Starting phenix.real_space_refine on Tue Nov 19 06:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bqv_44825/11_2024/9bqv_44825.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bqv_44825/11_2024/9bqv_44825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bqv_44825/11_2024/9bqv_44825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bqv_44825/11_2024/9bqv_44825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bqv_44825/11_2024/9bqv_44825.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bqv_44825/11_2024/9bqv_44825.cif" } resolution = 3.2 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= -0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 11833 2.51 5 N 3274 2.21 5 O 3542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18697 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9373 Classifications: {'peptide': 1161} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1127} Chain breaks: 3 Chain: "F" Number of atoms: 9324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 9324 Classifications: {'peptide': 1155} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1121} Chain breaks: 3 Time building chain proxies: 12.32, per 1000 atoms: 0.66 Number of scatterers: 18697 At special positions: 0 Unit cell: (123.14, 145.7, 131.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 3542 8.00 N 3274 7.00 C 11833 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: 4.86 Conformation dependent library (CDL) restraints added in 2.5 seconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 26 sheets defined 54.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 35 Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.723A pdb=" N LYS A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 163 through 177 removed outlier: 4.108A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 208 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.052A pdb=" N ARG A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.605A pdb=" N ASP A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.676A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 401 through 433 Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.935A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.613A pdb=" N PHE A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.860A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 656 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 693 Processing helix chain 'A' and resid 704 through 711 removed outlier: 3.594A pdb=" N MET A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.839A pdb=" N ILE A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.732A pdb=" N GLY A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 737' Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 760 through 764 Processing helix chain 'A' and resid 789 through 807 removed outlier: 3.551A pdb=" N ASN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 removed outlier: 3.630A pdb=" N MET A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 836 removed outlier: 3.821A pdb=" N GLN A 834 " --> pdb=" O ARG A 830 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 853 removed outlier: 3.946A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.553A pdb=" N GLY A 857 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 858 " --> pdb=" O ARG A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'A' and resid 873 through 879 removed outlier: 4.049A pdb=" N ILE A 877 " --> pdb=" O GLY A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.109A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 901 Processing helix chain 'A' and resid 909 through 938 removed outlier: 3.580A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 1014 through 1019 removed outlier: 3.527A pdb=" N LEU A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.816A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1068 removed outlier: 3.829A pdb=" N ALA A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 removed outlier: 3.729A pdb=" N TYR A1081 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 removed outlier: 3.954A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 20 through 38 Processing helix chain 'F' and resid 54 through 78 Processing helix chain 'F' and resid 94 through 111 Processing helix chain 'F' and resid 121 through 131 removed outlier: 3.766A pdb=" N LYS F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 143 Processing helix chain 'F' and resid 146 through 157 Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 163 through 177 removed outlier: 4.138A pdb=" N ARG F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 209 removed outlier: 3.889A pdb=" N GLY F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 227 Processing helix chain 'F' and resid 229 through 234 removed outlier: 4.037A pdb=" N ARG F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 259 through 263 removed outlier: 3.602A pdb=" N ASP F 263 " --> pdb=" O PRO F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.736A pdb=" N VAL F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 322 through 336 Processing helix chain 'F' and resid 401 through 433 removed outlier: 4.362A pdb=" N GLY F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'F' and resid 464 through 472 removed outlier: 3.535A pdb=" N VAL F 468 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE F 472 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.844A pdb=" N HIS F 496 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 536 Processing helix chain 'F' and resid 556 through 565 Processing helix chain 'F' and resid 572 through 585 Processing helix chain 'F' and resid 604 through 616 removed outlier: 3.563A pdb=" N LEU F 608 " --> pdb=" O ARG F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 629 Processing helix chain 'F' and resid 636 through 656 Processing helix chain 'F' and resid 672 through 674 No H-bonds generated for 'chain 'F' and resid 672 through 674' Processing helix chain 'F' and resid 675 through 693 Processing helix chain 'F' and resid 704 through 711 Processing helix chain 'F' and resid 712 through 723 removed outlier: 3.768A pdb=" N ILE F 716 " --> pdb=" O GLY F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 739 removed outlier: 3.568A pdb=" N ALA F 738 " --> pdb=" O SER F 735 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY F 739 " --> pdb=" O MET F 736 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 760 through 764 removed outlier: 3.604A pdb=" N SER F 764 " --> pdb=" O VAL F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 807 removed outlier: 3.597A pdb=" N ASN F 793 " --> pdb=" O SER F 789 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 824 Processing helix chain 'F' and resid 827 through 836 removed outlier: 3.503A pdb=" N HIS F 836 " --> pdb=" O LEU F 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 838 through 853 removed outlier: 3.949A pdb=" N GLN F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 858 removed outlier: 3.533A pdb=" N GLY F 857 " --> pdb=" O GLY F 854 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG F 858 " --> pdb=" O ARG F 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 854 through 858' Processing helix chain 'F' and resid 873 through 880 removed outlier: 4.436A pdb=" N ILE F 877 " --> pdb=" O GLY F 873 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU F 880 " --> pdb=" O GLU F 876 " (cutoff:3.500A) Processing helix chain 'F' and resid 884 through 888 removed outlier: 4.107A pdb=" N LEU F 887 " --> pdb=" O ASP F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 889 through 901 Processing helix chain 'F' and resid 909 through 938 removed outlier: 3.808A pdb=" N ARG F 913 " --> pdb=" O ASP F 909 " (cutoff:3.500A) Processing helix chain 'F' and resid 943 through 960 Processing helix chain 'F' and resid 992 through 996 removed outlier: 4.133A pdb=" N PHE F 996 " --> pdb=" O PRO F 993 " (cutoff:3.500A) Processing helix chain 'F' and resid 1014 through 1019 Processing helix chain 'F' and resid 1023 through 1032 removed outlier: 3.843A pdb=" N TRP F1027 " --> pdb=" O TYR F1023 " (cutoff:3.500A) Processing helix chain 'F' and resid 1045 through 1052 Processing helix chain 'F' and resid 1052 through 1068 removed outlier: 3.814A pdb=" N ALA F1068 " --> pdb=" O ALA F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1081 removed outlier: 3.736A pdb=" N TYR F1081 " --> pdb=" O ASN F1078 " (cutoff:3.500A) Processing helix chain 'F' and resid 1117 through 1127 removed outlier: 3.965A pdb=" N GLU F1125 " --> pdb=" O LEU F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.051A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 269 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE A 542 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 271 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.788A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.591A pdb=" N GLU A 503 " --> pdb=" O LYS A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344 removed outlier: 6.731A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 382 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.518A pdb=" N VAL A 595 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU A 868 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR A 597 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 870 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS A 599 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET A 663 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER A 731 " --> pdb=" O MET A 663 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER A 665 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 743 through 745 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 757 removed outlier: 3.573A pdb=" N LYS A 862 " --> pdb=" O ILE A 756 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.637A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 982 through 985 Processing sheet with id=AB3, first strand: chain 'A' and resid 1071 through 1074 removed outlier: 3.640A pdb=" N ARG A1087 " --> pdb=" O GLU A1074 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1162 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1137 through 1138 removed outlier: 3.696A pdb=" N GLY A1138 " --> pdb=" O ILE A1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.072A pdb=" N ALA F 43 " --> pdb=" O ILE F 539 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLY F 541 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU F 269 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE F 542 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE F 271 " --> pdb=" O ILE F 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 89 through 91 removed outlier: 5.794A pdb=" N TYR F 90 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AB8, first strand: chain 'F' and resid 251 through 252 Processing sheet with id=AB9, first strand: chain 'F' and resid 291 through 292 removed outlier: 3.563A pdb=" N GLU F 503 " --> pdb=" O LYS F 517 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 342 through 344 removed outlier: 7.224A pdb=" N ASN F 343 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 382 " --> pdb=" O ASP F 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 595 through 601 removed outlier: 6.398A pdb=" N VAL F 595 " --> pdb=" O ILE F 866 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU F 868 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR F 597 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL F 870 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS F 599 " --> pdb=" O VAL F 870 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE F 774 " --> pdb=" O PHE F 869 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP F 871 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU F 776 " --> pdb=" O ASP F 871 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET F 663 " --> pdb=" O VAL F 729 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER F 731 " --> pdb=" O MET F 663 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER F 665 " --> pdb=" O SER F 731 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS F 698 " --> pdb=" O VAL F 728 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE F 730 " --> pdb=" O LYS F 698 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE F 700 " --> pdb=" O PHE F 730 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N THR F 732 " --> pdb=" O PHE F 700 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 743 through 745 Processing sheet with id=AC4, first strand: chain 'F' and resid 755 through 757 Processing sheet with id=AC5, first strand: chain 'F' and resid 962 through 963 removed outlier: 3.653A pdb=" N ASN F1042 " --> pdb=" O VAL F 963 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 983 through 985 Processing sheet with id=AC7, first strand: chain 'F' and resid 1071 through 1074 removed outlier: 3.703A pdb=" N ARG F1087 " --> pdb=" O GLU F1074 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F1162 " --> pdb=" O PHE F1131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 1137 through 1138 removed outlier: 3.764A pdb=" N GLY F1138 " --> pdb=" O ILE F1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 916 hydrogen bonds defined for protein. 2613 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: 8.75 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3678 1.32 - 1.44: 4908 1.44 - 1.56: 10398 1.56 - 1.69: 5 1.69 - 1.81: 76 Bond restraints: 19065 Sorted by residual: bond pdb=" CB VAL F 91 " pdb=" CG2 VAL F 91 " ideal model delta sigma weight residual 1.521 1.365 0.156 3.30e-02 9.18e+02 2.22e+01 bond pdb=" CA LYS A 382 " pdb=" CB LYS A 382 " ideal model delta sigma weight residual 1.536 1.439 0.097 2.08e-02 2.31e+03 2.16e+01 bond pdb=" CB VAL A 91 " pdb=" CG2 VAL A 91 " ideal model delta sigma weight residual 1.521 1.378 0.143 3.30e-02 9.18e+02 1.88e+01 bond pdb=" CB VAL A 514 " pdb=" CG1 VAL A 514 " ideal model delta sigma weight residual 1.521 1.381 0.140 3.30e-02 9.18e+02 1.80e+01 bond pdb=" CB VAL F 514 " pdb=" CG1 VAL F 514 " ideal model delta sigma weight residual 1.521 1.384 0.137 3.30e-02 9.18e+02 1.71e+01 ... (remaining 19060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 24690 2.97 - 5.94: 921 5.94 - 8.91: 116 8.91 - 11.88: 36 11.88 - 14.85: 4 Bond angle restraints: 25767 Sorted by residual: angle pdb=" C SER F 361 " pdb=" N PHE F 362 " pdb=" CA PHE F 362 " ideal model delta sigma weight residual 121.54 133.24 -11.70 1.91e+00 2.74e-01 3.75e+01 angle pdb=" C HIS F 238 " pdb=" CA HIS F 238 " pdb=" CB HIS F 238 " ideal model delta sigma weight residual 110.56 100.29 10.27 1.83e+00 2.99e-01 3.15e+01 angle pdb=" C HIS A 238 " pdb=" CA HIS A 238 " pdb=" CB HIS A 238 " ideal model delta sigma weight residual 111.03 100.91 10.12 1.87e+00 2.86e-01 2.93e+01 angle pdb=" CB ARG A 305 " pdb=" CG ARG A 305 " pdb=" CD ARG A 305 " ideal model delta sigma weight residual 111.30 99.63 11.67 2.30e+00 1.89e-01 2.58e+01 angle pdb=" CA ARG A 563 " pdb=" CB ARG A 563 " pdb=" CG ARG A 563 " ideal model delta sigma weight residual 114.10 124.15 -10.05 2.00e+00 2.50e-01 2.52e+01 ... (remaining 25762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10440 17.95 - 35.90: 854 35.90 - 53.85: 180 53.85 - 71.80: 33 71.80 - 89.75: 22 Dihedral angle restraints: 11529 sinusoidal: 4719 harmonic: 6810 Sorted by residual: dihedral pdb=" CA VAL A 711 " pdb=" C VAL A 711 " pdb=" N GLY A 712 " pdb=" CA GLY A 712 " ideal model delta harmonic sigma weight residual 180.00 -140.35 -39.65 0 5.00e+00 4.00e-02 6.29e+01 dihedral pdb=" CA VAL F 711 " pdb=" C VAL F 711 " pdb=" N GLY F 712 " pdb=" CA GLY F 712 " ideal model delta harmonic sigma weight residual -180.00 -143.13 -36.87 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA GLU F 440 " pdb=" C GLU F 440 " pdb=" N ASN F 441 " pdb=" CA ASN F 441 " ideal model delta harmonic sigma weight residual 180.00 144.59 35.41 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 11526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1847 0.067 - 0.134: 822 0.134 - 0.201: 137 0.201 - 0.268: 32 0.268 - 0.335: 9 Chirality restraints: 2847 Sorted by residual: chirality pdb=" CB VAL F 239 " pdb=" CA VAL F 239 " pdb=" CG1 VAL F 239 " pdb=" CG2 VAL F 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL F 91 " pdb=" CA VAL F 91 " pdb=" CG1 VAL F 91 " pdb=" CG2 VAL F 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL A 91 " pdb=" CA VAL A 91 " pdb=" CG1 VAL A 91 " pdb=" CG2 VAL A 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2844 not shown) Planarity restraints: 3349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F1033 " 0.021 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE F1033 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE F1033 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE F1033 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F1033 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F1033 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE F1033 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 312 " 0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO A 313 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 238 " 0.017 2.00e-02 2.50e+03 2.62e-02 1.03e+01 pdb=" CG HIS F 238 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS F 238 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS F 238 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS F 238 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS F 238 " 0.005 2.00e-02 2.50e+03 ... (remaining 3346 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1404 2.70 - 3.25: 18243 3.25 - 3.80: 29364 3.80 - 4.35: 37726 4.35 - 4.90: 65536 Nonbonded interactions: 152273 Sorted by model distance: nonbonded pdb=" OH TYR A 427 " pdb=" OE2 GLU A 450 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR F 427 " pdb=" OE2 GLU F 450 " model vdw 2.169 3.040 nonbonded pdb=" O PHE F 999 " pdb=" N ARG F1001 " model vdw 2.171 3.120 nonbonded pdb=" O PHE A 999 " pdb=" N ARG A1001 " model vdw 2.171 3.120 nonbonded pdb=" OE1 GLU A 440 " pdb=" NH2 ARG A 442 " model vdw 2.176 3.120 ... (remaining 152268 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' and (resid 1 through 387 or resid 400 through 478 or resid 489 throug \ h 1190)) selection = chain 'F' } 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: 2.800 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: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 45.450 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.021 0.156 19065 Z= 1.365 Angle : 1.348 14.853 25767 Z= 0.727 Chirality : 0.074 0.335 2847 Planarity : 0.007 0.083 3349 Dihedral : 14.531 89.748 7109 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.27 (0.15), residues: 2300 helix: -1.28 (0.13), residues: 1144 sheet: -1.50 (0.32), residues: 241 loop : -1.58 (0.18), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP A 707 HIS 0.035 0.004 HIS F 238 PHE 0.057 0.005 PHE F1033 TYR 0.030 0.004 TYR F 559 ARG 0.039 0.002 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.434 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: A 700 PHE cc_start: 0.7479 (m-80) cc_final: 0.7179 (m-80) REVERT: F 641 ARG cc_start: 0.8673 (mtp-110) cc_final: 0.7908 (mtp-110) REVERT: F 1132 ILE cc_start: 0.9174 (mt) cc_final: 0.8848 (mm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3976 time to fit residues: 97.0518 Evaluate side-chains 96 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 238 HIS A 522 ASN A 923 ASN F 238 HIS F 522 ASN F 592 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19065 Z= 0.212 Angle : 0.571 8.673 25767 Z= 0.303 Chirality : 0.041 0.174 2847 Planarity : 0.004 0.051 3349 Dihedral : 5.350 45.384 2536 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.61 % Favored : 97.22 % Rotamer: Outliers : 0.83 % Allowed : 5.06 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.48 (0.17), residues: 2300 helix: 0.59 (0.15), residues: 1142 sheet: -1.21 (0.31), residues: 279 loop : -1.11 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 707 HIS 0.009 0.001 HIS F 623 PHE 0.026 0.002 PHE A 362 TYR 0.014 0.001 TYR A1081 ARG 0.004 0.001 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 LEU cc_start: 0.9121 (mt) cc_final: 0.8669 (mt) REVERT: A 700 PHE cc_start: 0.7603 (m-80) cc_final: 0.7394 (m-80) REVERT: A 1023 TYR cc_start: 0.7972 (m-80) cc_final: 0.7622 (m-80) REVERT: F 1 MET cc_start: 0.7511 (pmm) cc_final: 0.7185 (pmm) REVERT: F 641 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.7892 (mtp-110) REVERT: F 1084 PHE cc_start: 0.8081 (m-80) cc_final: 0.7867 (m-80) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 0.3583 time to fit residues: 81.0620 Evaluate side-chains 105 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 348 ASN A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 HIS ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 938 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19065 Z= 0.253 Angle : 0.532 8.102 25767 Z= 0.280 Chirality : 0.040 0.173 2847 Planarity : 0.004 0.042 3349 Dihedral : 4.899 42.898 2536 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.61 % Rotamer: Outliers : 1.07 % Allowed : 7.25 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.31 (0.17), residues: 2300 helix: 1.34 (0.15), residues: 1148 sheet: -1.01 (0.31), residues: 280 loop : -0.84 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 643 HIS 0.018 0.001 HIS F1188 PHE 0.029 0.002 PHE F 472 TYR 0.016 0.001 TYR F1133 ARG 0.004 0.000 ARG F1025 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 648 LEU cc_start: 0.9156 (mt) cc_final: 0.8816 (mt) REVERT: A 700 PHE cc_start: 0.7677 (m-80) cc_final: 0.7469 (m-80) REVERT: A 1023 TYR cc_start: 0.7964 (m-80) cc_final: 0.7686 (m-80) REVERT: F 1 MET cc_start: 0.7494 (pmm) cc_final: 0.7120 (pmm) REVERT: F 608 LEU cc_start: 0.8160 (tp) cc_final: 0.7545 (pp) REVERT: F 641 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.7841 (mtp-110) outliers start: 22 outliers final: 8 residues processed: 136 average time/residue: 0.3300 time to fit residues: 69.4463 Evaluate side-chains 99 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 947 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 238 HIS A 584 HIS A 938 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 HIS F 291 GLN F 584 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19065 Z= 0.230 Angle : 0.509 8.078 25767 Z= 0.268 Chirality : 0.040 0.167 2847 Planarity : 0.003 0.035 3349 Dihedral : 4.654 42.344 2536 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.91 % Favored : 96.91 % Rotamer: Outliers : 1.41 % Allowed : 8.32 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.18), residues: 2300 helix: 1.70 (0.15), residues: 1151 sheet: -0.73 (0.31), residues: 296 loop : -0.57 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 643 HIS 0.010 0.001 HIS F1188 PHE 0.024 0.002 PHE A 362 TYR 0.014 0.001 TYR A1081 ARG 0.004 0.000 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: A 648 LEU cc_start: 0.9071 (mt) cc_final: 0.8684 (mt) REVERT: A 1023 TYR cc_start: 0.7932 (m-80) cc_final: 0.7684 (m-80) REVERT: F 1 MET cc_start: 0.7585 (pmm) cc_final: 0.7225 (pmm) REVERT: F 2 ASN cc_start: 0.7623 (m-40) cc_final: 0.7242 (p0) REVERT: F 608 LEU cc_start: 0.8044 (tp) cc_final: 0.7664 (pp) REVERT: F 648 LEU cc_start: 0.9128 (mt) cc_final: 0.8849 (mt) REVERT: F 1084 PHE cc_start: 0.7691 (m-80) cc_final: 0.7470 (m-10) outliers start: 29 outliers final: 19 residues processed: 133 average time/residue: 0.3373 time to fit residues: 69.3346 Evaluate side-chains 109 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 930 ILE Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 1029 GLU Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 584 HIS A 592 ASN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 19065 Z= 0.364 Angle : 0.562 7.836 25767 Z= 0.293 Chirality : 0.042 0.177 2847 Planarity : 0.003 0.035 3349 Dihedral : 4.729 41.086 2536 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 1.51 % Allowed : 9.14 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.90 (0.18), residues: 2300 helix: 1.80 (0.15), residues: 1152 sheet: -0.64 (0.31), residues: 284 loop : -0.57 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 643 HIS 0.016 0.001 HIS F 238 PHE 0.029 0.002 PHE A 472 TYR 0.015 0.001 TYR F1133 ARG 0.009 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 2.394 Fit side-chains revert: symmetry clash REVERT: A 648 LEU cc_start: 0.9064 (mt) cc_final: 0.8698 (mt) REVERT: A 1023 TYR cc_start: 0.7968 (m-80) cc_final: 0.7666 (m-80) REVERT: F 1 MET cc_start: 0.7619 (pmm) cc_final: 0.7245 (pmm) REVERT: F 2 ASN cc_start: 0.7802 (m-40) cc_final: 0.7320 (p0) REVERT: F 641 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8148 (mtp-110) REVERT: F 648 LEU cc_start: 0.9086 (mt) cc_final: 0.8736 (mt) REVERT: F 1084 PHE cc_start: 0.7825 (m-80) cc_final: 0.7592 (m-10) outliers start: 31 outliers final: 24 residues processed: 120 average time/residue: 0.3097 time to fit residues: 60.9167 Evaluate side-chains 111 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 930 ILE Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 1029 GLU Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 0.0000 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 HIS ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19065 Z= 0.153 Angle : 0.472 7.516 25767 Z= 0.249 Chirality : 0.039 0.158 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.416 41.998 2536 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.43 % Favored : 97.39 % Rotamer: Outliers : 1.61 % Allowed : 9.82 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.31 (0.18), residues: 2300 helix: 2.14 (0.15), residues: 1156 sheet: -0.70 (0.31), residues: 310 loop : -0.26 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 643 HIS 0.019 0.001 HIS A1188 PHE 0.022 0.001 PHE A 362 TYR 0.015 0.001 TYR F1133 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 2.222 Fit side-chains revert: symmetry clash REVERT: A 641 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7924 (mtp85) REVERT: A 648 LEU cc_start: 0.9041 (mt) cc_final: 0.8682 (mt) REVERT: A 1023 TYR cc_start: 0.7929 (m-80) cc_final: 0.7658 (m-80) REVERT: F 2 ASN cc_start: 0.7680 (m-40) cc_final: 0.7233 (p0) REVERT: F 641 ARG cc_start: 0.8538 (mtm110) cc_final: 0.8128 (mtp-110) REVERT: F 648 LEU cc_start: 0.9035 (mt) cc_final: 0.8645 (mt) REVERT: F 1084 PHE cc_start: 0.7756 (m-80) cc_final: 0.7513 (m-10) outliers start: 33 outliers final: 23 residues processed: 134 average time/residue: 0.3138 time to fit residues: 66.8500 Evaluate side-chains 115 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1029 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19065 Z= 0.234 Angle : 0.506 7.898 25767 Z= 0.263 Chirality : 0.040 0.166 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.429 40.014 2536 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.87 % Favored : 96.96 % Rotamer: Outliers : 1.61 % Allowed : 10.70 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.40 (0.18), residues: 2300 helix: 2.21 (0.15), residues: 1155 sheet: -0.56 (0.31), residues: 297 loop : -0.26 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 643 HIS 0.007 0.001 HIS F 238 PHE 0.022 0.001 PHE A 362 TYR 0.013 0.001 TYR A1081 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: A 641 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7940 (mtp85) REVERT: A 648 LEU cc_start: 0.9040 (mt) cc_final: 0.8680 (mt) REVERT: A 666 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7648 (mm) REVERT: A 1023 TYR cc_start: 0.7888 (m-80) cc_final: 0.7648 (m-80) REVERT: F 2 ASN cc_start: 0.7641 (m-40) cc_final: 0.7220 (p0) REVERT: F 648 LEU cc_start: 0.9054 (mt) cc_final: 0.8661 (mt) REVERT: F 1084 PHE cc_start: 0.7807 (m-80) cc_final: 0.7573 (m-10) outliers start: 33 outliers final: 24 residues processed: 125 average time/residue: 0.2907 time to fit residues: 59.7642 Evaluate side-chains 118 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1029 GLU Chi-restraints excluded: chain F residue 1043 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19065 Z= 0.240 Angle : 0.506 7.593 25767 Z= 0.263 Chirality : 0.040 0.172 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.378 38.249 2536 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.74 % Favored : 97.09 % Rotamer: Outliers : 1.70 % Allowed : 10.55 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.47 (0.18), residues: 2300 helix: 2.29 (0.15), residues: 1156 sheet: -0.57 (0.31), residues: 297 loop : -0.26 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 643 HIS 0.005 0.001 HIS A1188 PHE 0.022 0.001 PHE A 362 TYR 0.013 0.001 TYR F1133 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: A 641 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7945 (mtp85) REVERT: A 648 LEU cc_start: 0.9027 (mt) cc_final: 0.8664 (mt) REVERT: A 666 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7726 (mm) REVERT: A 1023 TYR cc_start: 0.7959 (m-80) cc_final: 0.7700 (m-80) REVERT: F 2 ASN cc_start: 0.7658 (m-40) cc_final: 0.7230 (p0) REVERT: F 641 ARG cc_start: 0.8571 (mtm110) cc_final: 0.8272 (mtp-110) REVERT: F 648 LEU cc_start: 0.9054 (mt) cc_final: 0.8658 (mt) outliers start: 35 outliers final: 25 residues processed: 125 average time/residue: 0.3049 time to fit residues: 61.1515 Evaluate side-chains 115 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1029 GLU Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 506 HIS A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 GLN ** F 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19065 Z= 0.270 Angle : 0.521 8.313 25767 Z= 0.270 Chirality : 0.040 0.177 2847 Planarity : 0.003 0.032 3349 Dihedral : 4.420 38.122 2536 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.61 % Rotamer: Outliers : 1.65 % Allowed : 10.85 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.47 (0.18), residues: 2300 helix: 2.30 (0.15), residues: 1153 sheet: -0.57 (0.32), residues: 297 loop : -0.26 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1186 HIS 0.005 0.001 HIS F1188 PHE 0.023 0.001 PHE F 362 TYR 0.015 0.001 TYR A1146 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 2.052 Fit side-chains revert: symmetry clash REVERT: A 641 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7951 (mtp85) REVERT: A 648 LEU cc_start: 0.9026 (mt) cc_final: 0.8667 (mt) REVERT: A 666 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7710 (mm) REVERT: A 1023 TYR cc_start: 0.7981 (m-80) cc_final: 0.7711 (m-80) REVERT: F 2 ASN cc_start: 0.7738 (m-40) cc_final: 0.7259 (p0) REVERT: F 648 LEU cc_start: 0.9062 (mt) cc_final: 0.8669 (mt) REVERT: F 669 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7679 (ptp-110) outliers start: 34 outliers final: 26 residues processed: 118 average time/residue: 0.3169 time to fit residues: 58.8158 Evaluate side-chains 111 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 669 ARG Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1029 GLU Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 145 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1060 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19065 Z= 0.159 Angle : 0.481 9.088 25767 Z= 0.250 Chirality : 0.039 0.177 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.234 38.507 2536 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.48 % Favored : 97.35 % Rotamer: Outliers : 1.36 % Allowed : 11.33 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.66 (0.18), residues: 2300 helix: 2.46 (0.15), residues: 1155 sheet: -0.62 (0.31), residues: 313 loop : -0.09 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1186 HIS 0.005 0.001 HIS A1188 PHE 0.030 0.001 PHE A1071 TYR 0.012 0.001 TYR F 629 ARG 0.003 0.000 ARG A 475 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 641 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7843 (mtp85) REVERT: A 648 LEU cc_start: 0.8998 (mt) cc_final: 0.8644 (mt) REVERT: A 663 MET cc_start: 0.7799 (ttp) cc_final: 0.7244 (ttp) REVERT: A 666 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7659 (mm) REVERT: A 1023 TYR cc_start: 0.7941 (m-80) cc_final: 0.7716 (m-80) REVERT: F 2 ASN cc_start: 0.7746 (m-40) cc_final: 0.7262 (p0) REVERT: F 648 LEU cc_start: 0.9042 (mt) cc_final: 0.8659 (mt) REVERT: F 1084 PHE cc_start: 0.7438 (m-80) cc_final: 0.7223 (m-10) outliers start: 28 outliers final: 18 residues processed: 118 average time/residue: 0.3231 time to fit residues: 60.9991 Evaluate side-chains 107 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 761 VAL Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 1029 GLU Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 161 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.110635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073792 restraints weight = 48499.495| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.47 r_work: 0.3042 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19065 Z= 0.160 Angle : 0.488 8.915 25767 Z= 0.253 Chirality : 0.039 0.172 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.171 37.765 2536 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.52 % Favored : 97.30 % Rotamer: Outliers : 1.17 % Allowed : 11.48 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.78 (0.18), residues: 2300 helix: 2.55 (0.15), residues: 1154 sheet: -0.53 (0.31), residues: 313 loop : -0.04 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1186 HIS 0.005 0.001 HIS A1188 PHE 0.024 0.001 PHE F 362 TYR 0.014 0.001 TYR A1081 ARG 0.003 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.53 seconds wall clock time: 67 minutes 39.67 seconds (4059.67 seconds total)