Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 01:32:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/04_2023/7ry3_24732_trim_updated.pdb" } resolution = 2.91 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= 0.217 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 102 5.16 5 C 15423 2.51 5 N 3973 2.21 5 O 4463 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23964 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 7979 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 47, 'TRANS': 999} Chain: "B" Number of atoms: 7958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 7958 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 47, 'TRANS': 997} Chain: "C" Number of atoms: 8027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8027 Unusual residues: {'80P': 1} Classifications: {'peptide': 1048, 'undetermined': 1} Link IDs: {'PTRANS': 48, 'TRANS': 999, None: 1} Not linked: pdbres="PRO C1048 " pdbres="80P C1101 " Time building chain proxies: 12.20, per 1000 atoms: 0.51 Number of scatterers: 23964 At special positions: 0 Unit cell: (126.36, 124.2, 154.44, 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 102 16.00 F 3 9.00 O 4463 8.00 N 3973 7.00 C 15423 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: 10.39 Conformation dependent library (CDL) restraints added in 3.9 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 25 sheets defined 55.3% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.581A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.616A pdb=" N GLN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.535A pdb=" N VAL A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 190 through 196 removed outlier: 3.680A pdb=" N TYR A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.019A pdb=" N LYS A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.565A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 removed outlier: 4.009A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.610A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.723A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.901A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 451 removed outlier: 3.567A pdb=" N GLN A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 458 No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 461 through 496 removed outlier: 3.661A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 538 removed outlier: 3.853A pdb=" N ASP A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 586 through 602 removed outlier: 3.602A pdb=" N VAL A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 645 through 658 removed outlier: 3.807A pdb=" N ALA A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N MET A 657 " --> pdb=" O MET A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 778 through 781 Processing helix chain 'A' and resid 784 through 789 Processing helix chain 'A' and resid 802 through 805 No H-bonds generated for 'chain 'A' and resid 802 through 805' Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.638A pdb=" N LEU A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Proline residue: A 853 - end of helix Processing helix chain 'A' and resid 867 through 897 removed outlier: 3.661A pdb=" N ALA A 878 " --> pdb=" O SER A 874 " (cutoff:3.500A) Proline residue: A 879 - end of helix Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 928 removed outlier: 4.076A pdb=" N GLY A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 966 removed outlier: 3.506A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1001 removed outlier: 4.706A pdb=" N ARG A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Proline residue: A 985 - end of helix Proline residue: A 999 - end of helix Processing helix chain 'A' and resid 1008 through 1027 removed outlier: 3.780A pdb=" N GLY A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1043 Proline residue: A1034 - end of helix removed outlier: 3.534A pdb=" N TYR A1037 " --> pdb=" O ILE A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.887A pdb=" N GLN B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 removed outlier: 4.819A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 190 through 196 removed outlier: 4.042A pdb=" N TYR B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 316 removed outlier: 4.282A pdb=" N LYS B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 386 removed outlier: 3.603A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 422 removed outlier: 4.215A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 458 removed outlier: 3.609A pdb=" N GLN B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 462 through 486 removed outlier: 3.512A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 510 through 539 removed outlier: 3.888A pdb=" N SER B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 645 through 658 removed outlier: 3.775A pdb=" N LEU B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET B 657 " --> pdb=" O MET B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 710 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 744 through 755 Processing helix chain 'B' and resid 778 through 781 No H-bonds generated for 'chain 'B' and resid 778 through 781' Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 802 through 805 No H-bonds generated for 'chain 'B' and resid 802 through 805' Processing helix chain 'B' and resid 838 through 855 removed outlier: 3.708A pdb=" N LEU B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) Proline residue: B 853 - end of helix Processing helix chain 'B' and resid 866 through 897 removed outlier: 3.527A pdb=" N GLU B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA B 878 " --> pdb=" O SER B 874 " (cutoff:3.500A) Proline residue: B 879 - end of helix removed outlier: 3.666A pdb=" N TYR B 882 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 886 " --> pdb=" O TYR B 882 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 927 removed outlier: 3.973A pdb=" N VAL B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 909 " --> pdb=" O SER B 905 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 910 " --> pdb=" O VAL B 906 " (cutoff:3.500A) Proline residue: B 911 - end of helix removed outlier: 3.565A pdb=" N VAL B 914 " --> pdb=" O VAL B 910 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 917 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 967 Processing helix chain 'B' and resid 971 through 1001 removed outlier: 4.702A pdb=" N ARG B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Proline residue: B 985 - end of helix removed outlier: 3.650A pdb=" N THR B 990 " --> pdb=" O ILE B 986 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) Proline residue: B 999 - end of helix Processing helix chain 'B' and resid 1008 through 1043 removed outlier: 4.267A pdb=" N PHE B1031 " --> pdb=" O PHE B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.576A pdb=" N THR C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.780A pdb=" N GLN C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 113 removed outlier: 4.358A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.645A pdb=" N GLN C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 299 through 316 removed outlier: 4.306A pdb=" N LYS C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 358 removed outlier: 3.723A pdb=" N PHE C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 386 removed outlier: 4.132A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 422 removed outlier: 4.311A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 458 removed outlier: 3.580A pdb=" N GLN C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.816A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.646A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 510 through 538 Processing helix chain 'C' and resid 540 through 559 removed outlier: 3.555A pdb=" N GLN C 559 " --> pdb=" O VAL C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 603 Processing helix chain 'C' and resid 645 through 658 removed outlier: 4.098A pdb=" N ALA C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN C 656 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET C 657 " --> pdb=" O MET C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 710 removed outlier: 3.697A pdb=" N SER C 709 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 710 " --> pdb=" O GLY C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 744 through 754 Processing helix chain 'C' and resid 778 through 781 Processing helix chain 'C' and resid 784 through 789 Processing helix chain 'C' and resid 802 through 805 No H-bonds generated for 'chain 'C' and resid 802 through 805' Processing helix chain 'C' and resid 838 through 855 removed outlier: 4.214A pdb=" N LEU C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Proline residue: C 853 - end of helix Processing helix chain 'C' and resid 866 through 874 removed outlier: 3.616A pdb=" N SER C 874 " --> pdb=" O GLU C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 897 Processing helix chain 'C' and resid 902 through 927 removed outlier: 3.600A pdb=" N LEU C 908 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 909 " --> pdb=" O VAL C 906 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 910 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Proline residue: C 911 - end of helix removed outlier: 4.110A pdb=" N ILE C 915 " --> pdb=" O LEU C 912 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 916 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 920 " --> pdb=" O ALA C 917 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 923 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 924 " --> pdb=" O THR C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 966 Processing helix chain 'C' and resid 971 through 1001 removed outlier: 4.506A pdb=" N ARG C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Proline residue: C 985 - end of helix removed outlier: 3.594A pdb=" N ALA C 992 " --> pdb=" O MET C 988 " (cutoff:3.500A) Proline residue: C 999 - end of helix Processing helix chain 'C' and resid 1008 through 1043 removed outlier: 3.944A pdb=" N PHE C1031 " --> pdb=" O PHE C1027 " (cutoff:3.500A) Proline residue: C1034 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.762A pdb=" N GLN A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 12.706A pdb=" N ARG A 816 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N ASN A 827 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 818 " --> pdb=" O SER A 825 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.517A pdb=" N GLN A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 141 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU A 325 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 143 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP A 323 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.900A pdb=" N ASN A 761 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 774 " --> pdb=" O TYR A 759 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR A 759 " --> pdb=" O VAL A 774 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.648A pdb=" N LYS A 631 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 610 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 629 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A 612 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 627 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 718 through 720 removed outlier: 4.366A pdb=" N ASN A 827 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 725 through 732 Processing sheet with id= G, first strand: chain 'A' and resid 791 through 793 Processing sheet with id= H, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.596A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.736A pdb=" N GLN B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 321 through 325 removed outlier: 3.559A pdb=" N GLU B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.619A pdb=" N TYR B 182 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 771 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN B 761 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 774 " --> pdb=" O TYR B 759 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR B 759 " --> pdb=" O VAL B 774 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.768A pdb=" N LYS B 631 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 610 " --> pdb=" O PHE B 629 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE B 629 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 612 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 627 " --> pdb=" O THR B 612 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER B 614 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA B 625 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 824 through 830 removed outlier: 4.031A pdb=" N SER B 824 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 725 through 732 Processing sheet with id= O, first strand: chain 'B' and resid 791 through 793 Processing sheet with id= P, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.603A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.789A pdb=" N GLN C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 77 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.966A pdb=" N VAL C 769 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N MET C 184 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS C 771 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE C 186 " --> pdb=" O LYS C 771 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 773 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU C 188 " --> pdb=" O TYR C 773 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLN C 775 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 278 through 281 removed outlier: 6.547A pdb=" N LYS C 631 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE C 610 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 629 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR C 612 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 627 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER C 614 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA C 625 " --> pdb=" O SER C 614 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 825 through 830 Processing sheet with id= U, first strand: chain 'C' and resid 725 through 732 Processing sheet with id= V, first strand: chain 'C' and resid 791 through 793 Processing sheet with id= W, first strand: chain 'C' and resid 322 through 328 removed outlier: 6.338A pdb=" N VAL C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP C 328 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU C 137 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 289 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA C 141 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA C 287 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C 288 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 215 through 218 removed outlier: 4.334A pdb=" N VAL C 216 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL C 234 " --> pdb=" O VAL C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.094A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1354 hydrogen bonds defined for protein. 3903 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: 10.34 Time building geometry restraints manager: 11.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4015 1.31 - 1.44: 6301 1.44 - 1.56: 13909 1.56 - 1.69: 19 1.69 - 1.81: 198 Bond restraints: 24442 Sorted by residual: bond pdb=" C04 80P C1101 " pdb=" C21 80P C1101 " ideal model delta sigma weight residual 1.360 1.675 -0.315 2.00e-02 2.50e+03 2.48e+02 bond pdb=" C08 80P C1101 " pdb=" C09 80P C1101 " ideal model delta sigma weight residual 1.332 1.647 -0.315 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C11 80P C1101 " pdb=" C12 80P C1101 " ideal model delta sigma weight residual 1.240 1.554 -0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C09 80P C1101 " pdb=" C10 80P C1101 " ideal model delta sigma weight residual 1.097 1.374 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C26 80P C1101 " pdb=" C30 80P C1101 " ideal model delta sigma weight residual 1.293 1.553 -0.260 2.00e-02 2.50e+03 1.70e+02 ... (remaining 24437 not shown) Histogram of bond angle deviations from ideal: 97.01 - 105.07: 629 105.07 - 113.12: 12617 113.12 - 121.17: 14406 121.17 - 129.23: 5441 129.23 - 137.28: 154 Bond angle restraints: 33247 Sorted by residual: angle pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 110.42 122.13 -11.71 9.60e-01 1.09e+00 1.49e+02 angle pdb=" N LYS C 796 " pdb=" CA LYS C 796 " pdb=" C LYS C 796 " ideal model delta sigma weight residual 113.30 97.52 15.78 1.34e+00 5.57e-01 1.39e+02 angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 110.72 120.59 -9.87 1.01e+00 9.80e-01 9.54e+01 angle pdb=" N GLN A 276 " pdb=" CA GLN A 276 " pdb=" C GLN A 276 " ideal model delta sigma weight residual 111.36 121.72 -10.36 1.09e+00 8.42e-01 9.03e+01 angle pdb=" N ALA A 236 " pdb=" CA ALA A 236 " pdb=" C ALA A 236 " ideal model delta sigma weight residual 108.00 121.88 -13.88 1.48e+00 4.57e-01 8.79e+01 ... (remaining 33242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 14055 26.60 - 53.19: 457 53.19 - 79.78: 39 79.78 - 106.38: 0 106.38 - 132.97: 1 Dihedral angle restraints: 14552 sinusoidal: 5571 harmonic: 8981 Sorted by residual: dihedral pdb=" C VAL A 172 " pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" CB VAL A 172 " ideal model delta harmonic sigma weight residual -122.00 -136.68 14.68 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C VAL C 454 " pdb=" N VAL C 454 " pdb=" CA VAL C 454 " pdb=" CB VAL C 454 " ideal model delta harmonic sigma weight residual -122.00 -135.39 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N VAL C 454 " pdb=" C VAL C 454 " pdb=" CA VAL C 454 " pdb=" CB VAL C 454 " ideal model delta harmonic sigma weight residual 123.40 136.50 -13.10 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 14549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.123: 3912 1.123 - 2.246: 0 2.246 - 3.368: 0 3.368 - 4.491: 0 4.491 - 5.614: 1 Chirality restraints: 3913 Sorted by residual: chirality pdb=" C08 80P C1101 " pdb=" C07 80P C1101 " pdb=" C09 80P C1101 " pdb=" C21 80P C1101 " both_signs ideal model delta sigma weight residual False 2.49 -3.13 5.61 2.00e-01 2.50e+01 7.88e+02 chirality pdb=" CA LEU C 852 " pdb=" N LEU C 852 " pdb=" C LEU C 852 " pdb=" CB LEU C 852 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA ALA B 222 " pdb=" N ALA B 222 " pdb=" C ALA B 222 " pdb=" CB ALA B 222 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 3910 not shown) Planarity restraints: 4261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 233 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C THR C 233 " -0.059 2.00e-02 2.50e+03 pdb=" O THR C 233 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL C 234 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 926 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE B 926 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE B 926 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 927 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 852 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO C 853 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 853 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 853 " 0.049 5.00e-02 4.00e+02 ... (remaining 4258 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7095 2.81 - 3.34: 23315 3.34 - 3.86: 40601 3.86 - 4.38: 49790 4.38 - 4.90: 79622 Nonbonded interactions: 200423 Sorted by model distance: nonbonded pdb=" N LYS C 796 " pdb=" N GLY C 797 " model vdw 2.293 2.560 nonbonded pdb=" N GLN B 775 " pdb=" O GLN B 775 " model vdw 2.395 2.496 nonbonded pdb=" N ASN C 509 " pdb=" O ASN C 509 " model vdw 2.412 2.496 nonbonded pdb=" N GLY A 756 " pdb=" O GLY A 756 " model vdw 2.433 2.496 nonbonded pdb=" OG1 THR B 589 " pdb=" O GLN B 623 " model vdw 2.455 2.440 ... (remaining 200418 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 1045) selection = chain 'B' selection = (chain 'C' and resid 1 through 1045) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.100 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: 0.010 Extract box with map and model: 3.100 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 63.020 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.012 0.315 24442 Z= 0.807 Angle : 1.585 23.530 33247 Z= 1.073 Chirality : 0.144 5.614 3913 Planarity : 0.009 0.083 4261 Dihedral : 12.549 132.974 8788 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.37 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.49 % 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: 0.46 (0.14), residues: 3134 helix: 0.66 (0.12), residues: 1720 sheet: 0.86 (0.23), residues: 453 loop : -0.43 (0.19), residues: 961 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 720 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 21 residues processed: 775 average time/residue: 1.0928 time to fit residues: 1001.0250 Evaluate side-chains 571 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 550 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 5 average time/residue: 0.5871 time to fit residues: 7.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 283 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 87 GLN A 104 GLN A 108 GLN A 125 GLN A 231 ASN A 274 ASN A 298 ASN A 308 GLN A 531 ASN A 559 GLN A 669 GLN B 87 GLN B 108 GLN B 138 GLN B 391 ASN B 415 ASN B 729 GLN B 731 ASN C 123 GLN C 125 GLN C 138 GLN C 274 ASN C 531 ASN C 795 ASN C 829 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 24442 Z= 0.248 Angle : 0.690 25.595 33247 Z= 0.345 Chirality : 0.054 1.940 3913 Planarity : 0.006 0.062 4261 Dihedral : 5.679 113.565 3334 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 4.87 % 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: 1.34 (0.14), residues: 3134 helix: 1.55 (0.12), residues: 1707 sheet: 0.81 (0.24), residues: 423 loop : -0.11 (0.19), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 590 time to evaluate : 2.670 Fit side-chains revert: symmetry clash outliers start: 126 outliers final: 41 residues processed: 665 average time/residue: 1.0525 time to fit residues: 834.6086 Evaluate side-chains 565 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 524 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 33 residues processed: 10 average time/residue: 0.3848 time to fit residues: 9.6129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 68 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 208 GLN A 241 GLN A 316 ASN A 749 ASN B 87 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN B 415 ASN C 93 ASN C 138 GLN C 148 ASN C 176 GLN C 274 ASN C 531 ASN C 579 GLN C 795 ASN C 829 GLN C 953 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.107 24442 Z= 0.361 Angle : 0.713 23.491 33247 Z= 0.356 Chirality : 0.056 2.069 3913 Planarity : 0.005 0.053 4261 Dihedral : 5.624 108.379 3334 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 6.07 % 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: 1.38 (0.15), residues: 3134 helix: 1.66 (0.12), residues: 1706 sheet: 0.49 (0.24), residues: 453 loop : -0.09 (0.20), residues: 975 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 541 time to evaluate : 2.752 Fit side-chains revert: symmetry clash outliers start: 157 outliers final: 76 residues processed: 629 average time/residue: 1.0479 time to fit residues: 788.4287 Evaluate side-chains 596 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 520 time to evaluate : 2.519 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 49 residues processed: 29 average time/residue: 0.7392 time to fit residues: 30.6191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 147 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 208 GLN A 241 GLN A 722 GLN A 749 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 415 ASN C 148 ASN C 176 GLN C 274 ASN C 531 ASN C 583 ASN C 795 ASN C 953 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 24442 Z= 0.240 Angle : 0.644 23.558 33247 Z= 0.310 Chirality : 0.053 1.998 3913 Planarity : 0.005 0.053 4261 Dihedral : 5.447 105.460 3334 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 5.22 % 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 (0.15), residues: 3134 helix: 1.93 (0.12), residues: 1697 sheet: 0.41 (0.23), residues: 455 loop : -0.04 (0.20), residues: 982 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 547 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 80 residues processed: 632 average time/residue: 1.0886 time to fit residues: 823.6413 Evaluate side-chains 599 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 519 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 61 residues processed: 22 average time/residue: 0.4731 time to fit residues: 18.6734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 224 optimal weight: 0.0000 chunk 124 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 208 GLN A 977 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 148 ASN C 274 ASN C 531 ASN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 24442 Z= 0.289 Angle : 0.668 23.743 33247 Z= 0.322 Chirality : 0.053 1.992 3913 Planarity : 0.005 0.053 4261 Dihedral : 5.453 104.003 3334 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 5.45 % 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: 1.57 (0.15), residues: 3134 helix: 1.92 (0.12), residues: 1696 sheet: 0.41 (0.24), residues: 445 loop : -0.11 (0.20), residues: 993 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 528 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 96 residues processed: 614 average time/residue: 1.0716 time to fit residues: 790.1354 Evaluate side-chains 618 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 522 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 70 residues processed: 28 average time/residue: 0.3668 time to fit residues: 19.5451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 138 GLN A 208 GLN A 241 GLN A 722 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 795 ASN C 829 GLN C 953 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 24442 Z= 0.342 Angle : 0.694 23.805 33247 Z= 0.336 Chirality : 0.055 1.983 3913 Planarity : 0.005 0.058 4261 Dihedral : 5.544 103.732 3334 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 5.56 % 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: 1.41 (0.15), residues: 3134 helix: 1.79 (0.12), residues: 1699 sheet: 0.38 (0.24), residues: 435 loop : -0.23 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 530 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 92 residues processed: 625 average time/residue: 1.1022 time to fit residues: 820.3280 Evaluate side-chains 609 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 517 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 69 residues processed: 27 average time/residue: 0.4853 time to fit residues: 22.4264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0040 chunk 34 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 254 optimal weight: 0.0870 chunk 168 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN A 208 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 274 ASN C 531 ASN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24442 Z= 0.196 Angle : 0.635 23.355 33247 Z= 0.300 Chirality : 0.052 2.026 3913 Planarity : 0.004 0.051 4261 Dihedral : 5.277 103.178 3334 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 4.33 % 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: 1.72 (0.15), residues: 3134 helix: 2.10 (0.12), residues: 1694 sheet: 0.38 (0.24), residues: 443 loop : -0.12 (0.19), residues: 997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 538 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 76 residues processed: 615 average time/residue: 1.0935 time to fit residues: 805.4752 Evaluate side-chains 590 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 514 time to evaluate : 2.932 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 66 residues processed: 13 average time/residue: 0.5802 time to fit residues: 14.3456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 191 optimal weight: 0.0270 chunk 204 optimal weight: 0.3980 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 236 optimal weight: 0.8980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 722 GLN B 108 GLN B 112 GLN B 384 ASN B 720 ASN B 827 ASN C 148 ASN C 274 ASN C 415 ASN C 531 ASN C 598 ASN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN C 953 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 24442 Z= 0.151 Angle : 0.617 23.568 33247 Z= 0.287 Chirality : 0.052 2.031 3913 Planarity : 0.004 0.050 4261 Dihedral : 5.042 103.051 3334 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 3.75 % 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: 1.93 (0.15), residues: 3134 helix: 2.30 (0.12), residues: 1695 sheet: 0.44 (0.24), residues: 450 loop : -0.07 (0.20), residues: 989 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 540 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 66 residues processed: 609 average time/residue: 1.0689 time to fit residues: 780.8933 Evaluate side-chains 574 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 508 time to evaluate : 2.485 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 55 residues processed: 14 average time/residue: 0.6487 time to fit residues: 15.8402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 7.9990 chunk 288 optimal weight: 0.0040 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 265 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 208 GLN B 720 ASN B 827 ASN C 138 GLN C 148 ASN C 274 ASN C 531 ASN C 598 ASN C 795 ASN C 953 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 24442 Z= 0.282 Angle : 0.684 23.779 33247 Z= 0.324 Chirality : 0.054 1.991 3913 Planarity : 0.005 0.048 4261 Dihedral : 5.282 103.703 3334 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.71 (0.15), residues: 3134 helix: 2.07 (0.12), residues: 1697 sheet: 0.45 (0.24), residues: 442 loop : -0.11 (0.20), residues: 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 523 time to evaluate : 2.750 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 66 residues processed: 585 average time/residue: 1.1395 time to fit residues: 793.0195 Evaluate side-chains 576 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 510 time to evaluate : 2.724 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 56 residues processed: 13 average time/residue: 0.6851 time to fit residues: 15.0748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 286 optimal weight: 0.6980 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 191 optimal weight: 50.0000 chunk 151 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 208 GLN A 722 GLN B 720 ASN B 827 ASN C 148 ASN C 274 ASN C 531 ASN C 598 ASN C 795 ASN C 953 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 24442 Z= 0.305 Angle : 0.700 23.896 33247 Z= 0.334 Chirality : 0.055 1.993 3913 Planarity : 0.005 0.048 4261 Dihedral : 5.405 103.626 3334 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.67 % 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: 1.50 (0.15), residues: 3134 helix: 1.91 (0.12), residues: 1692 sheet: 0.35 (0.24), residues: 444 loop : -0.20 (0.19), residues: 998 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 522 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 61 residues processed: 580 average time/residue: 1.1336 time to fit residues: 785.7759 Evaluate side-chains 582 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 521 time to evaluate : 2.758 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 55 residues processed: 8 average time/residue: 0.4383 time to fit residues: 9.2226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 254 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN B 827 ASN C 148 ASN C 274 ASN C 531 ASN C 598 ASN C 795 ASN C 953 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.160457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.130180 restraints weight = 25406.653| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.26 r_work: 0.3093 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 24442 Z= 0.252 Angle : 0.677 23.994 33247 Z= 0.321 Chirality : 0.054 2.009 3913 Planarity : 0.005 0.048 4261 Dihedral : 5.332 103.557 3334 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.67 % 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: 1.55 (0.15), residues: 3134 helix: 1.96 (0.12), residues: 1693 sheet: 0.32 (0.24), residues: 441 loop : -0.18 (0.19), residues: 1000 =============================================================================== Job complete usr+sys time: 11026.86 seconds wall clock time: 195 minutes 31.84 seconds (11731.84 seconds total)