Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 20 17:33:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgt_10184/07_2023/6sgt_10184_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgt_10184/07_2023/6sgt_10184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgt_10184/07_2023/6sgt_10184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgt_10184/07_2023/6sgt_10184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgt_10184/07_2023/6sgt_10184_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgt_10184/07_2023/6sgt_10184_neut.pdb" } resolution = 3.46 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= 0.009 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 134 5.16 5 C 16626 2.51 5 N 4294 2.21 5 O 4827 1.98 5 H 26299 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 810": "OE1" <-> "OE2" Residue "C GLU 640": "OE1" <-> "OE2" Residue "C ARG 792": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1032": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 52180 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 15858 Classifications: {'peptide': 1034} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 988} Chain: "B" Number of atoms: 15849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15849 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 45, 'TRANS': 987} Chain: "D" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2336 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2287 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Time building chain proxies: 18.97, per 1000 atoms: 0.36 Number of scatterers: 52180 At special positions: 0 Unit cell: (151.723, 132.625, 144.296, 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 134 16.00 O 4827 8.00 N 4294 7.00 C 16626 6.00 H 26299 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.01 Conformation dependent library (CDL) restraints added in 3.7 seconds 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6224 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 23 sheets defined 55.5% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 8 through 28 removed outlier: 4.075A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.543A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.669A pdb=" N GLN A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.715A pdb=" N THR A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.722A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 359 removed outlier: 3.679A pdb=" N THR A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.635A pdb=" N THR A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.647A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 4.458A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 463 through 488 removed outlier: 4.224A pdb=" N TYR A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.741A pdb=" N GLU A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 509 " --> pdb=" O GLY A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 538 removed outlier: 4.045A pdb=" N TRP A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 removed outlier: 3.893A pdb=" N VAL A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 removed outlier: 3.845A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.631A pdb=" N SER A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 708 removed outlier: 4.430A pdb=" N ALA A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 837 through 849 Processing helix chain 'A' and resid 860 through 868 removed outlier: 4.849A pdb=" N GLU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 893 removed outlier: 5.141A pdb=" N ILE A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 903 removed outlier: 4.246A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 919 removed outlier: 4.391A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 912 " --> pdb=" O GLY A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 956 removed outlier: 3.783A pdb=" N LEU A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 991 removed outlier: 3.503A pdb=" N ALA A 963 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 968 " --> pdb=" O THR A 964 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 996 through 1009 removed outlier: 3.990A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1018 removed outlier: 3.552A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1033 removed outlier: 4.023A pdb=" N VAL A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A1033 " --> pdb=" O VAL A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.751A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.675A pdb=" N VAL B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 150 through 160 removed outlier: 4.134A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.953A pdb=" N LYS B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.719A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.535A pdb=" N ALA B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 removed outlier: 4.213A pdb=" N ILE B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 386 removed outlier: 4.480A 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 391 through 400 removed outlier: 3.619A pdb=" N MET B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 423 removed outlier: 3.746A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 3.767A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.834A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 488 removed outlier: 4.031A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 511 through 537 removed outlier: 3.671A pdb=" N TRP B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 556 Processing helix chain 'B' and resid 583 through 601 removed outlier: 3.745A pdb=" N THR B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.265A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 Processing helix chain 'B' and resid 733 through 738 removed outlier: 3.758A pdb=" N GLN B 737 " --> pdb=" O GLN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.634A pdb=" N THR B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 785 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 836 through 845 removed outlier: 3.826A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 removed outlier: 3.595A pdb=" N LYS B 850 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 851 " --> pdb=" O ALA B 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 847 through 851' Processing helix chain 'B' and resid 861 through 868 removed outlier: 3.936A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 867 " --> pdb=" O SER B 863 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 868 " --> pdb=" O TYR B 864 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 861 through 868' Processing helix chain 'B' and resid 872 through 893 Processing helix chain 'B' and resid 897 through 903 removed outlier: 4.230A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 919 removed outlier: 3.760A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 955 removed outlier: 3.553A pdb=" N LEU B 944 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE B 945 " --> pdb=" O ASN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 992 removed outlier: 4.711A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 996 through 1017 removed outlier: 4.045A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1033 removed outlier: 3.596A pdb=" N VAL B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.673A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.731A pdb=" N GLN C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.596A pdb=" N ASN C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.757A pdb=" N ALA C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 337 through 359 Processing helix chain 'C' and resid 361 through 386 removed outlier: 4.542A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.642A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.610A pdb=" N GLY C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.314A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 removed outlier: 4.064A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 452 removed outlier: 3.799A pdb=" N GLY C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 438 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 485 removed outlier: 4.022A pdb=" N ALA C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 493 removed outlier: 4.020A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 535 removed outlier: 3.684A pdb=" N TRP C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 558 Processing helix chain 'C' and resid 583 through 601 removed outlier: 3.560A pdb=" N THR C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 655 Processing helix chain 'C' and resid 691 through 708 removed outlier: 3.514A pdb=" N LEU C 695 " --> pdb=" O GLY C 691 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 708 " --> pdb=" O ALA C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.093A pdb=" N LEU C 750 " --> pdb=" O ILE C 746 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 787 Processing helix chain 'C' and resid 802 through 804 No H-bonds generated for 'chain 'C' and resid 802 through 804' Processing helix chain 'C' and resid 836 through 850 removed outlier: 3.636A pdb=" N ALA C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 880 removed outlier: 3.567A pdb=" N GLN C 865 " --> pdb=" O GLY C 861 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 867 " --> pdb=" O SER C 863 " (cutoff:3.500A) Proline residue: C 874 - end of helix removed outlier: 3.697A pdb=" N ALA C 878 " --> pdb=" O PRO C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 893 removed outlier: 3.640A pdb=" N CYS C 887 " --> pdb=" O VAL C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 903 removed outlier: 3.832A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 919 removed outlier: 3.951A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 919 " --> pdb=" O ALA C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 955 removed outlier: 4.306A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 971 through 985 Processing helix chain 'C' and resid 986 through 991 removed outlier: 3.513A pdb=" N VAL C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1017 removed outlier: 4.485A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C1016 " --> pdb=" O VAL C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing helix chain 'D' and resid 14 through 25 removed outlier: 3.580A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.088A pdb=" N LEU D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.580A pdb=" N LEU D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 4.232A pdb=" N VAL D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.592A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 148 through 156 removed outlier: 3.583A pdb=" N ILE D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 165 removed outlier: 3.827A pdb=" N LEU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.632A pdb=" N GLU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 37 Processing helix chain 'E' and resid 49 through 58 Processing helix chain 'E' and resid 59 through 67 removed outlier: 3.921A pdb=" N VAL E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 4.025A pdb=" N PHE E 90 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.566A pdb=" N GLU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.566A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.523A pdb=" N ILE E 152 " --> pdb=" O THR E 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 165 removed outlier: 3.732A pdb=" N LEU E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.601A pdb=" N SER A 80 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 824 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.677A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.677A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 286 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 removed outlier: 5.820A pdb=" N ILE A 235 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 731 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.899A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 717 through 718 removed outlier: 3.666A pdb=" N ASP A 858 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 805 through 812 removed outlier: 4.165A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 760 through 764 removed outlier: 4.293A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 131 removed outlier: 3.517A pdb=" N GLU B 130 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 43 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B 93 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 80 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 12.335A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP B 681 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.217A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.217A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 286 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 608 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 266 through 271 removed outlier: 6.341A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.201A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 232 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.617A pdb=" N SER C 80 " --> pdb=" O ARG C 818 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP C 681 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.798A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 267 through 269 removed outlier: 6.124A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 252 through 253 removed outlier: 3.688A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.388A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 573 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 790 through 792 1397 hydrogen bonds defined for protein. 4005 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: 22.49 Time building geometry restraints manager: 39.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26293 1.03 - 1.22: 15 1.22 - 1.42: 10636 1.42 - 1.61: 15462 1.61 - 1.81: 262 Bond restraints: 52668 Sorted by residual: bond pdb=" C ASP B 407 " pdb=" O ASP B 407 " ideal model delta sigma weight residual 1.237 1.162 0.074 1.19e-02 7.06e+03 3.91e+01 bond pdb=" C ASP B 164 " pdb=" O ASP B 164 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.16e-02 7.43e+03 3.86e+01 bond pdb=" C MET B 355 " pdb=" O MET B 355 " ideal model delta sigma weight residual 1.236 1.166 0.070 1.29e-02 6.01e+03 2.92e+01 bond pdb=" C TYR A 545 " pdb=" O TYR A 545 " ideal model delta sigma weight residual 1.237 1.192 0.044 1.17e-02 7.31e+03 1.43e+01 bond pdb=" C ALA B 26 " pdb=" O ALA B 26 " ideal model delta sigma weight residual 1.235 1.188 0.046 1.25e-02 6.40e+03 1.37e+01 ... (remaining 52663 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.82: 589 105.82 - 112.89: 62775 112.89 - 119.95: 14499 119.95 - 127.01: 17426 127.01 - 134.07: 242 Bond angle restraints: 95531 Sorted by residual: angle pdb=" CA TYR A 545 " pdb=" C TYR A 545 " pdb=" O TYR A 545 " ideal model delta sigma weight residual 120.55 114.27 6.28 1.06e+00 8.90e-01 3.51e+01 angle pdb=" N ILE D 62 " pdb=" CA ILE D 62 " pdb=" C ILE D 62 " ideal model delta sigma weight residual 111.62 107.42 4.20 7.90e-01 1.60e+00 2.82e+01 angle pdb=" N ILE C 827 " pdb=" CA ILE C 827 " pdb=" C ILE C 827 " ideal model delta sigma weight residual 113.53 108.43 5.10 9.80e-01 1.04e+00 2.71e+01 angle pdb=" C ASP B 164 " pdb=" N ALA B 165 " pdb=" CA ALA B 165 " ideal model delta sigma weight residual 120.44 126.42 -5.98 1.30e+00 5.92e-01 2.12e+01 angle pdb=" CA TYR B 811 " pdb=" C TYR B 811 " pdb=" O TYR B 811 " ideal model delta sigma weight residual 121.58 116.75 4.83 1.12e+00 7.97e-01 1.86e+01 ... (remaining 95526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 18862 17.39 - 34.77: 1713 34.77 - 52.16: 215 52.16 - 69.55: 38 69.55 - 86.94: 10 Dihedral angle restraints: 20838 sinusoidal: 9645 harmonic: 11193 Sorted by residual: dihedral pdb=" CA PHE A 388 " pdb=" C PHE A 388 " pdb=" N SER A 389 " pdb=" CA SER A 389 " ideal model delta harmonic sigma weight residual 180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ALA A 832 " pdb=" C ALA A 832 " pdb=" N PRO A 833 " pdb=" CA PRO A 833 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PHE B 804 " pdb=" C PHE B 804 " pdb=" N SER B 805 " pdb=" CA SER B 805 " ideal model delta harmonic sigma weight residual -180.00 -154.23 -25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 20835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3336 0.045 - 0.091: 669 0.091 - 0.136: 195 0.136 - 0.181: 10 0.181 - 0.227: 2 Chirality restraints: 4212 Sorted by residual: chirality pdb=" CA TYR B 811 " pdb=" N TYR B 811 " pdb=" C TYR B 811 " pdb=" CB TYR B 811 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B1019 " pdb=" CA ILE B1019 " pdb=" CG1 ILE B1019 " pdb=" CG2 ILE B1019 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA LEU A 219 " pdb=" N LEU A 219 " pdb=" C LEU A 219 " pdb=" CB LEU A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 4209 not shown) Planarity restraints: 7858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 27 " -0.033 2.00e-02 2.50e+03 6.48e-02 4.20e+01 pdb=" N ASP E 28 " 0.111 2.00e-02 2.50e+03 pdb=" CA ASP E 28 " -0.028 2.00e-02 2.50e+03 pdb=" H ASP E 28 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 535 " 0.023 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" N ARG A 536 " -0.076 2.00e-02 2.50e+03 pdb=" CA ARG A 536 " 0.020 2.00e-02 2.50e+03 pdb=" H ARG A 536 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 164 " 0.022 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" N ALA C 165 " -0.072 2.00e-02 2.50e+03 pdb=" CA ALA C 165 " 0.019 2.00e-02 2.50e+03 pdb=" H ALA C 165 " 0.031 2.00e-02 2.50e+03 ... (remaining 7855 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2064 2.16 - 2.77: 103970 2.77 - 3.38: 145639 3.38 - 3.99: 189719 3.99 - 4.60: 301607 Nonbonded interactions: 742999 Sorted by model distance: nonbonded pdb=" OE1 GLU E 127 " pdb=" H GLU E 127 " model vdw 1.549 1.850 nonbonded pdb=" OE1 GLU E 94 " pdb=" H GLU E 94 " model vdw 1.602 1.850 nonbonded pdb="HE21 GLN B 181 " pdb=" OE2 GLU B 273 " model vdw 1.604 1.850 nonbonded pdb=" O GLY A 766 " pdb="HE22 GLN B 63 " model vdw 1.612 1.850 nonbonded pdb=" O ILE A 235 " pdb=" H ILE B 729 " model vdw 1.615 1.850 ... (remaining 742994 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 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 146 through 1033)) selection = (chain 'B' and (resid 1 through 355 or (resid 356 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD \ 1 or name HD2 or name HE1 or name HE2)) or resid 357 through 666 or (resid 667 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3)) or resid 668 through 1033 \ )) selection = (chain 'C' and (resid 1 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 146 through 355 or (resid 356 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA or n \ ame HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2)) or resid 3 \ 57 through 666 or (resid 667 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name H \ B3)) or resid 668 through 1033)) } ncs_group { reference = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 16 through 166)) selection = chain 'E' } 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: 1.370 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: 0.590 Extract box with map and model: 9.620 Check model and map are aligned: 0.720 Set scattering table: 0.400 Process input model: 135.470 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.004 0.074 26369 Z= 0.281 Angle : 0.721 6.702 35814 Z= 0.447 Chirality : 0.040 0.227 4212 Planarity : 0.004 0.041 4596 Dihedral : 12.561 86.936 9508 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -4.71 (0.11), residues: 3398 helix: -2.87 (0.09), residues: 1761 sheet: -2.73 (0.21), residues: 411 loop : -3.38 (0.14), residues: 1226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 796 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 788 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 794 average time/residue: 0.9330 time to fit residues: 1123.3651 Evaluate side-chains 479 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 3.303 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4668 time to fit residues: 4.7005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 7.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 307 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 642 ASN A 667 ASN A 846 GLN ** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 284 GLN B 697 GLN B 700 ASN C 161 ASN C 191 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 298 ASN C 360 GLN C 415 ASN C 526 HIS C 605 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN C1001 ASN D 102 ASN D 156 ASN E 74 ASN E 102 ASN E 166 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 26369 Z= 0.307 Angle : 0.637 10.178 35814 Z= 0.340 Chirality : 0.043 0.168 4212 Planarity : 0.004 0.046 4596 Dihedral : 5.267 29.124 3609 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -3.06 (0.13), residues: 3398 helix: -1.37 (0.11), residues: 1778 sheet: -2.23 (0.22), residues: 434 loop : -2.78 (0.16), residues: 1186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 542 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 493 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 34 residues processed: 531 average time/residue: 0.7594 time to fit residues: 644.2935 Evaluate side-chains 464 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 430 time to evaluate : 3.602 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.5964 time to fit residues: 41.0286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 308 optimal weight: 0.0980 chunk 333 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN B 569 GLN C 63 GLN C 67 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C 657 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 26369 Z= 0.260 Angle : 0.590 6.108 35814 Z= 0.311 Chirality : 0.042 0.168 4212 Planarity : 0.004 0.050 4596 Dihedral : 5.009 26.959 3609 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -2.14 (0.14), residues: 3398 helix: -0.57 (0.12), residues: 1798 sheet: -1.97 (0.22), residues: 431 loop : -2.39 (0.17), residues: 1169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 468 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 479 average time/residue: 0.7507 time to fit residues: 576.7147 Evaluate side-chains 429 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 414 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5338 time to fit residues: 18.4270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 327 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 293 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 865 GLN B 719 ASN C 67 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 26369 Z= 0.217 Angle : 0.567 11.333 35814 Z= 0.297 Chirality : 0.041 0.162 4212 Planarity : 0.003 0.053 4596 Dihedral : 4.777 25.380 3609 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -1.59 (0.14), residues: 3398 helix: -0.11 (0.12), residues: 1803 sheet: -1.81 (0.23), residues: 425 loop : -2.13 (0.17), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 443 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 458 average time/residue: 0.7155 time to fit residues: 526.1640 Evaluate side-chains 419 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 406 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5926 time to fit residues: 17.7889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.0670 chunk 186 optimal weight: 0.0570 chunk 4 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 279 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN C 63 GLN C 213 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 166 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 26369 Z= 0.209 Angle : 0.551 7.215 35814 Z= 0.288 Chirality : 0.040 0.159 4212 Planarity : 0.003 0.054 4596 Dihedral : 4.672 25.298 3609 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -1.30 (0.14), residues: 3398 helix: 0.11 (0.13), residues: 1815 sheet: -1.68 (0.23), residues: 430 loop : -1.98 (0.18), residues: 1153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 426 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 438 average time/residue: 0.7912 time to fit residues: 556.4553 Evaluate side-chains 416 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 406 time to evaluate : 3.774 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6293 time to fit residues: 16.1363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN C 213 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 26369 Z= 0.248 Angle : 0.565 10.765 35814 Z= 0.296 Chirality : 0.041 0.225 4212 Planarity : 0.003 0.058 4596 Dihedral : 4.654 25.808 3609 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -1.10 (0.15), residues: 3398 helix: 0.28 (0.13), residues: 1818 sheet: -1.64 (0.23), residues: 424 loop : -1.88 (0.18), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 452 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 423 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 444 average time/residue: 0.7511 time to fit residues: 533.9420 Evaluate side-chains 419 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 398 time to evaluate : 2.961 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5453 time to fit residues: 24.0158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 276 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 326 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 26369 Z= 0.313 Angle : 0.589 6.669 35814 Z= 0.311 Chirality : 0.042 0.165 4212 Planarity : 0.003 0.059 4596 Dihedral : 4.749 26.759 3609 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3398 helix: 0.27 (0.13), residues: 1812 sheet: -1.70 (0.23), residues: 427 loop : -1.81 (0.18), residues: 1159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 412 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 426 average time/residue: 0.7250 time to fit residues: 494.6580 Evaluate side-chains 406 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 391 time to evaluate : 2.949 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.4868 time to fit residues: 17.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 0.0050 chunk 207 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN B 391 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 26369 Z= 0.218 Angle : 0.560 12.824 35814 Z= 0.292 Chirality : 0.041 0.159 4212 Planarity : 0.003 0.055 4596 Dihedral : 4.619 26.317 3609 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -0.87 (0.15), residues: 3398 helix: 0.44 (0.13), residues: 1813 sheet: -1.63 (0.24), residues: 403 loop : -1.68 (0.18), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 438 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 419 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 431 average time/residue: 0.7370 time to fit residues: 505.1456 Evaluate side-chains 411 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 400 time to evaluate : 2.983 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.5005 time to fit residues: 13.9186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 312 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 275 optimal weight: 8.9990 chunk 287 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN B 58 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 26369 Z= 0.196 Angle : 0.544 10.447 35814 Z= 0.283 Chirality : 0.040 0.159 4212 Planarity : 0.003 0.057 4596 Dihedral : 4.508 25.630 3609 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -0.68 (0.15), residues: 3398 helix: 0.58 (0.13), residues: 1814 sheet: -1.52 (0.24), residues: 407 loop : -1.60 (0.18), residues: 1177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 429 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 434 average time/residue: 0.7277 time to fit residues: 508.0833 Evaluate side-chains 412 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 409 time to evaluate : 3.798 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.5049 time to fit residues: 6.5798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 0.4980 chunk 199 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN B 391 ASN B 588 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS E 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 26369 Z= 0.324 Angle : 0.597 10.566 35814 Z= 0.314 Chirality : 0.042 0.168 4212 Planarity : 0.003 0.060 4596 Dihedral : 4.651 26.588 3609 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -0.83 (0.15), residues: 3398 helix: 0.46 (0.13), residues: 1809 sheet: -1.62 (0.23), residues: 430 loop : -1.64 (0.18), residues: 1159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 416 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 422 average time/residue: 0.7198 time to fit residues: 483.1601 Evaluate side-chains 411 residues out of total 2755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 405 time to evaluate : 2.946 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.4675 time to fit residues: 8.9450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 269 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117695 restraints weight = 103801.692| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.42 r_work: 0.3200 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 26369 Z= 0.276 Angle : 0.580 10.624 35814 Z= 0.304 Chirality : 0.042 0.163 4212 Planarity : 0.003 0.060 4596 Dihedral : 4.638 26.677 3609 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -0.76 (0.15), residues: 3398 helix: 0.53 (0.13), residues: 1814 sheet: -1.64 (0.24), residues: 414 loop : -1.61 (0.18), residues: 1170 =============================================================================== Job complete usr+sys time: 10852.99 seconds wall clock time: 188 minutes 54.21 seconds (11334.21 seconds total)