Starting phenix.real_space_refine on Mon Aug 5 09:10:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/08_2024/7unk_26625.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/08_2024/7unk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/08_2024/7unk_26625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/08_2024/7unk_26625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/08_2024/7unk_26625.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/08_2024/7unk_26625.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2586 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6968 2.51 5 N 1911 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 826": "OE1" <-> "OE2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8060 Classifications: {'peptide': 1047} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 68, 'TRANS': 978} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 990 Chain: "D" Number of atoms: 1318 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1203 Conformer: "C" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 137} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1203 Chain: "E" Number of atoms: 600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 568 Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N AASP C 81 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 81 " occ=0.50 residue: pdb=" N AGLN C 125 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 125 " occ=0.50 residue: pdb=" N ARG C 131 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 131 " occ=0.50 residue: pdb=" N ASER D 5 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 5 " occ=0.50 residue: pdb=" N ASER D 33 " occ=0.33 ... (16 atoms not shown) pdb=" OG CSER D 33 " occ=0.33 residue: pdb=" N AGLU D 56 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 56 " occ=0.50 residue: pdb=" N ASER D 80 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 80 " occ=0.50 residue: pdb=" N ALEU D 97 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU D 97 " occ=0.50 residue: pdb=" N ASER D 98 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 98 " occ=0.50 residue: pdb=" N ASER D 100 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 100 " occ=0.50 residue: pdb=" N AGLU D 124 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 124 " occ=0.50 residue: pdb=" N AGLU D 142 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 142 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 8.58, per 1000 atoms: 0.78 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 - 3.50 Amino acid : False - 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: 4.16 Conformation dependent library (CDL) restraints added in 2.9 seconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 6 sheets defined 70.0% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.552A pdb=" N LEU A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 45 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.549A pdb=" N ARG A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.937A pdb=" N ALA A 73 " --> pdb=" O ARG A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 76 through 89 Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 131 through 149 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.520A pdb=" N PHE A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.581A pdb=" N LEU A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.632A pdb=" N ALA A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Proline residue: A 204 - end of helix Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.983A pdb=" N ALA A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 260 through 278 removed outlier: 3.514A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 287 through 300 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 309 through 313 removed outlier: 4.065A pdb=" N GLN A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 removed outlier: 4.199A pdb=" N PHE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 Proline residue: A 351 - end of helix Proline residue: A 355 - end of helix removed outlier: 3.526A pdb=" N ARG A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.619A pdb=" N ARG A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.302A pdb=" N LEU A 396 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.317A pdb=" N SER A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 451 through 467 Processing helix chain 'A' and resid 468 through 474 Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.864A pdb=" N LEU A 487 " --> pdb=" O CYS A 483 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 488 " --> pdb=" O MET A 484 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.744A pdb=" N GLU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 537 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 559 through 575 removed outlier: 4.096A pdb=" N GLU A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.901A pdb=" N GLY A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 removed outlier: 4.295A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 669 through 687 removed outlier: 3.736A pdb=" N ASP A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 705 removed outlier: 4.198A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER A 697 " --> pdb=" O PRO A 693 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 710 through 735 removed outlier: 3.795A pdb=" N GLY A 722 " --> pdb=" O HIS A 718 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 758 Proline residue: A 753 - end of helix Processing helix chain 'A' and resid 764 through 782 removed outlier: 3.675A pdb=" N VAL A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 770 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 791 through 805 removed outlier: 3.554A pdb=" N GLU A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.697A pdb=" N LEU A 831 " --> pdb=" O TYR A 827 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 838 " --> pdb=" O HIS A 834 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Proline residue: A 840 - end of helix removed outlier: 3.542A pdb=" N GLY A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 866 removed outlier: 3.625A pdb=" N GLY A 857 " --> pdb=" O PRO A 853 " (cutoff:3.500A) Proline residue: A 860 - end of helix Processing helix chain 'A' and resid 871 through 890 Processing helix chain 'A' and resid 891 through 894 removed outlier: 3.870A pdb=" N ALA A 894 " --> pdb=" O ALA A 891 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 896 through 908 Proline residue: A 902 - end of helix Processing helix chain 'A' and resid 912 through 930 Processing helix chain 'A' and resid 931 through 936 removed outlier: 4.430A pdb=" N GLU A 936 " --> pdb=" O PRO A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 952 removed outlier: 3.784A pdb=" N PHE A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Proline residue: A 947 - end of helix removed outlier: 3.686A pdb=" N ALA A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 971 Processing helix chain 'A' and resid 981 through 988 removed outlier: 4.215A pdb=" N ALA A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 996 No H-bonds generated for 'chain 'A' and resid 994 through 996' Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.702A pdb=" N PHE A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1033 removed outlier: 3.617A pdb=" N LEU A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A1032 " --> pdb=" O SER A1028 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1051 removed outlier: 4.100A pdb=" N LYS A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1044 " --> pdb=" O THR A1040 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1066 removed outlier: 4.088A pdb=" N GLN A1060 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A1061 " --> pdb=" O ASP A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1077 removed outlier: 3.783A pdb=" N GLU A1073 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A1077 " --> pdb=" O GLU A1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.626A pdb=" N VAL D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.800A pdb=" N ARG D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 49 through 76 removed outlier: 3.709A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.536A pdb=" N LYS E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 622 through 626 removed outlier: 3.952A pdb=" N VAL A 623 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 662 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.170A pdb=" N ARG C 83 " --> pdb=" O VAL E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 10 removed outlier: 4.042A pdb=" N GLY D 8 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 27 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.598A pdb=" N ALA D 16 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG D 137 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 136 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 116 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 138 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR D 101 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 107 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 39 " --> pdb=" O ASER D 100 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU D 38 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU D 61 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TRP D 40 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER D 59 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU D 42 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.598A pdb=" N ALA D 16 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG D 137 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 136 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 116 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 138 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 145 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL D 146 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU E 97 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 95 " --> pdb=" O ARG D 148 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 4.60 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: 99.65 - 106.50: 379 106.50 - 113.36: 6176 113.36 - 120.22: 4073 120.22 - 127.07: 4463 127.07 - 133.93: 111 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- 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= 0.204 Angle : 0.659 8.302 15202 Z= 0.352 Chirality : 0.041 0.186 1779 Planarity : 0.006 0.097 1984 Dihedral : 15.440 89.676 4256 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.75 % Allowed : 0.42 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1422 helix: 1.56 (0.18), residues: 846 sheet: 1.60 (0.80), residues: 46 loop : -0.72 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 40 HIS 0.015 0.001 HIS D 36 PHE 0.029 0.001 PHE A 56 TYR 0.009 0.001 TYR A 179 ARG 0.008 0.001 ARG C 83 *********************** 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 fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.335 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: 0.2822 time to fit residues: 66.4310 Evaluate side-chains 130 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 HIS D 53 HIS E 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11197 Z= 0.192 Angle : 0.607 9.487 15202 Z= 0.299 Chirality : 0.041 0.177 1779 Planarity : 0.005 0.075 1984 Dihedral : 4.013 59.046 1542 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.08 % Allowed : 8.83 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.23), residues: 1422 helix: 1.66 (0.18), residues: 866 sheet: 1.59 (0.79), residues: 46 loop : -0.80 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 40 HIS 0.017 0.001 HIS D 53 PHE 0.018 0.001 PHE A 56 TYR 0.011 0.001 TYR A 179 ARG 0.007 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 1.208 Fit side-chains REVERT: A 187 MET cc_start: 0.8443 (ttp) cc_final: 0.8090 (ttm) REVERT: A 528 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7899 (tp30) REVERT: A 867 LYS cc_start: 0.8223 (tppt) cc_final: 0.7912 (mmmt) REVERT: C 8 ARG cc_start: 0.5716 (tpt170) cc_final: 0.5191 (tpt170) REVERT: C 26 ARG cc_start: 0.5204 (OUTLIER) cc_final: 0.2474 (tpt90) REVERT: D 54 ASP cc_start: 0.9083 (p0) cc_final: 0.8850 (p0) REVERT: D 136 VAL cc_start: 0.7256 (t) cc_final: 0.7018 (p) outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 0.2778 time to fit residues: 57.2963 Evaluate side-chains 133 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 42 optimal weight: 0.0670 chunk 100 optimal weight: 0.0870 overall best weight: 0.5896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1518 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= 0.176 Angle : 0.560 6.698 15202 Z= 0.275 Chirality : 0.040 0.170 1779 Planarity : 0.005 0.067 1984 Dihedral : 3.887 57.367 1542 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.58 % Allowed : 10.58 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1422 helix: 1.83 (0.19), residues: 859 sheet: 1.48 (0.78), residues: 46 loop : -0.71 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 40 HIS 0.008 0.001 HIS D 53 PHE 0.016 0.001 PHE A 877 TYR 0.011 0.001 TYR A 179 ARG 0.012 0.000 ARG D 137 *********************** 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 154 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.249 Fit side-chains REVERT: A 187 MET cc_start: 0.8378 (ttp) cc_final: 0.8014 (ttm) REVERT: A 528 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7984 (tp30) REVERT: C 26 ARG cc_start: 0.5190 (OUTLIER) cc_final: 0.2512 (tpt90) REVERT: D 101 TYR cc_start: 0.5519 (t80) cc_final: 0.5016 (t80) REVERT: D 136 VAL cc_start: 0.7191 (t) cc_final: 0.6955 (p) REVERT: D 137 ARG cc_start: 0.7365 (ptt180) cc_final: 0.7009 (ptt180) outliers start: 15 outliers final: 9 residues processed: 150 average time/residue: 0.2680 time to fit residues: 55.1103 Evaluate side-chains 137 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 0.0040 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11197 Z= 0.261 Angle : 0.595 7.022 15202 Z= 0.291 Chirality : 0.042 0.183 1779 Planarity : 0.005 0.062 1984 Dihedral : 3.947 56.887 1542 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.67 % Allowed : 13.42 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1422 helix: 1.79 (0.18), residues: 862 sheet: 1.31 (0.78), residues: 46 loop : -0.72 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 40 HIS 0.008 0.001 HIS D 53 PHE 0.016 0.001 PHE A1005 TYR 0.012 0.001 TYR A 179 ARG 0.006 0.001 ARG A1025 *********************** 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 143 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7116 (mtt180) REVERT: C 26 ARG cc_start: 0.5103 (OUTLIER) cc_final: 0.2443 (tpt90) outliers start: 16 outliers final: 13 residues processed: 137 average time/residue: 0.2712 time to fit residues: 51.1564 Evaluate side-chains 134 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 75 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11197 Z= 0.309 Angle : 0.619 7.044 15202 Z= 0.303 Chirality : 0.042 0.173 1779 Planarity : 0.005 0.060 1984 Dihedral : 4.059 56.961 1542 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 14.50 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1422 helix: 1.65 (0.18), residues: 858 sheet: 1.08 (0.77), residues: 46 loop : -0.79 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 40 HIS 0.006 0.001 HIS A 454 PHE 0.013 0.001 PHE A 699 TYR 0.014 0.001 TYR A 179 ARG 0.004 0.000 ARG A 70 *********************** 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 160 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 389 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: A 562 LEU cc_start: 0.8639 (tt) cc_final: 0.8382 (tt) REVERT: A 648 MET cc_start: 0.5776 (ptp) cc_final: 0.5524 (ptp) REVERT: C 26 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.2539 (tpt90) REVERT: D 137 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7202 (ptt180) outliers start: 28 outliers final: 14 residues processed: 151 average time/residue: 0.2677 time to fit residues: 55.6628 Evaluate side-chains 138 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 253 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 623 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 137 ARG 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 120 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2428 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= 0.178 Angle : 0.570 6.978 15202 Z= 0.278 Chirality : 0.040 0.157 1779 Planarity : 0.005 0.059 1984 Dihedral : 3.919 56.881 1542 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.00 % Allowed : 15.83 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.23), residues: 1422 helix: 1.88 (0.18), residues: 855 sheet: 0.88 (0.74), residues: 46 loop : -0.61 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 40 HIS 0.005 0.001 HIS D 53 PHE 0.017 0.001 PHE D 106 TYR 0.012 0.001 TYR A 179 ARG 0.006 0.000 ARG A 68 *********************** 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 152 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 389 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: A 562 LEU cc_start: 0.8562 (tt) cc_final: 0.8264 (tt) REVERT: C 26 ARG cc_start: 0.4938 (OUTLIER) cc_final: 0.2465 (tpt90) REVERT: D 89 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8963 (mt) REVERT: D 137 ARG cc_start: 0.7527 (ptt180) cc_final: 0.7277 (ptt180) REVERT: E 39 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8304 (mmm-85) REVERT: E 45 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.8038 (mtp-110) outliers start: 21 outliers final: 11 residues processed: 143 average time/residue: 0.2861 time to fit residues: 55.2353 Evaluate side-chains 141 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 15 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2505 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= 0.186 Angle : 0.568 7.380 15202 Z= 0.277 Chirality : 0.040 0.156 1779 Planarity : 0.005 0.059 1984 Dihedral : 3.844 56.618 1542 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 16.42 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1422 helix: 1.95 (0.18), residues: 855 sheet: 0.85 (0.73), residues: 46 loop : -0.66 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 40 HIS 0.007 0.001 HIS D 53 PHE 0.011 0.001 PHE A1005 TYR 0.011 0.001 TYR A 179 ARG 0.007 0.000 ARG E 36 *********************** 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 fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.8395 (ttp) cc_final: 0.7888 (ttm) REVERT: A 389 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7307 (mt0) REVERT: A 559 MET cc_start: 0.8750 (ttt) cc_final: 0.8387 (ttt) REVERT: A 562 LEU cc_start: 0.8495 (tt) cc_final: 0.8173 (tt) REVERT: C 26 ARG cc_start: 0.4949 (OUTLIER) cc_final: 0.2489 (tpt90) REVERT: C 76 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: D 137 ARG cc_start: 0.7544 (ptt180) cc_final: 0.7276 (ptt180) REVERT: E 39 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8305 (mmm-85) outliers start: 20 outliers final: 11 residues processed: 141 average time/residue: 0.2847 time to fit residues: 54.6302 Evaluate side-chains 139 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2580 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= 0.186 Angle : 0.567 7.035 15202 Z= 0.275 Chirality : 0.040 0.155 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.810 56.585 1542 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.83 % Allowed : 17.00 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1422 helix: 1.96 (0.18), residues: 858 sheet: 0.80 (0.73), residues: 46 loop : -0.68 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 40 HIS 0.006 0.001 HIS D 53 PHE 0.013 0.001 PHE A1005 TYR 0.015 0.001 TYR D 112 ARG 0.008 0.000 ARG A 70 *********************** 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 fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.8438 (ttp) cc_final: 0.7908 (ttm) REVERT: A 389 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: C 26 ARG cc_start: 0.4863 (OUTLIER) cc_final: 0.2427 (tpt90) REVERT: C 76 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: D 89 LEU cc_start: 0.9118 (mt) cc_final: 0.8669 (mt) REVERT: E 39 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8245 (mmm-85) outliers start: 19 outliers final: 13 residues processed: 141 average time/residue: 0.2861 time to fit residues: 54.8202 Evaluate side-chains 140 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 389 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 688 SER 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 C residue 107 THR Chi-restraints excluded: chain E residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7454 > 50: distance: 11 - 12: 3.559 distance: 12 - 13: 3.125 distance: 13 - 119: 5.791 distance: 17 - 18: 3.131 distance: 19 - 20: 4.879 distance: 20 - 21: 3.770 distance: 20 - 23: 3.769 distance: 21 - 22: 5.178 distance: 21 - 26: 7.686 distance: 23 - 24: 4.315 distance: 23 - 25: 6.562 distance: 26 - 27: 13.309 distance: 27 - 28: 9.658 distance: 27 - 30: 8.030 distance: 28 - 29: 15.399 distance: 28 - 34: 10.807 distance: 30 - 31: 9.657 distance: 31 - 32: 10.729 distance: 31 - 33: 16.936 distance: 34 - 35: 4.653 distance: 35 - 38: 11.042 distance: 36 - 37: 16.873 distance: 36 - 42: 13.309 distance: 38 - 39: 9.607 distance: 39 - 40: 11.038 distance: 39 - 41: 5.100 distance: 42 - 43: 13.471 distance: 43 - 44: 7.960 distance: 43 - 46: 28.953 distance: 44 - 45: 8.280 distance: 44 - 50: 18.399 distance: 46 - 47: 37.659 distance: 47 - 48: 15.845 distance: 47 - 49: 6.219 distance: 50 - 51: 16.619 distance: 50 - 56: 16.767 distance: 51 - 52: 19.496 distance: 51 - 54: 25.990 distance: 52 - 53: 19.201 distance: 52 - 57: 17.097 distance: 54 - 55: 9.753 distance: 55 - 56: 23.441 distance: 57 - 58: 12.839 distance: 58 - 59: 16.107 distance: 58 - 61: 12.384 distance: 59 - 60: 13.639 distance: 59 - 62: 19.816 distance: 62 - 63: 9.558 distance: 63 - 64: 14.355 distance: 63 - 66: 7.734 distance: 64 - 65: 12.846 distance: 64 - 71: 8.193 distance: 66 - 67: 16.353 distance: 67 - 68: 7.054 distance: 68 - 69: 14.893 distance: 69 - 70: 13.262 distance: 72 - 73: 3.489 distance: 72 - 75: 6.420 distance: 73 - 74: 6.553 distance: 73 - 82: 5.356 distance: 76 - 78: 6.139 distance: 77 - 79: 4.242 distance: 78 - 80: 3.176 distance: 79 - 81: 5.698 distance: 80 - 81: 4.127 distance: 82 - 83: 14.548 distance: 83 - 84: 6.618 distance: 83 - 86: 14.383 distance: 84 - 85: 13.783 distance: 84 - 89: 8.953 distance: 86 - 87: 5.963 distance: 86 - 88: 7.987