Starting phenix.real_space_refine (version: dev) on Sun May 15 08:51:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkt_21229/05_2022/6vkt_21229_updated.pdb" } resolution = 2.72 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= 0.000 sd= 1.000 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 None Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 24331 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7761 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 39, 'TRANS': 997} Chain breaks: 1 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7813 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 40, 'TRANS': 1002} Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7806 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 40, 'TRANS': 1001} Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 264 Unusual residues: {'PTY': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "B" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 373 Unusual residues: {'ERY': 1, 'PTY': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 78 Chain: "C" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 314 Unusual residues: {'PTY': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 13.87, per 1000 atoms: 0.57 Number of scatterers: 24331 At special positions: 0 Unit cell: (122.04, 144.72, 152.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 20 15.00 O 4548 8.00 N 3906 7.00 C 15722 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: 9.37 Conformation dependent library (CDL) restraints added in 3.5 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 22 sheets defined 51.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.654A pdb=" N TRP A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 removed outlier: 5.226A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.896A 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 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 241 through 246 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: 4.377A pdb=" N LYS A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 357 removed outlier: 3.627A pdb=" N PHE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 383 removed outlier: 4.905A 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 391 through 421 removed outlier: 3.782A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 455 removed outlier: 5.603A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 5.072A 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 493 Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 509 through 533 removed outlier: 3.573A pdb=" N LYS A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.672A pdb=" N SER A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 removed outlier: 3.658A pdb=" N GLY A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 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 751 removed outlier: 4.241A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 782 No H-bonds generated for 'chain 'A' and resid 780 through 782' Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 863 through 865 No H-bonds generated for 'chain 'A' and resid 863 through 865' Processing helix chain 'A' and resid 870 through 873 No H-bonds generated for 'chain 'A' and resid 870 through 873' Processing helix chain 'A' and resid 876 through 889 removed outlier: 4.053A pdb=" N VAL A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 922 removed outlier: 3.641A pdb=" N VAL A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) Proline residue: A 903 - end of helix removed outlier: 3.822A pdb=" N LEU A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 958 removed outlier: 3.549A pdb=" N ALA A 947 " --> pdb=" O MET A 943 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 997 removed outlier: 4.858A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1004 through 1040 removed outlier: 3.844A pdb=" N THR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix removed outlier: 3.626A pdb=" N PHE A1040 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 54 through 68 removed outlier: 5.275A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 161 through 164 No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 188 through 194 Processing helix chain 'B' and resid 198 through 207 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 260 through 263 No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 298 through 314 removed outlier: 4.036A pdb=" N TYR B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 357 removed outlier: 3.605A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 3.584A pdb=" N THR B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 390 through 421 removed outlier: 4.552A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 456 removed outlier: 5.743A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Proline residue: B 453 - end of helix removed outlier: 4.037A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 493 removed outlier: 3.805A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.348A 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 502 through 505 No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 509 through 531 Processing helix chain 'B' and resid 535 through 554 Processing helix chain 'B' and resid 581 through 595 Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'B' and resid 639 through 651 Processing helix chain 'B' and resid 668 through 670 No H-bonds generated for 'chain 'B' and resid 668 through 670' Processing helix chain 'B' and resid 688 through 703 Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 740 through 750 removed outlier: 3.561A pdb=" N ARG B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 834 through 847 Processing helix chain 'B' and resid 858 through 863 removed outlier: 3.664A pdb=" N ARG B 861 " --> pdb=" O GLY B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 889 Processing helix chain 'B' and resid 894 through 922 removed outlier: 3.629A pdb=" N LEU B 900 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 901 " --> pdb=" O ALA B 897 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N MET B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Proline residue: B 903 - end of helix removed outlier: 3.580A pdb=" N LEU B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 961 Processing helix chain 'B' and resid 967 through 997 removed outlier: 4.989A 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 1005 through 1039 removed outlier: 3.773A pdb=" N THR B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 9 through 28 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.627A pdb=" N VAL C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 198 through 207 Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.804A pdb=" N ASN C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 314 removed outlier: 4.439A pdb=" N LYS C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 357 Processing helix chain 'C' and resid 363 through 383 Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 405 through 421 Processing helix chain 'C' and resid 425 through 435 removed outlier: 3.558A pdb=" N THR C 429 " --> pdb=" O PRO C 425 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 455 removed outlier: 3.881A pdb=" N ILE C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 450 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 3.915A 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 460 through 493 removed outlier: 3.950A pdb=" N THR C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 4.222A 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 531 removed outlier: 3.831A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 554 Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.630A pdb=" N SER C 597 " --> pdb=" O GLN C 593 " (cutoff:3.500A) 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 removed outlier: 3.515A pdb=" N GLY C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 702 Processing helix chain 'C' and resid 730 through 736 Processing helix chain 'C' and resid 740 through 750 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 859 through 866 Processing helix chain 'C' and resid 869 through 889 Processing helix chain 'C' and resid 894 through 923 removed outlier: 3.781A pdb=" N LEU C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL C 901 " --> pdb=" O ALA C 897 " (cutoff:3.500A) removed outlier: 4.806A 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 961 removed outlier: 3.930A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 997 removed outlier: 5.125A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix removed outlier: 3.572A pdb=" N PHE C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1004 through 1039 removed outlier: 3.774A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 127 through 130 removed outlier: 4.961A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 83 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 270 removed outlier: 8.584A pdb=" N ARG A 180 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG A 767 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 757 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL A 770 " --> pdb=" O TYR A 755 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR A 755 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 215 through 217 removed outlier: 3.709A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 276 through 279 removed outlier: 6.950A pdb=" N ILE A 625 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 623 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 606 " --> pdb=" O MET A 621 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A 621 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N SER A 608 " --> pdb=" O MET A 619 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N MET A 619 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 821 through 826 removed outlier: 3.745A pdb=" N LEU A 676 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 677 " --> pdb=" O GLY A 857 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 721 through 725 Processing sheet with id= G, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.057A pdb=" N VAL A 289 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 139 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N MET A 287 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 812 through 816 removed outlier: 6.934A pdb=" N THR B 93 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET B 78 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 89 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 264 through 270 removed outlier: 7.819A pdb=" N ARG B 180 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG B 767 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 215 through 217 removed outlier: 4.328A pdb=" N GLY B 215 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 276 through 279 removed outlier: 6.902A pdb=" N ILE B 625 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 623 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR B 606 " --> pdb=" O MET B 621 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET B 621 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER B 608 " --> pdb=" O MET B 619 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N MET B 619 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 821 through 826 Processing sheet with id= M, first strand: chain 'B' and resid 721 through 723 Processing sheet with id= N, first strand: chain 'B' and resid 726 through 728 Processing sheet with id= O, first strand: chain 'B' and resid 136 through 143 removed outlier: 6.864A pdb=" N VAL B 289 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 139 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET B 287 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B 141 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR B 285 " --> pdb=" O MET B 141 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY B 286 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.790A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 320 through 322 removed outlier: 6.928A pdb=" N VAL C 289 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE C 139 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N MET C 287 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET C 141 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR C 285 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 264 through 270 removed outlier: 8.670A pdb=" N ARG C 180 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG C 767 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 757 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 282 through 284 removed outlier: 4.351A pdb=" N THR C 277 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE C 625 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE C 623 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR C 606 " --> pdb=" O MET C 621 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET C 621 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER C 608 " --> pdb=" O MET C 619 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET C 619 " --> pdb=" O SER C 608 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 820 through 826 Processing sheet with id= U, first strand: chain 'C' and resid 721 through 728 Processing sheet with id= V, first strand: chain 'C' and resid 248 through 251 removed outlier: 6.874A pdb=" N ILE C 258 " --> pdb=" O LEU C 249 " (cutoff:3.500A) 1276 hydrogen bonds defined for protein. 3768 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: 10.40 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3911 1.32 - 1.44: 6074 1.44 - 1.56: 14440 1.56 - 1.69: 40 1.69 - 1.81: 267 Bond restraints: 24732 Sorted by residual: bond pdb=" C8 PTY C1109 " pdb=" O10 PTY C1109 " ideal model delta sigma weight residual 1.205 1.455 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C30 PTY B1107 " pdb=" O4 PTY B1107 " ideal model delta sigma weight residual 1.331 1.465 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C8 PTY B1108 " pdb=" O7 PTY B1108 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C8 PTY C1105 " pdb=" O7 PTY C1105 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C8 PTY B1107 " pdb=" O7 PTY B1107 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 24727 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.37: 686 106.37 - 113.27: 13941 113.27 - 120.18: 8392 120.18 - 127.08: 10148 127.08 - 133.98: 186 Bond angle restraints: 33353 Sorted by residual: angle pdb=" O11 PTY B1107 " pdb=" P1 PTY B1107 " pdb=" O14 PTY B1107 " ideal model delta sigma weight residual 92.90 108.61 -15.71 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O11 PTY C1105 " pdb=" P1 PTY C1105 " pdb=" O14 PTY C1105 " ideal model delta sigma weight residual 92.90 107.23 -14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C PHE B1040 " pdb=" N LYS B1041 " pdb=" CA LYS B1041 " ideal model delta sigma weight residual 120.82 114.55 6.27 1.41e+00 5.03e-01 1.97e+01 angle pdb=" O11 PTY B1102 " pdb=" P1 PTY B1102 " pdb=" O14 PTY B1102 " ideal model delta sigma weight residual 92.90 105.81 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" O11 PTY A1104 " pdb=" P1 PTY A1104 " pdb=" O14 PTY A1104 " ideal model delta sigma weight residual 92.90 105.37 -12.47 3.00e+00 1.11e-01 1.73e+01 ... (remaining 33348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 14601 34.99 - 69.98: 164 69.98 - 104.97: 30 104.97 - 139.95: 11 139.95 - 174.94: 9 Dihedral angle restraints: 14815 sinusoidal: 5937 harmonic: 8878 Sorted by residual: dihedral pdb=" C3 PTY C1102 " pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O12 PTY C1102 " ideal model delta sinusoidal sigma weight residual -59.77 115.17 -174.94 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N1 PTY A1103 " pdb=" C2 PTY A1103 " pdb=" C3 PTY A1103 " pdb=" O11 PTY A1103 " ideal model delta sinusoidal sigma weight residual 65.33 -108.18 173.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PTY A1106 " pdb=" O11 PTY A1106 " pdb=" P1 PTY A1106 " pdb=" O12 PTY A1106 " ideal model delta sinusoidal sigma weight residual -59.77 106.18 -165.95 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 14812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.073: 3862 1.073 - 2.146: 0 2.146 - 3.218: 0 3.218 - 4.291: 0 4.291 - 5.364: 4 Chirality restraints: 3866 Sorted by residual: chirality pdb=" C12 ERY B1101 " pdb=" C11 ERY B1101 " pdb=" C13 ERY B1101 " pdb=" C35 ERY B1101 " both_signs ideal model delta sigma weight residual False -2.75 2.62 -5.36 2.00e-01 2.50e+01 7.19e+02 chirality pdb=" C16 ERY B1101 " pdb=" C15 ERY B1101 " pdb=" C17 ERY B1101 " pdb=" C19 ERY B1101 " both_signs ideal model delta sigma weight residual False 2.69 -2.68 5.36 2.00e-01 2.50e+01 7.19e+02 chirality pdb=" C6 ERY B1101 " pdb=" C32 ERY B1101 " pdb=" C5 ERY B1101 " pdb=" C7 ERY B1101 " both_signs ideal model delta sigma weight residual False -2.74 2.57 -5.32 2.00e-01 2.50e+01 7.07e+02 ... (remaining 3863 not shown) Planarity restraints: 4154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 67 " -0.649 9.50e-02 1.11e+02 2.91e-01 5.17e+01 pdb=" NE ARG B 67 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 67 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 67 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 67 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 916 " -0.489 9.50e-02 1.11e+02 2.19e-01 2.94e+01 pdb=" NE ARG A 916 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 916 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 916 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 916 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 744 " 0.430 9.50e-02 1.11e+02 1.93e-01 2.27e+01 pdb=" NE ARG C 744 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 744 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 744 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 744 " 0.015 2.00e-02 2.50e+03 ... (remaining 4151 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 5 2.13 - 2.82: 7407 2.82 - 3.52: 33302 3.52 - 4.21: 54694 4.21 - 4.90: 101676 Nonbonded interactions: 197084 Sorted by model distance: nonbonded pdb=" OG SER A 893 " pdb=" O12 PTY A1106 " model vdw 1.442 2.440 nonbonded pdb=" O13 PTY C1101 " pdb=" O10 PTY C1106 " model vdw 1.817 3.040 nonbonded pdb=" O MET C 433 " pdb=" OG SER C 437 " model vdw 2.107 2.440 nonbonded pdb=" OH TYR C 465 " pdb=" OE1 GLN C 936 " model vdw 2.109 2.440 nonbonded pdb=" OG SER A 148 " pdb=" OE1 GLU A 151 " model vdw 2.111 2.440 ... (remaining 197079 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 1042 or (resid 1101 and (name C1 or 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 C2 or name C20 or name C3 or name C30 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 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 C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 \ or name O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1103 and \ (name C1 or 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 C5 or name C6 or name C8 or name O10 or name O30 or name O4 or name O7 )) o \ r resid 1104 or (resid 1105 and (name C2 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 O30 \ or name O4 )) or (resid 1106 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 \ C21 or name C22 or name C8 or name O10 or name O7 )))) selection = (chain 'B' and (resid 1 through 498 or resid 508 through 1042 or (resid 1104 and \ (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C20 or name C3 or name \ C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C5 or na \ me C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or n \ ame O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1105 and (name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or n \ ame C17 or name C18 or name C19 or name C2 or name C20 or name C3 or name C30 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 1106 and (name C1 or name C11 or name C12 or name C13 or name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e 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 C5 or name C6 or name C8 or name O10 or name O30 o \ r name O4 or name O7 )) or (resid 1107 and (name C1 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 3 or 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 name C40 or name C5 or name C6 or n \ ame C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or \ name O30 or name O4 or name O7 or name P1 )) or (resid 1108 and (name C2 or nam \ e 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 O30 or name O4 )) or (resid 1109 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 C21 or name C22 or name C8 or name O10 or name \ O7 )))) selection = (chain 'C' and (resid 1 through 498 or resid 508 through 1042 or resid 1104 thro \ ugh 1105 or (resid 1106 and (name C1 or 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 C5 or name C6 or name C8 or name O10 or name O3 \ 0 or name O4 or name O7 )) or (resid 1107 and (name C1 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C \ 19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or nam \ e C3 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 C40 or name C5 or name C6 o \ r name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 \ or name O30 or name O4 or name O7 or name P1 )) or (resid 1108 and (name C2 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 O30 or name O4 )) or resid 1109)) } 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 135 5.16 5 C 15722 2.51 5 N 3906 2.21 5 O 4548 1.98 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: 2.500 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: 0.030 Extract box with map and model: 11.830 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.220 Process input model: 63.670 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.006 0.250 24732 Z= 0.379 Angle : 0.796 15.705 33353 Z= 0.358 Chirality : 0.172 5.364 3866 Planarity : 0.009 0.291 4154 Dihedral : 13.655 174.943 9127 Min Nonbonded Distance : 1.442 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.00 % 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: -1.19 (0.14), residues: 3114 helix: 0.34 (0.12), residues: 1655 sheet: -1.14 (0.24), residues: 440 loop : -2.46 (0.16), residues: 1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 2.974 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 4 residues processed: 511 average time/residue: 1.3646 time to fit residues: 801.5440 Evaluate side-chains 333 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 329 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 3 average time/residue: 0.2629 time to fit residues: 4.9592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 0.0040 chunk 181 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 192 GLN A 317 GLN A 358 GLN A 574 GLN A 617 GLN A 681 GLN A 688 HIS ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN B 179 GLN B 293 ASN B 317 GLN B 617 GLN B 681 GLN B 762 GLN B 779 GLN B 785 ASN B 807 GLN B 917 ASN C 55 GLN C 104 GLN C 123 GLN C 124 GLN C 283 ASN C 463 ASN C 617 GLN C 762 GLN C 766 GLN C 869 GLN C 961 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 24732 Z= 0.181 Angle : 0.676 29.259 33353 Z= 0.291 Chirality : 0.069 2.102 3866 Planarity : 0.004 0.111 4154 Dihedral : 14.249 178.365 3904 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.56 % 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: -0.01 (0.15), residues: 3114 helix: 1.29 (0.13), residues: 1669 sheet: -0.50 (0.24), residues: 435 loop : -2.00 (0.17), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 349 time to evaluate : 2.684 Fit side-chains outliers start: 64 outliers final: 19 residues processed: 383 average time/residue: 1.3654 time to fit residues: 602.4468 Evaluate side-chains 334 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 315 time to evaluate : 2.536 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 8 average time/residue: 0.4062 time to fit residues: 8.1623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 77 optimal weight: 0.0040 chunk 282 optimal weight: 0.9980 chunk 305 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 211 GLN A 317 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 700 GLN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN B 109 ASN B 179 GLN B 681 GLN B 836 GLN C 108 GLN C 463 ASN C 688 HIS C 766 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24732 Z= 0.218 Angle : 0.669 26.732 33353 Z= 0.292 Chirality : 0.069 2.057 3866 Planarity : 0.004 0.105 4154 Dihedral : 13.063 176.095 3904 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 3.08 % 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: 0.60 (0.15), residues: 3114 helix: 1.69 (0.13), residues: 1662 sheet: -0.07 (0.25), residues: 429 loop : -1.58 (0.18), residues: 1023 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 334 time to evaluate : 3.007 Fit side-chains outliers start: 77 outliers final: 31 residues processed: 373 average time/residue: 1.3778 time to fit residues: 593.3893 Evaluate side-chains 336 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 305 time to evaluate : 2.752 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 19 residues processed: 13 average time/residue: 0.4837 time to fit residues: 12.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 135 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 300 optimal weight: 0.5980 chunk 148 optimal weight: 0.3980 chunk 269 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 211 GLN A 317 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN C 766 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 24732 Z= 0.171 Angle : 0.645 26.945 33353 Z= 0.279 Chirality : 0.068 2.053 3866 Planarity : 0.004 0.089 4154 Dihedral : 12.124 178.104 3904 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 3.24 % 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: 0.93 (0.16), residues: 3114 helix: 1.83 (0.13), residues: 1686 sheet: 0.11 (0.25), residues: 438 loop : -1.30 (0.19), residues: 990 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 324 time to evaluate : 2.789 Fit side-chains outliers start: 81 outliers final: 38 residues processed: 369 average time/residue: 1.3692 time to fit residues: 584.9244 Evaluate side-chains 338 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 300 time to evaluate : 2.602 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 13 average time/residue: 0.5486 time to fit residues: 13.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.0470 chunk 170 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 chunk 207 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 211 GLN A 317 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN A 836 GLN A 859 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN C 630 ASN C 696 ASN C 766 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.002 0.028 24732 Z= 0.146 Angle : 0.632 26.802 33353 Z= 0.272 Chirality : 0.068 2.058 3866 Planarity : 0.004 0.080 4154 Dihedral : 11.498 176.752 3904 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 3.28 % 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: 1.15 (0.16), residues: 3114 helix: 1.96 (0.13), residues: 1689 sheet: 0.30 (0.26), residues: 415 loop : -1.12 (0.19), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 313 time to evaluate : 2.604 Fit side-chains outliers start: 82 outliers final: 40 residues processed: 365 average time/residue: 1.3719 time to fit residues: 579.5759 Evaluate side-chains 340 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 300 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 28 residues processed: 12 average time/residue: 0.3783 time to fit residues: 10.4782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 176 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 249 optimal weight: 0.3980 chunk 139 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 211 GLN A 317 GLN A 358 GLN A 514 ASN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN B 165 GLN C 630 ASN C 766 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 24732 Z= 0.164 Angle : 0.640 26.548 33353 Z= 0.276 Chirality : 0.067 2.062 3866 Planarity : 0.004 0.075 4154 Dihedral : 11.025 173.619 3904 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 3.24 % 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 (0.16), residues: 3114 helix: 2.06 (0.13), residues: 1696 sheet: 0.33 (0.26), residues: 426 loop : -0.98 (0.19), residues: 992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 321 time to evaluate : 2.853 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 47 residues processed: 374 average time/residue: 1.4001 time to fit residues: 610.8242 Evaluate side-chains 346 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 299 time to evaluate : 2.837 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 37 residues processed: 11 average time/residue: 0.4070 time to fit residues: 10.5966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 253 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 299 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 211 GLN A 317 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN A 836 GLN A 859 GLN B 681 GLN B 817 ASN C 630 ASN C 766 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 24732 Z= 0.176 Angle : 0.650 26.334 33353 Z= 0.281 Chirality : 0.068 2.066 3866 Planarity : 0.004 0.073 4154 Dihedral : 10.652 169.293 3904 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 3.16 % 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: 1.41 (0.16), residues: 3114 helix: 2.11 (0.13), residues: 1685 sheet: 0.36 (0.26), residues: 423 loop : -0.87 (0.19), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 303 time to evaluate : 2.893 Fit side-chains outliers start: 79 outliers final: 45 residues processed: 359 average time/residue: 1.3774 time to fit residues: 573.2687 Evaluate side-chains 338 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 293 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 35 residues processed: 10 average time/residue: 0.7684 time to fit residues: 12.8732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN C 630 ASN C 766 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 24732 Z= 0.254 Angle : 0.682 26.016 33353 Z= 0.301 Chirality : 0.068 2.069 3866 Planarity : 0.004 0.070 4154 Dihedral : 10.506 164.848 3904 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 2.60 % 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: 1.33 (0.16), residues: 3114 helix: 2.07 (0.13), residues: 1680 sheet: 0.07 (0.25), residues: 458 loop : -0.80 (0.20), residues: 976 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 308 time to evaluate : 2.832 Fit side-chains outliers start: 65 outliers final: 43 residues processed: 354 average time/residue: 1.4290 time to fit residues: 585.2168 Evaluate side-chains 336 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 293 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.5335 time to fit residues: 7.7486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 0.8980 chunk 262 optimal weight: 0.0970 chunk 279 optimal weight: 2.9990 chunk 168 optimal weight: 0.0670 chunk 121 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 252 optimal weight: 0.4980 chunk 264 optimal weight: 0.9990 chunk 278 optimal weight: 0.0070 chunk 183 optimal weight: 5.9990 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN A 358 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN B 165 GLN B 812 GLN C 630 ASN C 766 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.061 24732 Z= 0.135 Angle : 0.650 26.028 33353 Z= 0.283 Chirality : 0.067 2.075 3866 Planarity : 0.004 0.070 4154 Dihedral : 9.933 162.472 3904 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 2.12 % 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 (0.16), residues: 3114 helix: 2.22 (0.13), residues: 1677 sheet: 0.48 (0.27), residues: 413 loop : -0.75 (0.19), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 316 time to evaluate : 2.794 Fit side-chains outliers start: 53 outliers final: 34 residues processed: 363 average time/residue: 1.4093 time to fit residues: 602.4695 Evaluate side-chains 331 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 297 time to evaluate : 2.707 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 33 residues processed: 1 average time/residue: 0.2320 time to fit residues: 4.0879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 205 optimal weight: 0.7980 chunk 309 optimal weight: 0.7980 chunk 285 optimal weight: 0.0870 chunk 246 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 190 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 317 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN B 165 GLN C 630 ASN C 766 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 24732 Z= 0.152 Angle : 0.653 25.850 33353 Z= 0.283 Chirality : 0.067 2.076 3866 Planarity : 0.004 0.070 4154 Dihedral : 9.637 159.946 3904 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.76 % 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: 1.61 (0.16), residues: 3114 helix: 2.24 (0.13), residues: 1686 sheet: 0.44 (0.26), residues: 419 loop : -0.70 (0.20), residues: 1009 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 300 time to evaluate : 2.726 Fit side-chains outliers start: 44 outliers final: 33 residues processed: 337 average time/residue: 1.4492 time to fit residues: 562.1582 Evaluate side-chains 325 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 292 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 33 residues processed: 0 time to fit residues: 3.6755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 317 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 859 GLN B 463 ASN B1007 GLN C 630 ASN C 766 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.082430 restraints weight = 34143.365| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.19 r_work: 0.3010 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work: 0.2992 rms_B_bonded: 2.02 restraints_weight: 0.1250 r_work: 0.2983 rms_B_bonded: 2.06 restraints_weight: 0.0625 r_work: 0.2974 rms_B_bonded: 2.12 restraints_weight: 0.0312 r_work: 0.2964 rms_B_bonded: 2.20 restraints_weight: 0.0156 r_work: 0.2954 rms_B_bonded: 2.30 restraints_weight: 0.0078 r_work: 0.2944 rms_B_bonded: 2.41 restraints_weight: 0.0039 r_work: 0.2933 rms_B_bonded: 2.54 restraints_weight: 0.0020 r_work: 0.2923 rms_B_bonded: 2.68 restraints_weight: 0.0010 r_work: 0.2911 rms_B_bonded: 2.84 restraints_weight: 0.0005 r_work: 0.2899 rms_B_bonded: 3.02 restraints_weight: 0.0002 r_work: 0.2887 rms_B_bonded: 3.21 restraints_weight: 0.0001 r_work: 0.2874 rms_B_bonded: 3.43 restraints_weight: 0.0001 r_work: 0.2861 rms_B_bonded: 3.66 restraints_weight: 0.0000 r_work: 0.2847 rms_B_bonded: 3.91 restraints_weight: 0.0000 r_work: 0.2832 rms_B_bonded: 4.19 restraints_weight: 0.0000 r_work: 0.2817 rms_B_bonded: 4.48 restraints_weight: 0.0000 r_work: 0.2801 rms_B_bonded: 4.81 restraints_weight: 0.0000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 24732 Z= 0.204 Angle : 0.673 25.861 33353 Z= 0.296 Chirality : 0.067 2.077 3866 Planarity : 0.004 0.114 4154 Dihedral : 9.579 158.095 3904 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.72 % 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: 1.62 (0.16), residues: 3114 helix: 2.24 (0.13), residues: 1682 sheet: 0.36 (0.25), residues: 442 loop : -0.64 (0.20), residues: 990 =============================================================================== Job complete usr+sys time: 8948.81 seconds wall clock time: 159 minutes 19.10 seconds (9559.10 seconds total)