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 8.61 r_work: 0.2935 rms_B_bonded: 6.94 restraints_weight: 2.0000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 11197 Z= 0.285 Angle : 0.704 7.587 15202 Z= 0.348 Chirality : 0.046 0.192 1779 Planarity : 0.006 0.062 1984 Dihedral : 4.307 57.836 1542 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.25 % Allowed : 13.42 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1422 helix: 1.41 (0.18), residues: 861 sheet: 1.44 (0.73), residues: 51 loop : -0.91 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 69 HIS 0.008 0.001 HIS D 53 PHE 0.019 0.002 PHE A 699 TYR 0.015 0.002 TYR A 460 ARG 0.005 0.001 ARG A1025 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 612) hydrogen bonds : angle 4.39401 ( 1801) covalent geometry : bond 0.00718 (11197) covalent geometry : angle 0.70405 (15202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7682 (ptp90) REVERT: A 187 MET cc_start: 0.9165 (ttp) cc_final: 0.8965 (ttm) REVERT: A 434 ARG cc_start: 0.9074 (tmm160) cc_final: 0.8721 (tpt-90) REVERT: A 700 GLU cc_start: 0.8841 (tp30) cc_final: 0.8612 (mm-30) REVERT: A 867 LYS cc_start: 0.8010 (tppt) cc_final: 0.7638 (mmmt) REVERT: C 26 ARG cc_start: 0.4507 (OUTLIER) cc_final: 0.1982 (tpt90) REVERT: D 136 VAL cc_start: 0.7552 (t) cc_final: 0.7230 (p) REVERT: D 137 ARG cc_start: 0.7392 (ptt180) cc_final: 0.7176 (ptt180) outliers start: 23 outliers final: 15 residues processed: 145 average time/residue: 0.2661 time to fit residues: 53.3539 Evaluate side-chains 143 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 118 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 408 GLN A 454 HIS D 53 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.170784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115488 restraints weight = 108305.909| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 8.55 r_work: 0.2994 rms_B_bonded: 6.97 restraints_weight: 2.0000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11197 Z= 0.139 Angle : 0.592 9.583 15202 Z= 0.288 Chirality : 0.041 0.169 1779 Planarity : 0.005 0.060 1984 Dihedral : 4.095 57.560 1542 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.58 % Allowed : 15.00 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1422 helix: 1.68 (0.18), residues: 859 sheet: 1.00 (0.76), residues: 46 loop : -0.78 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 153 HIS 0.009 0.001 HIS D 53 PHE 0.012 0.001 PHE A 332 TYR 0.013 0.001 TYR A 179 ARG 0.004 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 612) hydrogen bonds : angle 4.05886 ( 1801) covalent geometry : bond 0.00336 (11197) covalent geometry : angle 0.59158 (15202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.9076 (ttp) cc_final: 0.8819 (ttm) REVERT: A 389 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: A 434 ARG cc_start: 0.9004 (tmm160) cc_final: 0.8673 (tpt-90) REVERT: C 26 ARG cc_start: 0.4262 (OUTLIER) cc_final: 0.1898 (tpt90) REVERT: C 76 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: D 136 VAL cc_start: 0.7469 (t) cc_final: 0.7144 (p) outliers start: 28 outliers final: 16 residues processed: 144 average time/residue: 0.2831 time to fit residues: 56.1243 Evaluate side-chains 140 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 38 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 121 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 453 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116845 restraints weight = 100405.340| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 8.26 r_work: 0.3007 rms_B_bonded: 6.88 restraints_weight: 2.0000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11197 Z= 0.129 Angle : 0.579 7.686 15202 Z= 0.281 Chirality : 0.040 0.160 1779 Planarity : 0.005 0.059 1984 Dihedral : 3.996 57.196 1542 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.08 % Allowed : 16.17 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1422 helix: 1.79 (0.18), residues: 859 sheet: 0.88 (0.75), residues: 46 loop : -0.75 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 153 HIS 0.006 0.001 HIS D 53 PHE 0.010 0.001 PHE C 67 TYR 0.012 0.001 TYR A 179 ARG 0.009 0.000 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 612) hydrogen bonds : angle 3.95470 ( 1801) covalent geometry : bond 0.00308 (11197) covalent geometry : angle 0.57894 (15202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9048 (ttp) cc_final: 0.8795 (ttm) REVERT: A 389 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: A 434 ARG cc_start: 0.8980 (tmm160) cc_final: 0.8665 (tpt-90) REVERT: C 26 ARG cc_start: 0.4118 (OUTLIER) cc_final: 0.1790 (tpt90) REVERT: C 76 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7485 (mp10) outliers start: 22 outliers final: 14 residues processed: 139 average time/residue: 0.2891 time to fit residues: 54.9843 Evaluate side-chains 141 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 118 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.171897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116136 restraints weight = 102020.732| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 8.28 r_work: 0.3025 rms_B_bonded: 6.75 restraints_weight: 2.0000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11197 Z= 0.126 Angle : 0.577 6.848 15202 Z= 0.280 Chirality : 0.040 0.156 1779 Planarity : 0.005 0.059 1984 Dihedral : 3.924 56.647 1542 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.08 % Allowed : 16.75 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.23), residues: 1422 helix: 1.86 (0.18), residues: 863 sheet: 0.86 (0.73), residues: 46 loop : -0.79 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 40 HIS 0.005 0.001 HIS D 53 PHE 0.010 0.001 PHE C 67 TYR 0.016 0.001 TYR D 112 ARG 0.005 0.000 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 612) hydrogen bonds : angle 3.89081 ( 1801) covalent geometry : bond 0.00303 (11197) covalent geometry : angle 0.57652 (15202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9073 (ttp) cc_final: 0.8807 (ttm) REVERT: A 389 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: A 434 ARG cc_start: 0.8995 (tmm160) cc_final: 0.8679 (tpt-90) REVERT: C 26 ARG cc_start: 0.4230 (OUTLIER) cc_final: 0.1951 (tpt90) REVERT: C 76 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: D 89 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8682 (mt) outliers start: 22 outliers final: 14 residues processed: 145 average time/residue: 0.3026 time to fit residues: 60.1553 Evaluate side-chains 146 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 827 TYR Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.172597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136148 restraints weight = 120974.879| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 9.91 r_work: 0.2922 rms_B_bonded: 8.82 restraints_weight: 2.0000 r_work: 0.3103 rms_B_bonded: 5.66 restraints_weight: 4.0000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11197 Z= 0.119 Angle : 0.572 7.618 15202 Z= 0.277 Chirality : 0.040 0.156 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.858 56.500 1542 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.00 % Allowed : 17.33 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1422 helix: 1.94 (0.18), residues: 857 sheet: 0.83 (0.73), residues: 46 loop : -0.70 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 40 HIS 0.007 0.001 HIS D 53 PHE 0.009 0.001 PHE A 332 TYR 0.023 0.001 TYR D 112 ARG 0.007 0.000 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 612) hydrogen bonds : angle 3.83964 ( 1801) covalent geometry : bond 0.00284 (11197) covalent geometry : angle 0.57179 (15202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7419 (ptp90) REVERT: A 187 MET cc_start: 0.9045 (ttp) cc_final: 0.8793 (ttm) REVERT: A 389 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7376 (mt0) REVERT: A 434 ARG cc_start: 0.8871 (tmm160) cc_final: 0.8636 (tpt-90) REVERT: A 559 MET cc_start: 0.8926 (ttt) cc_final: 0.8552 (ttt) REVERT: C 26 ARG cc_start: 0.4202 (OUTLIER) cc_final: 0.1912 (tpt90) REVERT: C 76 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: D 89 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8666 (mt) REVERT: D 137 ARG cc_start: 0.7982 (ptt180) cc_final: 0.7761 (ptt180) outliers start: 21 outliers final: 14 residues processed: 142 average time/residue: 0.2777 time to fit residues: 54.4569 Evaluate side-chains 145 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 827 TYR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 62 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 79 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135150 restraints weight = 103475.299| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 9.47 r_work: 0.2921 rms_B_bonded: 8.63 restraints_weight: 2.0000 r_work: 0.3099 rms_B_bonded: 5.56 restraints_weight: 4.0000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11197 Z= 0.129 Angle : 0.579 7.850 15202 Z= 0.280 Chirality : 0.040 0.155 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.847 56.421 1542 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.17 % Allowed : 17.33 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1422 helix: 1.92 (0.18), residues: 864 sheet: 0.75 (0.72), residues: 46 loop : -0.72 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 40 HIS 0.006 0.001 HIS D 53 PHE 0.010 0.001 PHE A 332 TYR 0.022 0.001 TYR D 112 ARG 0.005 0.000 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 612) hydrogen bonds : angle 3.84395 ( 1801) covalent geometry : bond 0.00313 (11197) covalent geometry : angle 0.57883 (15202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9041 (ttp) cc_final: 0.8815 (ttm) REVERT: A 389 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: A 434 ARG cc_start: 0.8869 (tmm160) cc_final: 0.8637 (tpt-90) REVERT: A 559 MET cc_start: 0.8915 (ttt) cc_final: 0.8582 (ttt) REVERT: A 562 LEU cc_start: 0.8540 (tt) cc_final: 0.8234 (tt) REVERT: C 26 ARG cc_start: 0.4135 (OUTLIER) cc_final: 0.1872 (tpt90) REVERT: C 76 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: D 89 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8675 (mt) REVERT: D 137 ARG cc_start: 0.7888 (ptt180) cc_final: 0.7616 (ptt180) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.3219 time to fit residues: 61.5358 Evaluate side-chains 149 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 827 TYR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.172850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119285 restraints weight = 101677.907| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 8.60 r_work: 0.3037 rms_B_bonded: 6.99 restraints_weight: 2.0000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11197 Z= 0.115 Angle : 0.575 8.237 15202 Z= 0.278 Chirality : 0.039 0.154 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.814 56.398 1542 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.17 % Allowed : 17.33 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1422 helix: 1.99 (0.18), residues: 863 sheet: 0.68 (0.72), residues: 46 loop : -0.67 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 40 HIS 0.006 0.001 HIS D 53 PHE 0.010 0.001 PHE C 67 TYR 0.022 0.001 TYR D 112 ARG 0.005 0.000 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 612) hydrogen bonds : angle 3.79490 ( 1801) covalent geometry : bond 0.00267 (11197) covalent geometry : angle 0.57455 (15202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7495 (ptp90) REVERT: A 187 MET cc_start: 0.9085 (ttp) cc_final: 0.8823 (ttm) REVERT: A 389 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: A 434 ARG cc_start: 0.8970 (tmm160) cc_final: 0.8666 (tpt-90) REVERT: A 559 MET cc_start: 0.8947 (ttt) cc_final: 0.8599 (ttt) REVERT: A 562 LEU cc_start: 0.8529 (tt) cc_final: 0.8233 (tt) REVERT: C 26 ARG cc_start: 0.3985 (OUTLIER) cc_final: 0.1762 (tpt90) REVERT: C 76 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: C 108 ASN cc_start: 0.8509 (t0) cc_final: 0.8300 (t0) REVERT: D 89 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8668 (mt) REVERT: D 137 ARG cc_start: 0.7865 (ptt180) cc_final: 0.7596 (ptt180) REVERT: E 84 MET cc_start: 0.8702 (mmm) cc_final: 0.8386 (tmm) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.4029 time to fit residues: 78.6031 Evaluate side-chains 148 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 827 TYR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.172747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135638 restraints weight = 101509.301| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 9.44 r_work: 0.2934 rms_B_bonded: 8.62 restraints_weight: 2.0000 r_work: 0.3115 rms_B_bonded: 5.49 restraints_weight: 4.0000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11197 Z= 0.120 Angle : 0.575 8.266 15202 Z= 0.278 Chirality : 0.040 0.154 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.799 56.348 1542 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.25 % Allowed : 17.42 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1422 helix: 1.97 (0.18), residues: 870 sheet: 0.65 (0.72), residues: 46 loop : -0.71 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 40 HIS 0.006 0.001 HIS D 53 PHE 0.010 0.001 PHE C 67 TYR 0.021 0.001 TYR D 112 ARG 0.005 0.000 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 612) hydrogen bonds : angle 3.79148 ( 1801) covalent geometry : bond 0.00288 (11197) covalent geometry : angle 0.57536 (15202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.68 seconds wall clock time: 114 minutes 44.46 seconds (6884.46 seconds total)