Starting phenix.real_space_refine on Wed Mar 4 10:51:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7unk_26625/03_2026/7unk_26625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7unk_26625/03_2026/7unk_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_26625/03_2026/7unk_26625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7unk_26625/03_2026/7unk_26625.map" model { file = "/net/cci-nas-00/data/ceres_data/7unk_26625/03_2026/7unk_26625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7unk_26625/03_2026/7unk_26625.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.36, per 1000 atoms: 0.31 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: 0.86 Conformation dependent library (CDL) restraints added in 737.7 milliseconds 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: 0.38 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: 1.56 Time building geometry restraints manager: 1.08 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (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 ARG 0.008 0.001 ARG C 83 TYR 0.009 0.001 TYR A 179 PHE 0.029 0.001 PHE A 56 TRP 0.008 0.001 TRP D 40 HIS 0.015 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00310 (11197) covalent geometry : angle 0.65936 (15202) hydrogen bonds : bond 0.16654 ( 612) hydrogen bonds : angle 5.40287 ( 1801) *********************** 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 : 0.459 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: 0.1237 time to fit residues: 29.1148 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 : 0.389 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0060 chunk 55 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.177675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121672 restraints weight = 93969.810| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 7.42 r_work: 0.3173 rms_B_bonded: 6.48 restraints_weight: 2.0000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1198 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= 0.127 Angle : 0.603 9.529 15202 Z= 0.297 Chirality : 0.041 0.174 1779 Planarity : 0.005 0.074 1984 Dihedral : 3.991 59.074 1542 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.00 % Allowed : 8.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1422 helix: 1.69 (0.19), residues: 860 sheet: 1.57 (0.79), residues: 46 loop : -0.79 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 83 TYR 0.012 0.001 TYR A 179 PHE 0.018 0.001 PHE A 56 TRP 0.001 0.000 TRP D 40 HIS 0.017 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00284 (11197) covalent geometry : angle 0.60340 (15202) hydrogen bonds : bond 0.04130 ( 612) hydrogen bonds : angle 4.21994 ( 1801) *********************** 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 156 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.413 Fit side-chains REVERT: A 187 MET cc_start: 0.8972 (ttp) cc_final: 0.8563 (ttm) REVERT: A 528 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8309 (tp30) REVERT: A 867 LYS cc_start: 0.8055 (tppt) cc_final: 0.7748 (mmmt) REVERT: C 8 ARG cc_start: 0.5914 (tpt170) cc_final: 0.4735 (tpt170) REVERT: C 26 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.2013 (tpt90) REVERT: D 1 MET cc_start: 0.7706 (ppp) cc_final: 0.7469 (ppp) REVERT: D 54 ASP cc_start: 0.9180 (p0) cc_final: 0.8928 (p0) REVERT: D 136 VAL cc_start: 0.7369 (t) cc_final: 0.7071 (p) outliers start: 7 outliers final: 4 residues processed: 152 average time/residue: 0.1256 time to fit residues: 25.8610 Evaluate side-chains 132 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 356 MET Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain C residue 26 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 98 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.176021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122068 restraints weight = 112931.501| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 9.13 r_work: 0.3083 rms_B_bonded: 7.17 restraints_weight: 2.0000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11197 Z= 0.120 Angle : 0.562 6.802 15202 Z= 0.275 Chirality : 0.040 0.171 1779 Planarity : 0.005 0.067 1984 Dihedral : 3.883 57.083 1542 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.75 % Allowed : 10.50 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.23), residues: 1422 helix: 1.82 (0.19), residues: 860 sheet: 1.47 (0.78), residues: 46 loop : -0.73 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 137 TYR 0.011 0.001 TYR A 179 PHE 0.017 0.001 PHE A 877 TRP 0.007 0.001 TRP D 40 HIS 0.007 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00281 (11197) covalent geometry : angle 0.56212 (15202) hydrogen bonds : bond 0.03743 ( 612) hydrogen bonds : angle 3.99792 ( 1801) *********************** 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 158 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.392 Fit side-chains REVERT: A 187 MET cc_start: 0.8990 (ttp) cc_final: 0.8591 (ttm) REVERT: A 528 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8395 (tp30) REVERT: C 26 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.1966 (tpt90) REVERT: D 101 TYR cc_start: 0.5257 (t80) cc_final: 0.4807 (t80) REVERT: E 39 ARG cc_start: 0.8953 (mmm-85) cc_final: 0.8685 (mmm-85) REVERT: E 84 MET cc_start: 0.8618 (mmm) cc_final: 0.8398 (tpp) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 0.1205 time to fit residues: 25.0216 Evaluate side-chains 140 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 131 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 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 = 0.4083 r_free = 0.4083 target = 0.173749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119478 restraints weight = 102025.507| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 8.51 r_work: 0.3056 rms_B_bonded: 6.81 restraints_weight: 2.0000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11197 Z= 0.134 Angle : 0.570 6.701 15202 Z= 0.278 Chirality : 0.041 0.183 1779 Planarity : 0.005 0.062 1984 Dihedral : 3.867 56.668 1542 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.83 % Allowed : 12.75 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.23), residues: 1422 helix: 1.84 (0.18), residues: 867 sheet: 1.30 (0.78), residues: 46 loop : -0.68 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 137 TYR 0.011 0.001 TYR A 179 PHE 0.016 0.001 PHE A1005 TRP 0.005 0.001 TRP D 40 HIS 0.008 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00325 (11197) covalent geometry : angle 0.56959 (15202) hydrogen bonds : bond 0.03736 ( 612) hydrogen bonds : angle 3.94549 ( 1801) *********************** 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 151 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7208 (mtt180) REVERT: A 187 MET cc_start: 0.9017 (ttp) cc_final: 0.8724 (ttm) REVERT: A 437 MET cc_start: 0.9366 (tpt) cc_final: 0.8692 (tpt) REVERT: C 26 ARG cc_start: 0.4507 (OUTLIER) cc_final: 0.1947 (tpt90) REVERT: D 101 TYR cc_start: 0.5453 (t80) cc_final: 0.4950 (t80) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.1154 time to fit residues: 22.6597 Evaluate side-chains 138 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 356 MET 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 1024 LEU Chi-restraints excluded: chain C residue 26 ARG 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 132 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 22 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 76 optimal weight: 0.0570 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117669 restraints weight = 93562.814| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 7.79 r_work: 0.3059 rms_B_bonded: 6.63 restraints_weight: 2.0000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2053 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= 0.136 Angle : 0.565 6.747 15202 Z= 0.276 Chirality : 0.040 0.173 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.845 56.581 1542 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.42 % Allowed : 14.08 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.23), residues: 1422 helix: 1.85 (0.18), residues: 868 sheet: 1.17 (0.77), residues: 46 loop : -0.71 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 137 TYR 0.011 0.001 TYR A 179 PHE 0.013 0.001 PHE A1005 TRP 0.003 0.001 TRP D 40 HIS 0.005 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00334 (11197) covalent geometry : angle 0.56454 (15202) hydrogen bonds : bond 0.03690 ( 612) hydrogen bonds : angle 3.90817 ( 1801) *********************** 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: 26 poor density : 129 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.9035 (ttp) cc_final: 0.8748 (ttm) REVERT: A 389 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: A 562 LEU cc_start: 0.8589 (tt) cc_final: 0.8287 (tt) REVERT: A 648 MET cc_start: 0.5774 (ptp) cc_final: 0.5486 (ptt) REVERT: C 26 ARG cc_start: 0.4381 (OUTLIER) cc_final: 0.1928 (tpt90) REVERT: D 89 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8540 (mt) REVERT: D 137 ARG cc_start: 0.7941 (ptt180) cc_final: 0.7474 (ptt-90) outliers start: 26 outliers final: 13 residues processed: 146 average time/residue: 0.1161 time to fit residues: 23.3114 Evaluate side-chains 143 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 157 HIS 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 1024 LEU Chi-restraints excluded: chain C residue 26 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 154 GLN A 453 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130796 restraints weight = 107372.999| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 9.73 r_work: 0.2850 rms_B_bonded: 8.57 restraints_weight: 2.0000 r_work: 0.3030 rms_B_bonded: 5.48 restraints_weight: 4.0000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11197 Z= 0.224 Angle : 0.658 7.358 15202 Z= 0.321 Chirality : 0.044 0.168 1779 Planarity : 0.005 0.060 1984 Dihedral : 4.140 57.242 1542 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.42 % Allowed : 14.92 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1422 helix: 1.62 (0.18), residues: 865 sheet: 1.18 (0.70), residues: 51 loop : -0.83 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1025 TYR 0.014 0.002 TYR A 179 PHE 0.015 0.002 PHE D 106 TRP 0.005 0.001 TRP D 40 HIS 0.006 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00563 (11197) covalent geometry : angle 0.65811 (15202) hydrogen bonds : bond 0.04674 ( 612) hydrogen bonds : angle 4.17903 ( 1801) *********************** 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 156 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7514 (ptp90) REVERT: A 389 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: A 434 ARG cc_start: 0.8888 (tmm160) cc_final: 0.8652 (tpt-90) REVERT: A 827 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8363 (t80) REVERT: C 26 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.2085 (tpt90) REVERT: D 89 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8567 (mt) outliers start: 26 outliers final: 14 residues processed: 148 average time/residue: 0.1202 time to fit residues: 24.3601 Evaluate side-chains 143 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 769 MET Chi-restraints excluded: chain A residue 827 TYR Chi-restraints excluded: chain A residue 1001 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS A 408 GLN A 454 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.172403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118140 restraints weight = 95016.756| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 8.35 r_work: 0.3045 rms_B_bonded: 6.73 restraints_weight: 2.0000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11197 Z= 0.118 Angle : 0.581 8.747 15202 Z= 0.280 Chirality : 0.040 0.156 1779 Planarity : 0.005 0.059 1984 Dihedral : 3.929 57.307 1542 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.92 % Allowed : 16.50 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.23), residues: 1422 helix: 1.93 (0.18), residues: 853 sheet: 0.76 (0.73), residues: 46 loop : -0.63 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.012 0.001 TYR A 179 PHE 0.012 0.001 PHE C 67 TRP 0.003 0.001 TRP D 153 HIS 0.006 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00271 (11197) covalent geometry : angle 0.58095 (15202) hydrogen bonds : bond 0.03641 ( 612) hydrogen bonds : angle 3.88124 ( 1801) *********************** 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 151 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7441 (ptp90) REVERT: A 389 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: A 434 ARG cc_start: 0.8975 (tmm160) cc_final: 0.8675 (tpt-90) REVERT: C 26 ARG cc_start: 0.4145 (OUTLIER) cc_final: 0.1843 (tpt90) REVERT: C 76 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: D 89 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8615 (mt) REVERT: D 137 ARG cc_start: 0.7842 (ptt180) cc_final: 0.7407 (ptt-90) outliers start: 20 outliers final: 9 residues processed: 142 average time/residue: 0.1291 time to fit residues: 24.6839 Evaluate side-chains 140 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 257 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 73 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.172827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119002 restraints weight = 103398.478| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 8.68 r_work: 0.3032 rms_B_bonded: 7.11 restraints_weight: 2.0000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 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 = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11197 Z= 0.117 Angle : 0.569 7.767 15202 Z= 0.275 Chirality : 0.040 0.154 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.835 56.845 1542 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.92 % Allowed : 16.50 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.23), residues: 1422 helix: 2.01 (0.18), residues: 855 sheet: 0.68 (0.72), residues: 46 loop : -0.60 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 36 TYR 0.015 0.001 TYR D 112 PHE 0.012 0.001 PHE A1005 TRP 0.005 0.001 TRP D 40 HIS 0.007 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00275 (11197) covalent geometry : angle 0.56913 (15202) hydrogen bonds : bond 0.03500 ( 612) hydrogen bonds : angle 3.80159 ( 1801) *********************** 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 149 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7474 (ptp90) REVERT: A 389 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: A 434 ARG cc_start: 0.9019 (tmm160) cc_final: 0.8668 (tpt-90) REVERT: A 562 LEU cc_start: 0.8492 (tt) cc_final: 0.8238 (tt) REVERT: A 648 MET cc_start: 0.5878 (ptp) cc_final: 0.5595 (ptm) REVERT: A 769 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8690 (mtp) REVERT: A 994 ASP cc_start: 0.5512 (m-30) cc_final: 0.4921 (m-30) REVERT: C 26 ARG cc_start: 0.4026 (OUTLIER) cc_final: 0.1762 (tpt90) REVERT: C 76 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: D 89 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8612 (mt) REVERT: D 137 ARG cc_start: 0.7842 (ptt180) cc_final: 0.7394 (ptt-90) outliers start: 20 outliers final: 10 residues processed: 139 average time/residue: 0.1306 time to fit residues: 24.5625 Evaluate side-chains 142 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.173252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119319 restraints weight = 109646.112| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 8.70 r_work: 0.3039 rms_B_bonded: 6.98 restraints_weight: 2.0000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2622 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= 0.113 Angle : 0.568 7.715 15202 Z= 0.274 Chirality : 0.040 0.154 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.786 56.521 1542 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.58 % Allowed : 17.08 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1422 helix: 2.00 (0.18), residues: 861 sheet: 0.61 (0.72), residues: 46 loop : -0.52 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.022 0.001 TYR D 112 PHE 0.013 0.001 PHE A1005 TRP 0.010 0.001 TRP D 40 HIS 0.006 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00263 (11197) covalent geometry : angle 0.56831 (15202) hydrogen bonds : bond 0.03374 ( 612) hydrogen bonds : angle 3.75655 ( 1801) *********************** 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 144 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7467 (ptp90) REVERT: A 187 MET cc_start: 0.8947 (ttp) cc_final: 0.8506 (ttm) REVERT: A 389 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: A 434 ARG cc_start: 0.8965 (tmm160) cc_final: 0.8659 (tpt-90) REVERT: A 562 LEU cc_start: 0.8464 (tt) cc_final: 0.8195 (tt) REVERT: A 769 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8670 (mtp) REVERT: A 994 ASP cc_start: 0.5658 (m-30) cc_final: 0.5243 (m-30) REVERT: C 26 ARG cc_start: 0.3960 (OUTLIER) cc_final: 0.1733 (tpt90) REVERT: C 76 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: D 89 LEU cc_start: 0.9012 (mt) cc_final: 0.8621 (mt) REVERT: D 137 ARG cc_start: 0.7794 (ptt180) cc_final: 0.7486 (ptt-90) outliers start: 16 outliers final: 9 residues processed: 136 average time/residue: 0.1212 time to fit residues: 22.4449 Evaluate side-chains 138 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 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 E residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135849 restraints weight = 113026.246| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 9.98 r_work: 0.2921 rms_B_bonded: 8.95 restraints_weight: 2.0000 r_work: 0.3100 rms_B_bonded: 5.77 restraints_weight: 4.0000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 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 = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2683 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= 0.125 Angle : 0.582 8.234 15202 Z= 0.280 Chirality : 0.040 0.155 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.787 56.501 1542 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.92 % Allowed : 17.00 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1422 helix: 1.98 (0.18), residues: 873 sheet: 0.65 (0.72), residues: 46 loop : -0.56 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 36 TYR 0.022 0.001 TYR D 112 PHE 0.016 0.001 PHE A 877 TRP 0.008 0.001 TRP D 40 HIS 0.005 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00303 (11197) covalent geometry : angle 0.58187 (15202) hydrogen bonds : bond 0.03532 ( 612) hydrogen bonds : angle 3.79919 ( 1801) ********************** 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 146 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7414 (ptp90) REVERT: A 187 MET cc_start: 0.8930 (ttp) cc_final: 0.8479 (ttm) REVERT: A 389 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: A 434 ARG cc_start: 0.8882 (tmm160) cc_final: 0.8637 (tpt-90) REVERT: A 559 MET cc_start: 0.8922 (ttt) cc_final: 0.8538 (ttt) REVERT: A 562 LEU cc_start: 0.8483 (tt) cc_final: 0.8210 (tt) REVERT: A 769 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: A 994 ASP cc_start: 0.5498 (m-30) cc_final: 0.5120 (m-30) REVERT: C 26 ARG cc_start: 0.4003 (OUTLIER) cc_final: 0.1823 (tpt90) REVERT: C 76 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: D 89 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8645 (mt) REVERT: D 137 ARG cc_start: 0.7778 (ptt180) cc_final: 0.7462 (ptt-90) outliers start: 20 outliers final: 12 residues processed: 137 average time/residue: 0.1158 time to fit residues: 21.9567 Evaluate side-chains 143 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 139 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 VAL 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 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 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 8 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118673 restraints weight = 96018.890| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 8.29 r_work: 0.3041 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2740 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= 0.128 Angle : 0.581 8.205 15202 Z= 0.279 Chirality : 0.040 0.156 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.791 56.684 1542 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.92 % Allowed : 16.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1422 helix: 1.98 (0.18), residues: 874 sheet: 0.33 (0.70), residues: 55 loop : -0.49 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 36 TYR 0.021 0.001 TYR D 112 PHE 0.013 0.001 PHE A1005 TRP 0.008 0.001 TRP D 40 HIS 0.003 0.000 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00313 (11197) covalent geometry : angle 0.58146 (15202) hydrogen bonds : bond 0.03530 ( 612) hydrogen bonds : angle 3.80570 ( 1801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2835.57 seconds wall clock time: 49 minutes 3.69 seconds (2943.69 seconds total)