Starting phenix.real_space_refine (version: dev) on Thu Dec 22 13:02:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dew_27401/12_2022/8dew_27401_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dew_27401/12_2022/8dew_27401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dew_27401/12_2022/8dew_27401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dew_27401/12_2022/8dew_27401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dew_27401/12_2022/8dew_27401_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dew_27401/12_2022/8dew_27401_updated.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 1042": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 890": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C TYR 997": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 48792 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 16017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 16017 Classifications: {'peptide': 1058} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1017} Chain: "B" Number of atoms: 15746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 15746 Classifications: {'peptide': 1040} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 999} Chain: "C" Number of atoms: 16017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 16017 Classifications: {'peptide': 1058} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1017} Chain: "D" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 299 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 252 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PTY:plan-1': 4, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 285 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 176 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PTY:plan-1': 4, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 21.39, per 1000 atoms: 0.44 Number of scatterers: 48792 At special positions: 0 Unit cell: (155.52, 133.92, 135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 137 16.00 P 10 15.00 O 4534 8.00 N 3982 7.00 C 15834 6.00 H 24295 1.00 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: 41.13 Conformation dependent library (CDL) restraints added in 4.1 seconds 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5782 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 23 sheets defined 55.0% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 28 Processing helix chain 'A' and resid 54 through 68 removed outlier: 5.571A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 297 through 314 removed outlier: 4.265A pdb=" N LYS A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 357 Processing helix chain 'A' and resid 360 through 384 removed outlier: 4.476A pdb=" N ILE A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 390 through 421 removed outlier: 4.436A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 455 removed outlier: 5.752A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Proline residue: A 453 - end of helix Processing helix chain 'A' and resid 462 through 494 removed outlier: 4.520A pdb=" N THR A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 554 Processing helix chain 'A' and resid 581 through 596 Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 688 through 705 Processing helix chain 'A' and resid 730 through 733 No H-bonds generated for 'chain 'A' and resid 730 through 733' Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 870 through 889 Processing helix chain 'A' and resid 894 through 923 Proline residue: A 903 - end of helix removed outlier: 3.632A pdb=" N LEU A 922 " --> pdb=" O PHE A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 962 Processing helix chain 'A' and resid 967 through 992 removed outlier: 5.034A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Processing helix chain 'A' and resid 994 through 997 No H-bonds generated for 'chain 'A' and resid 994 through 997' Processing helix chain 'A' and resid 1004 through 1039 removed outlier: 3.618A pdb=" N THR A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.714A pdb=" N GLU A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A1049 " --> pdb=" O HIS A1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 54 through 68 removed outlier: 5.007A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 removed outlier: 3.688A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N THR B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 149 through 165 removed outlier: 4.879A pdb=" N VAL B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 188 through 194 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.506A pdb=" N ASN B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 297 through 314 removed outlier: 4.309A pdb=" N LYS B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 357 Processing helix chain 'B' and resid 361 through 383 removed outlier: 3.769A pdb=" N ILE B 365 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Proline residue: B 366 - end of helix removed outlier: 4.260A pdb=" N VAL B 370 " --> pdb=" O THR B 367 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 390 through 421 removed outlier: 4.431A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 455 removed outlier: 5.671A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Proline residue: B 453 - end of helix Processing helix chain 'B' and resid 460 through 494 removed outlier: 3.784A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 509 through 533 Processing helix chain 'B' and resid 536 through 554 Processing helix chain 'B' and resid 581 through 596 Processing helix chain 'B' and resid 639 through 653 removed outlier: 3.546A pdb=" N GLY B 652 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 742 through 750 Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 780 through 785 removed outlier: 3.886A pdb=" N LEU B 784 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 847 Processing helix chain 'B' and resid 858 through 864 removed outlier: 3.567A pdb=" N ALA B 864 " --> pdb=" O ARG B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 889 Processing helix chain 'B' and resid 894 through 923 removed outlier: 3.982A pdb=" N LEU B 900 " --> pdb=" O ALA B 897 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 901 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Proline residue: B 903 - end of helix Processing helix chain 'B' and resid 933 through 963 Processing helix chain 'B' and resid 967 through 997 removed outlier: 4.880A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1004 through 1039 removed outlier: 4.039A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 28 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 100 through 116 removed outlier: 4.189A pdb=" N SER C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 149 through 165 removed outlier: 4.598A pdb=" N VAL C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 198 through 207 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 297 through 314 removed outlier: 4.361A pdb=" N LYS C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TYR C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 357 Processing helix chain 'C' and resid 360 through 383 removed outlier: 3.671A pdb=" N ILE C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) Proline residue: C 366 - end of helix removed outlier: 3.675A pdb=" N VAL C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 370 " --> pdb=" O PRO C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 390 through 421 removed outlier: 4.500A pdb=" N GLY C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 455 removed outlier: 5.539A pdb=" N GLY C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ALA C 439 " --> pdb=" O GLN C 435 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Proline residue: C 453 - end of helix Processing helix chain 'C' and resid 459 through 493 removed outlier: 4.428A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix Processing helix chain 'C' and resid 509 through 532 Processing helix chain 'C' and resid 535 through 554 Processing helix chain 'C' and resid 581 through 597 Processing helix chain 'C' and resid 629 through 631 No H-bonds generated for 'chain 'C' and resid 629 through 631' Processing helix chain 'C' and resid 639 through 653 Processing helix chain 'C' and resid 668 through 670 No H-bonds generated for 'chain 'C' and resid 668 through 670' Processing helix chain 'C' and resid 688 through 702 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 740 through 751 removed outlier: 4.131A pdb=" N LEU C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 776 No H-bonds generated for 'chain 'C' and resid 774 through 776' Processing helix chain 'C' and resid 780 through 784 Processing helix chain 'C' and resid 798 through 801 No H-bonds generated for 'chain 'C' and resid 798 through 801' Processing helix chain 'C' and resid 834 through 848 Processing helix chain 'C' and resid 858 through 889 removed outlier: 3.599A pdb=" N GLY C 867 " --> pdb=" O ALA C 864 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER C 868 " --> pdb=" O LYS C 865 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C 869 " --> pdb=" O GLY C 866 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR C 870 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 923 removed outlier: 3.629A pdb=" N LEU C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 901 " --> pdb=" O ALA C 897 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET C 902 " --> pdb=" O VAL C 898 " (cutoff:3.500A) Proline residue: C 903 - end of helix Processing helix chain 'C' and resid 933 through 964 removed outlier: 3.751A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 997 removed outlier: 5.169A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1004 through 1039 removed outlier: 3.614A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix Processing helix chain 'C' and resid 1044 through 1057 removed outlier: 4.463A pdb=" N HIS C1053 " --> pdb=" O MET C1049 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS C1056 " --> pdb=" O ARG C1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.812A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A 83 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 138 through 141 removed outlier: 3.582A pdb=" N MET A 138 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 270 removed outlier: 8.719A pdb=" N ARG A 180 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 767 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 757 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 770 " --> pdb=" O TYR A 755 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR A 755 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 215 through 217 removed outlier: 3.998A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 276 through 279 removed outlier: 6.728A pdb=" N ILE A 625 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE A 623 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR A 606 " --> pdb=" O MET A 621 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET A 621 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N SER A 608 " --> pdb=" O MET A 619 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N MET A 619 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 821 through 826 Processing sheet with id= G, first strand: chain 'A' and resid 721 through 725 Processing sheet with id= H, first strand: chain 'A' and resid 248 through 251 removed outlier: 6.770A pdb=" N ILE A 258 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 320 through 322 removed outlier: 6.701A pdb=" N VAL B 289 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE B 139 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET B 287 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET B 141 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR B 285 " --> pdb=" O MET B 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 264 through 270 removed outlier: 7.581A pdb=" N ARG B 180 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG B 767 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 215 through 217 removed outlier: 3.730A pdb=" N GLY B 215 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 276 through 279 removed outlier: 6.540A pdb=" N ILE B 625 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE B 623 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR B 606 " --> pdb=" O MET B 621 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 621 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER B 608 " --> pdb=" O MET B 619 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N MET B 619 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 820 through 824 Processing sheet with id= N, first strand: chain 'B' and resid 721 through 728 Processing sheet with id= O, first strand: chain 'B' and resid 787 through 789 Processing sheet with id= P, first strand: chain 'B' and resid 75 through 82 removed outlier: 7.136A pdb=" N THR B 93 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET B 78 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER B 89 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.257A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 320 through 322 removed outlier: 3.668A pdb=" N MET C 138 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 264 through 270 removed outlier: 8.374A pdb=" N ARG C 180 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG C 767 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 276 through 279 removed outlier: 6.825A pdb=" N ILE C 625 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE C 623 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR C 606 " --> pdb=" O MET C 621 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET C 621 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER C 608 " --> pdb=" O MET C 619 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET C 619 " --> pdb=" O SER C 608 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 821 through 826 Processing sheet with id= V, first strand: chain 'C' and resid 721 through 728 Processing sheet with id= W, first strand: chain 'C' and resid 248 through 251 removed outlier: 6.711A pdb=" N ILE C 258 " --> pdb=" O LEU C 249 " (cutoff:3.500A) 1403 hydrogen bonds defined for protein. 3867 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: 20.28 Time building geometry restraints manager: 42.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 24292 1.01 - 1.21: 34 1.21 - 1.41: 9589 1.41 - 1.61: 14991 1.61 - 1.81: 289 Bond restraints: 49195 Sorted by residual: bond pdb=" C8 PTY C1107 " pdb=" O10 PTY C1107 " ideal model delta sigma weight residual 1.205 1.410 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C30 PTY B1106 " pdb=" O4 PTY B1106 " ideal model delta sigma weight residual 1.331 1.184 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C8 PTY C1105 " pdb=" O7 PTY C1105 " ideal model delta sigma weight residual 1.331 1.184 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C8 PTY C1107 " pdb=" O7 PTY C1107 " ideal model delta sigma weight residual 1.331 1.185 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C8 PTY A1106 " pdb=" O7 PTY A1106 " ideal model delta sigma weight residual 1.331 1.185 0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 49190 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.18: 455 105.18 - 112.39: 57798 112.39 - 119.61: 11861 119.61 - 126.82: 18255 126.82 - 134.03: 248 Bond angle restraints: 88617 Sorted by residual: angle pdb=" N PHE A 451 " pdb=" CA PHE A 451 " pdb=" C PHE A 451 " ideal model delta sigma weight residual 111.36 118.38 -7.02 1.09e+00 8.42e-01 4.15e+01 angle pdb=" N ASN C 293 " pdb=" CA ASN C 293 " pdb=" C ASN C 293 " ideal model delta sigma weight residual 110.23 100.92 9.31 1.45e+00 4.76e-01 4.13e+01 angle pdb=" O11 PTY B1101 " pdb=" P1 PTY B1101 " pdb=" O14 PTY B1101 " ideal model delta sigma weight residual 92.90 109.72 -16.82 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O11 PTY B1108 " pdb=" P1 PTY B1108 " pdb=" O14 PTY B1108 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PTY A1102 " pdb=" P1 PTY A1102 " pdb=" O14 PTY A1102 " ideal model delta sigma weight residual 92.90 109.56 -16.66 3.00e+00 1.11e-01 3.08e+01 ... (remaining 88612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 19305 31.94 - 63.89: 373 63.89 - 95.83: 42 95.83 - 127.78: 6 127.78 - 159.72: 3 Dihedral angle restraints: 19729 sinusoidal: 9362 harmonic: 10367 Sorted by residual: dihedral pdb=" CA LEU A 751 " pdb=" C LEU A 751 " pdb=" N SER A 752 " pdb=" CA SER A 752 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLN C 963 " pdb=" C GLN C 963 " pdb=" N GLY C 964 " pdb=" CA GLY C 964 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C VAL A 452 " pdb=" N VAL A 452 " pdb=" CA VAL A 452 " pdb=" CB VAL A 452 " ideal model delta harmonic sigma weight residual -122.00 -133.46 11.46 0 2.50e+00 1.60e-01 2.10e+01 ... (remaining 19726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3589 0.078 - 0.156: 286 0.156 - 0.234: 12 0.234 - 0.311: 2 0.311 - 0.389: 3 Chirality restraints: 3892 Sorted by residual: chirality pdb=" CA LEU C 220 " pdb=" N LEU C 220 " pdb=" C LEU C 220 " pdb=" CB LEU C 220 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA PHE A 451 " pdb=" N PHE A 451 " pdb=" C PHE A 451 " pdb=" CB PHE A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA VAL A 452 " pdb=" N VAL A 452 " pdb=" C VAL A 452 " pdb=" CB VAL A 452 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3889 not shown) Planarity restraints: 7256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 961 " -0.235 2.00e-02 2.50e+03 3.05e-01 1.39e+03 pdb=" CD GLN A 961 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN A 961 " 0.231 2.00e-02 2.50e+03 pdb=" NE2 GLN A 961 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 961 " 0.470 2.00e-02 2.50e+03 pdb="HE22 GLN A 961 " -0.477 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 30 " 0.252 2.00e-02 2.50e+03 2.65e-01 1.05e+03 pdb=" CG ASN D 30 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 30 " -0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN D 30 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN D 30 " -0.380 2.00e-02 2.50e+03 pdb="HD22 ASN D 30 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 22 " -0.157 2.00e-02 2.50e+03 1.79e-01 4.82e+02 pdb=" CD GLN D 22 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN D 22 " 0.156 2.00e-02 2.50e+03 pdb=" NE2 GLN D 22 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN D 22 " 0.268 2.00e-02 2.50e+03 pdb="HE22 GLN D 22 " -0.268 2.00e-02 2.50e+03 ... (remaining 7253 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2848 2.20 - 2.80: 98515 2.80 - 3.40: 133455 3.40 - 4.00: 176884 4.00 - 4.60: 276741 Nonbonded interactions: 688443 Sorted by model distance: nonbonded pdb=" OD1 ASP B 272 " pdb=" H TYR B 273 " model vdw 1.600 1.850 nonbonded pdb=" HG1 THR A 712 " pdb=" OG SER A 827 " model vdw 1.602 1.850 nonbonded pdb=" OE2 GLU A 412 " pdb=" HE ARG A 980 " model vdw 1.617 1.850 nonbonded pdb=" OD1 ASN A 729 " pdb=" H ALA A 732 " model vdw 1.621 1.850 nonbonded pdb=" O ALA A 999 " pdb=" HE ARG A1008 " model vdw 1.637 1.850 ... (remaining 688438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 694 or (resid 695 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 696 through 890 or (resid 891 and (name N or name CA or name C or name \ O or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resi \ d 892 through 1040 or (resid 1101 and (name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or n \ ame C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C30 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name C8 )) or (resid 1102 \ and (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C20 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C8 or name O10 or name O30 or name O4 or name O7 )) or (resid 1103 an \ d (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19)) or (resid 1104 and (name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or \ (resid 1105 and (name C11 or name C12 or name C13 or name C14 or name C15 or nam \ e C16 or name C17 or name C18 or name C19 or name C8 )) or (resid 1106 and (name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21)) or (resid 1107 and (name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C8 or name O10 or name O7 )))) selection = (chain 'B' and (resid 1 through 1040 or (resid 1101 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name C30 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C8 \ )) or (resid 1102 and (name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name C30 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C8 or name O10 or name O30 or name O4 or name O7 )) \ or (resid 1103 and (name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19)) or (resid 1104 and (name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39)) or (resid 1105 and (name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C8 )) or (re \ sid 1106 and (name C13 or name C14 or name C15 or name C16 or name C17 or name C \ 18 or name C19 or name C20 or name C21)) or (resid 1107 and (name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C8 or name O10 or name O7 )))) selection = (chain 'C' and (resid 1 through 694 or (resid 695 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 696 through 890 or (resid 891 and (name N or name CA or name C or name \ O or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resi \ d 892 through 1040 or resid 1101 or (resid 1102 and (name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C30 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name C39 or name C8 or name O10 or name \ O30 or name O4 or name O7 )) or (resid 1103 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 1104 \ and (name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39)) or (resid 1105 and (name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C8 )) or (resid 1106 and (name C13 or name C14 or name C15 or n \ ame C16 or name C17 or name C18 or name C19 or name C20 or name C21)) or (resid \ 1107 and (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C8 or name O10 or name O7 \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 137 5.16 5 C 15834 2.51 5 N 3982 2.21 5 O 4534 1.98 5 H 24295 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.720 Extract box with map and model: 13.800 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.400 Process input model: 147.450 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.005 0.205 24900 Z= 0.344 Angle : 0.853 16.820 33567 Z= 0.385 Chirality : 0.044 0.389 3892 Planarity : 0.004 0.062 4210 Dihedral : 14.635 159.723 9182 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.15), residues: 3164 helix: 2.05 (0.12), residues: 1787 sheet: 0.28 (0.23), residues: 499 loop : -0.54 (0.21), residues: 878 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 499 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 501 average time/residue: 2.5786 time to fit residues: 1518.7385 Evaluate side-chains 341 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 0.0470 chunk 183 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 211 GLN A 226 GLN A 961 GLN B 157 GLN B 936 GLN C 55 GLN C 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 24900 Z= 0.254 Angle : 0.532 7.349 33567 Z= 0.287 Chirality : 0.041 0.166 3892 Planarity : 0.005 0.065 4210 Dihedral : 10.760 177.740 3855 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.15), residues: 3164 helix: 1.91 (0.12), residues: 1778 sheet: 0.42 (0.23), residues: 506 loop : -0.49 (0.21), residues: 880 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 353 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 372 average time/residue: 2.7717 time to fit residues: 1217.0498 Evaluate side-chains 350 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 341 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 1.4087 time to fit residues: 12.0234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 179 GLN C 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 24900 Z= 0.299 Angle : 0.533 5.971 33567 Z= 0.285 Chirality : 0.041 0.161 3892 Planarity : 0.005 0.086 4210 Dihedral : 10.358 168.521 3855 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.15), residues: 3164 helix: 1.77 (0.12), residues: 1770 sheet: 0.35 (0.23), residues: 508 loop : -0.57 (0.21), residues: 886 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 349 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 12 residues processed: 368 average time/residue: 2.6505 time to fit residues: 1158.9354 Evaluate side-chains 348 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 336 time to evaluate : 3.750 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 1.6242 time to fit residues: 13.1520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 136 optimal weight: 0.0370 chunk 192 optimal weight: 0.9990 chunk 287 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 211 GLN B 672 ASN C 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24900 Z= 0.173 Angle : 0.478 7.592 33567 Z= 0.256 Chirality : 0.039 0.153 3892 Planarity : 0.004 0.071 4210 Dihedral : 9.529 162.511 3855 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.15), residues: 3164 helix: 1.95 (0.13), residues: 1772 sheet: 0.50 (0.24), residues: 501 loop : -0.47 (0.21), residues: 891 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 343 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 362 average time/residue: 2.6440 time to fit residues: 1122.6507 Evaluate side-chains 341 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 330 time to evaluate : 3.548 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.2121 time to fit residues: 7.7809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 273 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN C 779 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24900 Z= 0.214 Angle : 0.484 5.853 33567 Z= 0.258 Chirality : 0.040 0.152 3892 Planarity : 0.004 0.079 4210 Dihedral : 9.156 162.616 3855 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.15), residues: 3164 helix: 1.95 (0.13), residues: 1769 sheet: 0.46 (0.23), residues: 504 loop : -0.48 (0.21), residues: 891 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 328 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 346 average time/residue: 2.6192 time to fit residues: 1077.5262 Evaluate side-chains 328 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 316 time to evaluate : 4.202 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.1574 time to fit residues: 9.5423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 24900 Z= 0.223 Angle : 0.487 5.479 33567 Z= 0.260 Chirality : 0.040 0.148 3892 Planarity : 0.004 0.088 4210 Dihedral : 8.964 163.836 3855 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.15), residues: 3164 helix: 1.95 (0.13), residues: 1768 sheet: 0.45 (0.23), residues: 507 loop : -0.51 (0.21), residues: 889 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 322 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 343 average time/residue: 2.6085 time to fit residues: 1064.9396 Evaluate side-chains 339 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 323 time to evaluate : 3.650 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 1.2454 time to fit residues: 13.8371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 24900 Z= 0.337 Angle : 0.535 5.664 33567 Z= 0.286 Chirality : 0.042 0.153 3892 Planarity : 0.005 0.098 4210 Dihedral : 9.292 165.206 3855 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.15), residues: 3164 helix: 1.74 (0.12), residues: 1768 sheet: 0.39 (0.24), residues: 487 loop : -0.65 (0.20), residues: 909 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 329 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 346 average time/residue: 2.6770 time to fit residues: 1109.3105 Evaluate side-chains 336 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 321 time to evaluate : 3.765 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 1.4232 time to fit residues: 12.3161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 859 GLN C 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 24900 Z= 0.302 Angle : 0.524 6.361 33567 Z= 0.280 Chirality : 0.041 0.149 3892 Planarity : 0.005 0.097 4210 Dihedral : 9.202 165.173 3855 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.15), residues: 3164 helix: 1.71 (0.12), residues: 1767 sheet: 0.31 (0.23), residues: 511 loop : -0.64 (0.20), residues: 886 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 328 time to evaluate : 4.005 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 347 average time/residue: 2.4970 time to fit residues: 1024.7894 Evaluate side-chains 342 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 326 time to evaluate : 3.869 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 1.5530 time to fit residues: 15.0072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 222 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 267 optimal weight: 0.1980 chunk 281 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 859 GLN C 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 24900 Z= 0.152 Angle : 0.469 5.701 33567 Z= 0.250 Chirality : 0.039 0.148 3892 Planarity : 0.004 0.074 4210 Dihedral : 8.480 165.001 3855 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.15), residues: 3164 helix: 1.99 (0.13), residues: 1768 sheet: 0.50 (0.24), residues: 496 loop : -0.48 (0.20), residues: 900 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 328 time to evaluate : 4.402 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 341 average time/residue: 2.5912 time to fit residues: 1056.9931 Evaluate side-chains 332 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 319 time to evaluate : 3.720 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.6003 time to fit residues: 5.7379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 313 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24900 Z= 0.277 Angle : 0.506 5.951 33567 Z= 0.269 Chirality : 0.041 0.152 3892 Planarity : 0.004 0.101 4210 Dihedral : 8.652 165.929 3855 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3164 helix: 1.89 (0.13), residues: 1765 sheet: 0.42 (0.24), residues: 492 loop : -0.60 (0.20), residues: 907 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 321 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 335 average time/residue: 2.6589 time to fit residues: 1061.4143 Evaluate side-chains 329 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 316 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 1.9333 time to fit residues: 9.6116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 257 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.083849 restraints weight = 89489.547| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.48 r_work: 0.2985 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 24900 Z= 0.235 Angle : 0.497 5.905 33567 Z= 0.265 Chirality : 0.040 0.151 3892 Planarity : 0.004 0.093 4210 Dihedral : 8.602 165.875 3855 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3164 helix: 1.89 (0.13), residues: 1764 sheet: 0.41 (0.24), residues: 498 loop : -0.57 (0.20), residues: 902 =============================================================================== Job complete usr+sys time: 16995.01 seconds wall clock time: 296 minutes 3.26 seconds (17763.26 seconds total)