Starting phenix.real_space_refine on Sun Dec 10 05:38:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/12_2023/7unk_26625.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/12_2023/7unk_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_26625/12_2023/7unk_26625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/12_2023/7unk_26625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/12_2023/7unk_26625.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unk_26625/12_2023/7unk_26625.pdb" } 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-1.21rc1-5172/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: 7.85, per 1000 atoms: 0.71 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: 4.09 Conformation dependent library (CDL) restraints added in 2.7 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: 1.33 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: 3.42 Time building geometry restraints manager: 4.46 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 2.440 nonbonded pdb=" NZ LYS C 122 " pdb=" OG SER D 91 " model vdw 2.225 2.520 nonbonded pdb=" OG SER A 618 " pdb=" OE2 GLU A 620 " model vdw 2.250 2.440 nonbonded pdb=" O ALA A 950 " pdb=" NH2 ARG A 953 " model vdw 2.250 2.520 nonbonded pdb=" O VAL D 45 " pdb=" OG1 THR D 93 " model vdw 2.257 2.440 ... (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 ========== 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.040 Find NCS groups from input model: 0.290 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- 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 : 1.262 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 174 average time/residue: 0.2896 time to fit residues: 68.4778 Evaluate side-chains 128 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN D 36 HIS D 53 HIS E 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11197 Z= 0.232 Angle : 0.610 9.428 15202 Z= 0.301 Chirality : 0.042 0.178 1779 Planarity : 0.005 0.075 1984 Dihedral : 3.637 18.610 1538 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.00 % Allowed : 9.33 % Favored : 89.67 % 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: 1.18 (0.23), residues: 1422 helix: 1.62 (0.18), residues: 874 sheet: 1.60 (0.79), residues: 46 loop : -0.79 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 40 HIS 0.017 0.001 HIS D 53 PHE 0.018 0.001 PHE A 56 TYR 0.015 0.001 TYR D 101 ARG 0.007 0.000 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 145 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.328 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 142 average time/residue: 0.2904 time to fit residues: 56.4054 Evaluate side-chains 129 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1016 time to fit residues: 2.5086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 104 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 0.0270 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1588 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= 0.192 Angle : 0.561 6.661 15202 Z= 0.275 Chirality : 0.040 0.173 1779 Planarity : 0.005 0.068 1984 Dihedral : 3.546 19.216 1538 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.50 % Allowed : 10.83 % Favored : 87.67 % 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: 1.28 (0.23), residues: 1422 helix: 1.77 (0.19), residues: 862 sheet: 1.55 (0.78), residues: 46 loop : -0.80 (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 0.016 0.001 TYR D 101 ARG 0.005 0.000 ARG C 83 *********************** 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 146 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.181 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 140 average time/residue: 0.2768 time to fit residues: 53.2220 Evaluate side-chains 129 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1182 time to fit residues: 2.8728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 119 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11197 Z= 0.398 Angle : 0.670 7.446 15202 Z= 0.329 Chirality : 0.044 0.196 1779 Planarity : 0.005 0.060 1984 Dihedral : 3.880 22.486 1538 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.92 % Allowed : 13.92 % Favored : 84.17 % 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: 0.93 (0.23), residues: 1422 helix: 1.48 (0.18), residues: 857 sheet: 1.30 (0.73), residues: 51 loop : -0.93 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 69 HIS 0.009 0.001 HIS D 53 PHE 0.016 0.002 PHE A1005 TYR 0.013 0.002 TYR A 460 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 151 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.314 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 144 average time/residue: 0.2815 time to fit residues: 55.6539 Evaluate side-chains 134 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1020 time to fit residues: 3.6569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11197 Z= 0.224 Angle : 0.586 9.903 15202 Z= 0.283 Chirality : 0.041 0.178 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.714 21.563 1538 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.92 % Allowed : 16.00 % Favored : 83.08 % 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: 1.18 (0.23), residues: 1422 helix: 1.72 (0.18), residues: 856 sheet: 0.95 (0.69), residues: 51 loop : -0.84 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 153 HIS 0.005 0.001 HIS D 53 PHE 0.012 0.001 PHE A1005 TYR 0.011 0.001 TYR D 101 ARG 0.006 0.000 ARG D 137 *********************** 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 135 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.237 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 131 average time/residue: 0.2877 time to fit residues: 51.5515 Evaluate side-chains 125 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1165 time to fit residues: 2.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 11 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 HIS ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2398 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= 0.163 Angle : 0.557 8.030 15202 Z= 0.269 Chirality : 0.039 0.167 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.529 19.414 1538 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.58 % Allowed : 17.00 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1422 helix: 1.96 (0.18), residues: 855 sheet: 0.62 (0.72), residues: 46 loop : -0.79 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 69 HIS 0.005 0.000 HIS D 53 PHE 0.012 0.001 PHE C 67 TYR 0.010 0.001 TYR D 101 ARG 0.003 0.000 ARG C 83 *********************** 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 139 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.312 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 137 average time/residue: 0.2964 time to fit residues: 55.2447 Evaluate side-chains 128 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2496 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= 0.195 Angle : 0.561 6.995 15202 Z= 0.272 Chirality : 0.040 0.166 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.502 18.948 1538 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.75 % Allowed : 17.33 % Favored : 81.92 % 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: 1.40 (0.23), residues: 1422 helix: 1.93 (0.18), residues: 866 sheet: 0.43 (0.71), residues: 46 loop : -0.79 (0.27), residues: 510 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 0.014 0.001 PHE A 877 TYR 0.009 0.001 TYR D 101 ARG 0.005 0.000 ARG D 137 *********************** 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 135 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.288 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 131 average time/residue: 0.3021 time to fit residues: 53.9066 Evaluate side-chains 128 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2685 time to fit residues: 2.4150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 120 optimal weight: 9.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2549 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= 0.167 Angle : 0.559 7.602 15202 Z= 0.269 Chirality : 0.039 0.161 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.428 18.252 1538 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.75 % Allowed : 17.50 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1422 helix: 2.00 (0.18), residues: 864 sheet: 0.31 (0.70), residues: 46 loop : -0.77 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.005 0.000 HIS D 53 PHE 0.011 0.001 PHE C 67 TYR 0.009 0.001 TYR D 112 ARG 0.006 0.000 ARG E 36 *********************** 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 137 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.273 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 134 average time/residue: 0.2932 time to fit residues: 53.9014 Evaluate side-chains 131 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1370 time to fit residues: 2.4553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2633 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= 0.214 Angle : 0.578 7.687 15202 Z= 0.278 Chirality : 0.040 0.164 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.474 18.492 1538 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.42 % Allowed : 18.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1422 helix: 1.97 (0.18), residues: 867 sheet: 0.21 (0.70), residues: 46 loop : -0.77 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 40 HIS 0.004 0.001 HIS D 53 PHE 0.015 0.001 PHE A 877 TYR 0.013 0.001 TYR E 88 ARG 0.006 0.000 ARG D 137 *********************** 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 130 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.277 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.2973 time to fit residues: 53.1131 Evaluate side-chains 128 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 137 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 109 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11197 Z= 0.247 Angle : 0.605 8.348 15202 Z= 0.290 Chirality : 0.041 0.166 1779 Planarity : 0.005 0.058 1984 Dihedral : 3.576 19.335 1538 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.50 % Allowed : 18.17 % 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 (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: 1.38 (0.23), residues: 1422 helix: 1.88 (0.18), residues: 867 sheet: 0.48 (0.66), residues: 51 loop : -0.77 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 40 HIS 0.004 0.001 HIS D 53 PHE 0.011 0.001 PHE A 332 TYR 0.010 0.001 TYR A 179 ARG 0.005 0.000 ARG D 137 ********************** 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 130 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.231 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 128 average time/residue: 0.2893 time to fit residues: 51.0853 Evaluate side-chains 126 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1025 time to fit residues: 2.1325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.0040 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.172269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117015 restraints weight = 103202.636| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 8.21 r_work: 0.3045 rms_B_bonded: 6.70 restraints_weight: 2.0000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11197 Z= 0.193 Angle : 0.590 10.388 15202 Z= 0.283 Chirality : 0.040 0.162 1779 Planarity : 0.005 0.057 1984 Dihedral : 3.510 18.675 1538 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.58 % Allowed : 18.17 % Favored : 81.25 % 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: 1.47 (0.23), residues: 1422 helix: 1.98 (0.18), residues: 873 sheet: 0.05 (0.69), residues: 46 loop : -0.74 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 40 HIS 0.005 0.001 HIS D 53 PHE 0.015 0.001 PHE A 877 TYR 0.008 0.001 TYR D 112 ARG 0.005 0.000 ARG D 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.45 seconds wall clock time: 44 minutes 31.72 seconds (2671.72 seconds total)