Starting phenix.real_space_refine on Wed Nov 20 07:24:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sli_40578/11_2024/8sli_40578.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sli_40578/11_2024/8sli_40578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sli_40578/11_2024/8sli_40578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sli_40578/11_2024/8sli_40578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sli_40578/11_2024/8sli_40578.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sli_40578/11_2024/8sli_40578.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 Ca 8 9.91 5 S 40 5.16 5 C 13156 2.51 5 N 3876 2.21 5 O 3916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20996 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 5247 Classifications: {'peptide': 894} Incomplete info: {'truncation_to_alanine': 553} Link IDs: {'PTRANS': 34, 'TRANS': 859} Chain breaks: 17 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 2109 Unresolved non-hydrogen angles: 2702 Unresolved non-hydrogen dihedrals: 1753 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 36, 'TYR:plan': 16, 'ASN:plan1': 13, 'TRP:plan': 12, 'HIS:plan': 13, 'PHE:plan': 34, 'GLU:plan': 48, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 1164 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 12.79, per 1000 atoms: 0.61 Number of scatterers: 20996 At special positions: 0 Unit cell: (151.2, 151.2, 148.96, 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) Ca 8 19.99 S 40 16.00 O 3916 8.00 N 3876 7.00 C 13156 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 - 3.00 Amino acid : True - 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: 6.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 16 sheets defined 75.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 81 through 100 removed outlier: 4.569A pdb=" N VAL A 87 " --> pdb=" O TRP A 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.759A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.407A pdb=" N ARG A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.717A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL A 300 " --> pdb=" O TRP A 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.875A pdb=" N LEU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 443 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.574A pdb=" N SER A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 600 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.659A pdb=" N GLN A 629 " --> pdb=" O HIS A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 removed outlier: 3.607A pdb=" N CYS A 655 " --> pdb=" O GLY A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 717 through 728 Processing helix chain 'A' and resid 729 through 755 Processing helix chain 'A' and resid 760 through 787 removed outlier: 3.571A pdb=" N SER A 764 " --> pdb=" O PRO A 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 804 removed outlier: 4.135A pdb=" N ASP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 821 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.286A pdb=" N MET A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA A 853 " --> pdb=" O HIS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 895 removed outlier: 3.651A pdb=" N VAL A 872 " --> pdb=" O MET A 868 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.545A pdb=" N ARG A 907 " --> pdb=" O TRP A 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Proline residue: A 912 - end of helix removed outlier: 4.487A pdb=" N ILE A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 950 through 983 removed outlier: 3.660A pdb=" N MET A 970 " --> pdb=" O ASN A 966 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 974 " --> pdb=" O MET A 970 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL A 983 " --> pdb=" O TYR A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1006 Processing helix chain 'A' and resid 1010 through 1028 removed outlier: 4.041A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A1028 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1071 Processing helix chain 'A' and resid 1072 through 1092 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 81 through 100 removed outlier: 4.569A pdb=" N VAL D 87 " --> pdb=" O TRP D 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.758A pdb=" N ALA D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 238 through 250 removed outlier: 4.407A pdb=" N ARG D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 271 removed outlier: 3.716A pdb=" N VAL D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL D 300 " --> pdb=" O TRP D 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.876A pdb=" N LEU D 355 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 394 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 515 through 528 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 542 through 560 removed outlier: 3.573A pdb=" N SER D 558 " --> pdb=" O ILE D 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS D 559 " --> pdb=" O LYS D 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 600 Processing helix chain 'D' and resid 610 through 618 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.658A pdb=" N GLN D 629 " --> pdb=" O HIS D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 655 removed outlier: 3.606A pdb=" N CYS D 655 " --> pdb=" O GLY D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 665 Processing helix chain 'D' and resid 717 through 728 Processing helix chain 'D' and resid 729 through 755 Processing helix chain 'D' and resid 760 through 787 removed outlier: 3.571A pdb=" N SER D 764 " --> pdb=" O PRO D 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 766 " --> pdb=" O GLY D 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP D 773 " --> pdb=" O THR D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 804 removed outlier: 4.136A pdb=" N ASP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 821 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.285A pdb=" N MET D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE D 849 " --> pdb=" O THR D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA D 853 " --> pdb=" O HIS D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS D 861 " --> pdb=" O GLN D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 895 removed outlier: 3.650A pdb=" N VAL D 872 " --> pdb=" O MET D 868 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 892 " --> pdb=" O VAL D 888 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU D 893 " --> pdb=" O THR D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 918 removed outlier: 3.544A pdb=" N ARG D 907 " --> pdb=" O TRP D 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 908 " --> pdb=" O ILE D 904 " (cutoff:3.500A) Proline residue: D 912 - end of helix removed outlier: 4.487A pdb=" N ILE D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE D 917 " --> pdb=" O TYR D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 930 Processing helix chain 'D' and resid 950 through 983 removed outlier: 3.659A pdb=" N MET D 970 " --> pdb=" O ASN D 966 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 974 " --> pdb=" O MET D 970 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 975 " --> pdb=" O ASN D 971 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 976 " --> pdb=" O LEU D 972 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL D 983 " --> pdb=" O TYR D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 1006 Processing helix chain 'D' and resid 1010 through 1028 removed outlier: 4.042A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU D1016 " --> pdb=" O PRO D1012 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D1028 " --> pdb=" O LYS D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' and resid 1072 through 1092 Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 81 through 100 removed outlier: 4.569A pdb=" N VAL C 87 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.758A pdb=" N ALA C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 238 through 250 removed outlier: 4.408A pdb=" N ARG C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.717A pdb=" N VAL C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL C 300 " --> pdb=" O TRP C 296 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.874A pdb=" N LEU C 355 " --> pdb=" O TYR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 394 Processing helix chain 'C' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 429 through 443 Processing helix chain 'C' and resid 465 through 477 Processing helix chain 'C' and resid 515 through 528 Processing helix chain 'C' and resid 529 through 539 Processing helix chain 'C' and resid 542 through 560 removed outlier: 3.574A pdb=" N SER C 558 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS C 559 " --> pdb=" O LYS C 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 Processing helix chain 'C' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 600 Processing helix chain 'C' and resid 610 through 618 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.659A pdb=" N GLN C 629 " --> pdb=" O HIS C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 655 removed outlier: 3.608A pdb=" N CYS C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 665 Processing helix chain 'C' and resid 717 through 728 Processing helix chain 'C' and resid 729 through 755 Processing helix chain 'C' and resid 760 through 787 removed outlier: 3.571A pdb=" N SER C 764 " --> pdb=" O PRO C 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C 766 " --> pdb=" O GLY C 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP C 773 " --> pdb=" O THR C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 804 removed outlier: 4.135A pdb=" N ASP C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 821 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.286A pdb=" N MET C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE C 849 " --> pdb=" O THR C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA C 853 " --> pdb=" O HIS C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 895 removed outlier: 3.651A pdb=" N VAL C 872 " --> pdb=" O MET C 868 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C 892 " --> pdb=" O VAL C 888 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 893 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 918 removed outlier: 3.544A pdb=" N ARG C 907 " --> pdb=" O TRP C 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 908 " --> pdb=" O ILE C 904 " (cutoff:3.500A) Proline residue: C 912 - end of helix removed outlier: 4.487A pdb=" N ILE C 916 " --> pdb=" O PRO C 912 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE C 917 " --> pdb=" O TYR C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 930 Processing helix chain 'C' and resid 950 through 983 removed outlier: 3.660A pdb=" N MET C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 974 " --> pdb=" O MET C 970 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 975 " --> pdb=" O ASN C 971 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 983 " --> pdb=" O TYR C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1006 Processing helix chain 'C' and resid 1010 through 1028 removed outlier: 4.041A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C1028 " --> pdb=" O LYS C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' and resid 1072 through 1092 Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 81 through 100 removed outlier: 4.569A pdb=" N VAL B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.759A pdb=" N ALA B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.407A pdb=" N ARG B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.717A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.794A pdb=" N THR B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 311 removed outlier: 4.597A pdb=" N VAL B 300 " --> pdb=" O TRP B 296 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.510A pdb=" N SER B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.874A pdb=" N LEU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.704A pdb=" N VAL B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 429 through 443 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 515 through 528 Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 542 through 560 removed outlier: 3.574A pdb=" N SER B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 574 through 588 removed outlier: 3.604A pdb=" N LEU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 600 Processing helix chain 'B' and resid 610 through 618 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.659A pdb=" N GLN B 629 " --> pdb=" O HIS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 removed outlier: 3.607A pdb=" N CYS B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 729 through 755 Processing helix chain 'B' and resid 760 through 787 removed outlier: 3.570A pdb=" N SER B 764 " --> pdb=" O PRO B 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 773 " --> pdb=" O THR B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 804 removed outlier: 4.135A pdb=" N ASP B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 821 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.285A pdb=" N MET B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 849 removed outlier: 3.579A pdb=" N ILE B 849 " --> pdb=" O THR B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.783A pdb=" N ALA B 853 " --> pdb=" O HIS B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 4.018A pdb=" N LYS B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 895 removed outlier: 3.652A pdb=" N VAL B 872 " --> pdb=" O MET B 868 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.546A pdb=" N ARG B 907 " --> pdb=" O TRP B 903 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) Proline residue: B 912 - end of helix removed outlier: 4.488A pdb=" N ILE B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B 917 " --> pdb=" O TYR B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 930 Processing helix chain 'B' and resid 950 through 983 removed outlier: 3.661A pdb=" N MET B 970 " --> pdb=" O ASN B 966 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 974 " --> pdb=" O MET B 970 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 975 " --> pdb=" O ASN B 971 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1006 Processing helix chain 'B' and resid 1010 through 1028 removed outlier: 4.040A pdb=" N LEU B1015 " --> pdb=" O PRO B1011 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B1028 " --> pdb=" O LYS B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1092 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.673A pdb=" N LYS A 39 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 187 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 41 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA A 136 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE A 186 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 138 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 188 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA A 140 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 103 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET A 139 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 105 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER A 141 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 253 through 255 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 602 Processing sheet with id=AA5, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.673A pdb=" N LYS D 39 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 187 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL D 41 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA D 136 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE D 186 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY D 138 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL D 188 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA D 140 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE D 103 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET D 139 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 105 " --> pdb=" O MET D 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER D 141 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 70 Processing sheet with id=AA7, first strand: chain 'D' and resid 253 through 255 Processing sheet with id=AA8, first strand: chain 'D' and resid 601 through 602 Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.674A pdb=" N LYS C 39 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU C 187 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 41 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA C 136 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE C 186 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 138 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 188 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA C 140 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 103 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET C 139 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 105 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER C 141 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AB2, first strand: chain 'C' and resid 253 through 255 Processing sheet with id=AB3, first strand: chain 'C' and resid 601 through 602 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.673A pdb=" N LYS B 39 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU B 187 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 41 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA B 136 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE B 186 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 138 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 188 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA B 140 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 105 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N SER B 141 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB6, first strand: chain 'B' and resid 253 through 255 Processing sheet with id=AB7, first strand: chain 'B' and resid 601 through 602 1788 hydrogen bonds defined for protein. 5280 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: 8.90 Time building geometry restraints manager: 7.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7452 1.34 - 1.46: 4054 1.46 - 1.58: 9730 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 21292 Sorted by residual: bond pdb=" C LEU D 969 " pdb=" N MET D 970 " ideal model delta sigma weight residual 1.333 1.417 -0.084 1.26e-02 6.30e+03 4.45e+01 bond pdb=" C LEU C 969 " pdb=" N MET C 970 " ideal model delta sigma weight residual 1.333 1.416 -0.083 1.26e-02 6.30e+03 4.35e+01 bond pdb=" C LEU A 969 " pdb=" N MET A 970 " ideal model delta sigma weight residual 1.333 1.416 -0.083 1.26e-02 6.30e+03 4.35e+01 bond pdb=" C LEU B 969 " pdb=" N MET B 970 " ideal model delta sigma weight residual 1.333 1.416 -0.083 1.26e-02 6.30e+03 4.35e+01 bond pdb=" C TRP C 992 " pdb=" N LYS C 993 " ideal model delta sigma weight residual 1.335 1.368 -0.032 1.32e-02 5.74e+03 6.06e+00 ... (remaining 21287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 27978 1.13 - 2.27: 1175 2.27 - 3.40: 175 3.40 - 4.54: 68 4.54 - 5.67: 20 Bond angle restraints: 29416 Sorted by residual: angle pdb=" CA ARG D 911 " pdb=" C ARG D 911 " pdb=" N PRO D 912 " ideal model delta sigma weight residual 120.93 116.10 4.83 1.06e+00 8.90e-01 2.07e+01 angle pdb=" CA ARG A 911 " pdb=" C ARG A 911 " pdb=" N PRO A 912 " ideal model delta sigma weight residual 120.93 116.11 4.82 1.06e+00 8.90e-01 2.06e+01 angle pdb=" CA ARG B 911 " pdb=" C ARG B 911 " pdb=" N PRO B 912 " ideal model delta sigma weight residual 120.93 116.12 4.81 1.06e+00 8.90e-01 2.06e+01 angle pdb=" CA ARG C 911 " pdb=" C ARG C 911 " pdb=" N PRO C 912 " ideal model delta sigma weight residual 120.93 116.14 4.79 1.06e+00 8.90e-01 2.04e+01 angle pdb=" N PRO D 759 " pdb=" CA PRO D 759 " pdb=" C PRO D 759 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.48e+00 ... (remaining 29411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 11452 12.00 - 24.00: 588 24.00 - 36.00: 152 36.00 - 48.00: 32 48.00 - 60.00: 16 Dihedral angle restraints: 12240 sinusoidal: 1844 harmonic: 10396 Sorted by residual: dihedral pdb=" CA PRO B 759 " pdb=" C PRO B 759 " pdb=" N PRO B 760 " pdb=" CA PRO B 760 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO A 759 " pdb=" C PRO A 759 " pdb=" N PRO A 760 " pdb=" CA PRO A 760 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO C 759 " pdb=" C PRO C 759 " pdb=" N PRO C 760 " pdb=" CA PRO C 760 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 12237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2382 0.027 - 0.054: 825 0.054 - 0.082: 363 0.082 - 0.109: 138 0.109 - 0.136: 32 Chirality restraints: 3740 Sorted by residual: chirality pdb=" CA ASN C 394 " pdb=" N ASN C 394 " pdb=" C ASN C 394 " pdb=" CB ASN C 394 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ASN D 394 " pdb=" N ASN D 394 " pdb=" C ASN D 394 " pdb=" CB ASN D 394 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ASN A 394 " pdb=" N ASN A 394 " pdb=" C ASN A 394 " pdb=" CB ASN A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 3737 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 759 " -0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO B 760 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 760 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 760 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 759 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 760 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 759 " 0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO D 760 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 760 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 760 " 0.049 5.00e-02 4.00e+02 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1338 2.73 - 3.27: 25430 3.27 - 3.82: 35387 3.82 - 4.36: 35227 4.36 - 4.90: 55855 Nonbonded interactions: 153237 Sorted by model distance: nonbonded pdb=" O GLN D 761 " pdb=" OG SER D 764 " model vdw 2.188 3.040 nonbonded pdb=" O GLN A 761 " pdb=" OG SER A 764 " model vdw 2.188 3.040 nonbonded pdb=" O GLN B 761 " pdb=" OG SER B 764 " model vdw 2.188 3.040 nonbonded pdb=" O GLN C 761 " pdb=" OG SER C 764 " model vdw 2.188 3.040 nonbonded pdb=" O LEU C 421 " pdb=" OG SER C 424 " model vdw 2.192 3.040 ... (remaining 153232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 50.950 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 0.084 21292 Z= 0.258 Angle : 0.571 5.673 29416 Z= 0.370 Chirality : 0.037 0.136 3740 Planarity : 0.005 0.087 3956 Dihedral : 9.811 59.997 5376 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -2.65 (0.13), residues: 3432 helix: -1.11 (0.10), residues: 2380 sheet: -2.86 (0.32), residues: 176 loop : -2.91 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 378 HIS 0.009 0.001 HIS D 998 PHE 0.013 0.001 PHE D 372 TYR 0.006 0.001 TYR D 997 ARG 0.005 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 TRP cc_start: 0.8232 (m100) cc_final: 0.7798 (m100) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1480 time to fit residues: 12.5486 Evaluate side-chains 40 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 8.9990 chunk 269 optimal weight: 30.0000 chunk 149 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 40.0000 chunk 144 optimal weight: 6.9990 chunk 279 optimal weight: 50.0000 chunk 107 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 207 optimal weight: 0.0170 chunk 323 optimal weight: 2.9990 overall best weight: 3.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN B 349 GLN B 850 HIS ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21292 Z= 0.237 Angle : 0.513 5.507 29416 Z= 0.305 Chirality : 0.037 0.143 3740 Planarity : 0.005 0.090 3956 Dihedral : 4.618 23.491 3552 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.43 % Allowed : 3.04 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3432 helix: 0.61 (0.10), residues: 2396 sheet: -2.40 (0.35), residues: 168 loop : -2.24 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 773 HIS 0.008 0.002 HIS D 612 PHE 0.016 0.001 PHE B 372 TYR 0.007 0.001 TYR D 910 ARG 0.002 0.001 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 400 ARG cc_start: 0.9539 (ttm110) cc_final: 0.9256 (ttm110) REVERT: B 810 ASP cc_start: 0.8878 (m-30) cc_final: 0.8672 (m-30) REVERT: B 976 MET cc_start: 0.7921 (mmp) cc_final: 0.7630 (ppp) REVERT: B 1062 LEU cc_start: 0.9888 (mt) cc_final: 0.9390 (mt) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1325 time to fit residues: 10.6581 Evaluate side-chains 47 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 269 optimal weight: 30.0000 chunk 220 optimal weight: 0.0970 chunk 89 optimal weight: 50.0000 chunk 323 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 288 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21292 Z= 0.230 Angle : 0.487 6.081 29416 Z= 0.289 Chirality : 0.037 0.132 3740 Planarity : 0.005 0.088 3956 Dihedral : 4.381 23.454 3552 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3432 helix: 1.04 (0.10), residues: 2400 sheet: -2.37 (0.35), residues: 192 loop : -1.94 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 773 HIS 0.006 0.001 HIS C 612 PHE 0.017 0.001 PHE D 744 TYR 0.015 0.001 TYR C 587 ARG 0.001 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9521 (ttm110) cc_final: 0.9205 (ttm110) REVERT: D 748 PHE cc_start: 0.9627 (t80) cc_final: 0.9420 (t80) REVERT: D 976 MET cc_start: 0.7712 (mmp) cc_final: 0.7510 (ppp) REVERT: D 1062 LEU cc_start: 0.9820 (mt) cc_final: 0.9483 (mt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1487 time to fit residues: 10.2179 Evaluate side-chains 42 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 10.0000 chunk 243 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 217 optimal weight: 9.9990 chunk 325 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 308 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 349 GLN D 737 ASN ** D 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21292 Z= 0.155 Angle : 0.416 5.042 29416 Z= 0.244 Chirality : 0.036 0.125 3740 Planarity : 0.005 0.087 3956 Dihedral : 3.980 24.306 3552 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3432 helix: 1.27 (0.10), residues: 2428 sheet: -2.37 (0.33), residues: 192 loop : -1.67 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 773 HIS 0.003 0.001 HIS A 612 PHE 0.012 0.001 PHE A 536 TYR 0.012 0.001 TYR D 587 ARG 0.001 0.000 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9510 (ttm110) cc_final: 0.9188 (ttm110) REVERT: D 810 ASP cc_start: 0.9050 (m-30) cc_final: 0.8779 (m-30) REVERT: D 874 PHE cc_start: 0.9217 (m-10) cc_final: 0.8871 (m-80) REVERT: D 970 MET cc_start: 0.9004 (ttt) cc_final: 0.8726 (tmm) REVERT: D 1062 LEU cc_start: 0.9807 (mt) cc_final: 0.9447 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1120 time to fit residues: 9.0336 Evaluate side-chains 44 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 256 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 175 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21292 Z= 0.397 Angle : 0.653 13.771 29416 Z= 0.383 Chirality : 0.040 0.184 3740 Planarity : 0.006 0.088 3956 Dihedral : 4.983 23.170 3552 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.67 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.21 (0.14), residues: 3432 helix: -0.16 (0.10), residues: 2432 sheet: -2.49 (0.34), residues: 192 loop : -1.97 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 773 HIS 0.015 0.003 HIS C 612 PHE 0.025 0.002 PHE C 372 TYR 0.018 0.002 TYR B 997 ARG 0.002 0.001 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 355 LEU cc_start: 0.9580 (tt) cc_final: 0.9357 (pp) REVERT: A 400 ARG cc_start: 0.9549 (ttm110) cc_final: 0.9222 (ttm110) REVERT: A 970 MET cc_start: 0.8899 (ttt) cc_final: 0.8649 (tmm) REVERT: A 996 ARG cc_start: 0.9839 (ttt180) cc_final: 0.9609 (ttm170) REVERT: A 1062 LEU cc_start: 0.9818 (mt) cc_final: 0.9539 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1315 time to fit residues: 9.0714 Evaluate side-chains 38 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 202 optimal weight: 0.0980 chunk 84 optimal weight: 6.9990 chunk 344 optimal weight: 0.8980 chunk 285 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 0.0370 chunk 180 optimal weight: 20.0000 overall best weight: 2.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21292 Z= 0.158 Angle : 0.435 5.086 29416 Z= 0.253 Chirality : 0.036 0.123 3740 Planarity : 0.005 0.087 3956 Dihedral : 4.145 24.272 3552 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3432 helix: 1.08 (0.10), residues: 2412 sheet: -2.75 (0.34), residues: 192 loop : -1.68 (0.25), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 773 HIS 0.004 0.001 HIS D 612 PHE 0.015 0.001 PHE C 583 TYR 0.014 0.001 TYR B 587 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 382 ASP cc_start: 0.8927 (m-30) cc_final: 0.8358 (p0) REVERT: A 400 ARG cc_start: 0.9531 (ttm110) cc_final: 0.9191 (ttm110) REVERT: A 970 MET cc_start: 0.8813 (ttt) cc_final: 0.8604 (tmm) REVERT: A 1062 LEU cc_start: 0.9814 (mt) cc_final: 0.9542 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1169 time to fit residues: 9.2715 Evaluate side-chains 43 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 196 optimal weight: 30.0000 chunk 251 optimal weight: 40.0000 chunk 194 optimal weight: 0.0770 chunk 289 optimal weight: 0.0670 chunk 192 optimal weight: 0.0970 chunk 343 optimal weight: 0.0070 chunk 214 optimal weight: 20.0000 chunk 209 optimal weight: 0.0670 chunk 158 optimal weight: 0.0370 overall best weight: 0.0510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21292 Z= 0.125 Angle : 0.413 6.044 29416 Z= 0.231 Chirality : 0.035 0.119 3740 Planarity : 0.004 0.084 3956 Dihedral : 3.573 23.820 3552 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3432 helix: 1.49 (0.10), residues: 2380 sheet: -2.91 (0.35), residues: 132 loop : -1.48 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 773 HIS 0.004 0.001 HIS D 998 PHE 0.013 0.001 PHE B 536 TYR 0.004 0.001 TYR C 997 ARG 0.002 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.598 Fit side-chains REVERT: A 382 ASP cc_start: 0.8910 (m-30) cc_final: 0.8369 (p0) REVERT: A 400 ARG cc_start: 0.9514 (ttm110) cc_final: 0.9190 (ttp80) REVERT: A 966 ASN cc_start: 0.9737 (p0) cc_final: 0.9500 (p0) REVERT: A 996 ARG cc_start: 0.9687 (ttm-80) cc_final: 0.9450 (ptm160) REVERT: A 1062 LEU cc_start: 0.9783 (mt) cc_final: 0.9449 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1266 time to fit residues: 11.2088 Evaluate side-chains 47 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 30.0000 chunk 169 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21292 Z= 0.215 Angle : 0.465 7.644 29416 Z= 0.269 Chirality : 0.036 0.121 3740 Planarity : 0.005 0.086 3956 Dihedral : 3.689 23.872 3552 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3432 helix: 1.59 (0.10), residues: 2380 sheet: -2.66 (0.35), residues: 168 loop : -1.31 (0.25), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 773 HIS 0.012 0.002 HIS C 850 PHE 0.016 0.001 PHE A 372 TYR 0.022 0.002 TYR A 587 ARG 0.002 0.001 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9518 (ttm110) cc_final: 0.9162 (ttm110) REVERT: D 970 MET cc_start: 0.9371 (tmm) cc_final: 0.9136 (tmm) REVERT: D 1062 LEU cc_start: 0.9800 (mt) cc_final: 0.9502 (mt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1035 time to fit residues: 8.2194 Evaluate side-chains 43 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 20.0000 chunk 328 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 251 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 302 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 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 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21292 Z= 0.334 Angle : 0.584 10.263 29416 Z= 0.344 Chirality : 0.039 0.159 3740 Planarity : 0.005 0.086 3956 Dihedral : 4.561 24.120 3552 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3432 helix: 0.47 (0.10), residues: 2396 sheet: -2.87 (0.34), residues: 192 loop : -1.71 (0.24), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 773 HIS 0.013 0.003 HIS D 612 PHE 0.022 0.002 PHE A 372 TYR 0.017 0.002 TYR D 997 ARG 0.004 0.001 ARG B 996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 400 ARG cc_start: 0.9571 (ttm110) cc_final: 0.9211 (ttm110) REVERT: A 1062 LEU cc_start: 0.9821 (mt) cc_final: 0.9535 (mt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1100 time to fit residues: 7.8535 Evaluate side-chains 39 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 6.9990 chunk 338 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 326 optimal weight: 0.8980 chunk 282 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21292 Z= 0.176 Angle : 0.455 7.355 29416 Z= 0.261 Chirality : 0.036 0.126 3740 Planarity : 0.005 0.088 3956 Dihedral : 4.058 24.357 3552 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3432 helix: 1.29 (0.10), residues: 2368 sheet: -3.05 (0.37), residues: 144 loop : -1.53 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 773 HIS 0.004 0.001 HIS A 612 PHE 0.013 0.001 PHE C 583 TYR 0.010 0.001 TYR A 997 ARG 0.001 0.000 ARG D 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: D 400 ARG cc_start: 0.9511 (ttm110) cc_final: 0.9134 (ttm110) REVERT: D 748 PHE cc_start: 0.9564 (t80) cc_final: 0.9323 (t80) REVERT: D 970 MET cc_start: 0.9412 (tmm) cc_final: 0.9182 (tmm) REVERT: D 1062 LEU cc_start: 0.9819 (mt) cc_final: 0.9511 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1110 time to fit residues: 8.2875 Evaluate side-chains 42 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 8.9990 chunk 300 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 0.0870 chunk 282 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 290 optimal weight: 30.0000 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.076925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049133 restraints weight = 38738.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049688 restraints weight = 30369.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049866 restraints weight = 24600.014| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21292 Z= 0.194 Angle : 0.474 7.290 29416 Z= 0.268 Chirality : 0.036 0.120 3740 Planarity : 0.005 0.086 3956 Dihedral : 3.968 23.865 3552 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3432 helix: 1.28 (0.10), residues: 2372 sheet: -2.95 (0.37), residues: 144 loop : -1.40 (0.24), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 773 HIS 0.006 0.001 HIS B 612 PHE 0.014 0.001 PHE A 372 TYR 0.011 0.001 TYR D 997 ARG 0.001 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.99 seconds wall clock time: 42 minutes 50.57 seconds (2570.57 seconds total)