Starting phenix.real_space_refine on Fri Jul 3 08:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.map" model { file = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2026/7niw_12367.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 41 5.16 5 C 8055 2.51 5 N 2067 2.21 5 O 2311 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8831 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 29, 'TRANS': 1110} Chain breaks: 2 Chain: "B" Number of atoms: 1616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1610 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Conformer: "B" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1631 Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 234, 1757 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 273 Unusual residues: {'CLR': 6, 'DLP': 1, 'X2N': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.85, per 1000 atoms: 0.23 Number of scatterers: 12477 At special positions: 0 Unit cell: (120.12, 127.38, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 1 15.00 F 2 9.00 O 2311 8.00 N 2067 7.00 C 8055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.02 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 216 " distance=2.03 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: 1.04 Conformation dependent library (CDL) restraints added in 657.3 milliseconds 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 22 sheets defined 49.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 50 through 69 removed outlier: 4.008A pdb=" N LYS A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.251A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 159 removed outlier: 3.787A pdb=" N GLU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.640A pdb=" N ASN A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 190 removed outlier: 4.059A pdb=" N ASN A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 213 Processing helix chain 'A' and resid 213 through 252 removed outlier: 3.575A pdb=" N THR A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.548A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.531A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 325 removed outlier: 4.277A pdb=" N HIS A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.898A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 372 removed outlier: 3.502A pdb=" N ASP A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE A 357 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 485 through 495 removed outlier: 3.617A pdb=" N ASN A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 535 through 548 removed outlier: 4.032A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 577 removed outlier: 3.528A pdb=" N GLU A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 removed outlier: 3.739A pdb=" N LYS A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.867A pdb=" N ASN A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'A' and resid 707 through 723 Processing helix chain 'A' and resid 724 through 739 removed outlier: 3.813A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 796 removed outlier: 3.901A pdb=" N GLN A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.699A pdb=" N ASP A 805 " --> pdb=" O TRP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 853 removed outlier: 3.867A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 removed outlier: 3.787A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 902 removed outlier: 3.960A pdb=" N ILE A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY A 871 " --> pdb=" O ILE A 867 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 909 Processing helix chain 'A' and resid 911 through 966 removed outlier: 3.686A pdb=" N PHE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 4.181A pdb=" N HIS A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 951 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 952 " --> pdb=" O MET A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 992 removed outlier: 3.593A pdb=" N GLY A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1000 Processing helix chain 'A' and resid 1002 through 1013 removed outlier: 3.808A pdb=" N LEU A1010 " --> pdb=" O HIS A1006 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 3.930A pdb=" N LEU A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1104 through 1109 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1132 through 1134 No H-bonds generated for 'chain 'A' and resid 1132 through 1134' Processing helix chain 'A' and resid 1140 through 1151 Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.551A pdb=" N ILE A1157 " --> pdb=" O ILE A1153 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1158' Processing helix chain 'A' and resid 1179 through 1191 removed outlier: 3.628A pdb=" N ALA A1184 " --> pdb=" O LYS A1180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A1185 " --> pdb=" O GLN A1181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A1190 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG A1191 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1222 removed outlier: 4.662A pdb=" N GLU A1215 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'B' and resid 122 through 127 removed outlier: 4.361A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.616A pdb=" N SER C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 221 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 425 through 427 removed outlier: 6.379A pdb=" N ALA A 426 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE A 603 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 610 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 472 through 475 removed outlier: 6.446A pdb=" N LEU A 554 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE A 587 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 556 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1052 through 1053 removed outlier: 3.555A pdb=" N LEU A1057 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1052 through 1053 removed outlier: 5.659A pdb=" N GLU A1038 " --> pdb=" O THR A1092 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR A1092 " --> pdb=" O GLU A1038 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1113 through 1114 removed outlier: 7.283A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A1196 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1067 " --> pdb=" O VAL A1228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1094 through 1095 Processing sheet with id=AA8, first strand: chain 'A' and resid 1124 through 1125 removed outlier: 3.961A pdb=" N CYS A1124 " --> pdb=" O VAL A1168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1168 " --> pdb=" O CYS A1124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.598A pdb=" N SER B 115 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.598A pdb=" N SER B 115 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AB7, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.912A pdb=" N TYR C 122 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AC1, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.120A pdb=" N THR C 127 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.557A pdb=" N LEU C 161 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 201 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.557A pdb=" N LEU C 161 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 171 through 174 removed outlier: 3.561A pdb=" N CYS C 216 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 229 " --> pdb=" O CYS C 216 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1806 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: 2.57 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2020 1.31 - 1.44: 3442 1.44 - 1.57: 7203 1.57 - 1.70: 19 1.70 - 1.83: 64 Bond restraints: 12748 Sorted by residual: bond pdb=" CA LEU A1197 " pdb=" CB LEU A1197 " ideal model delta sigma weight residual 1.524 1.435 0.089 1.62e-02 3.81e+03 3.01e+01 bond pdb=" C31 DLP A1308 " pdb=" O2 DLP A1308 " ideal model delta sigma weight residual 1.331 1.438 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C11 DLP A1308 " pdb=" O3 DLP A1308 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CBL X2N A1306 " pdb=" NBT X2N A1306 " ideal model delta sigma weight residual 1.406 1.331 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CB GLN A 837 " pdb=" CG GLN A 837 " ideal model delta sigma weight residual 1.520 1.414 0.106 3.00e-02 1.11e+03 1.25e+01 ... (remaining 12743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 16124 2.35 - 4.70: 966 4.70 - 7.05: 157 7.05 - 9.40: 40 9.40 - 11.75: 8 Bond angle restraints: 17295 Sorted by residual: angle pdb=" N THR B 207 " pdb=" CA THR B 207 " pdb=" C THR B 207 " ideal model delta sigma weight residual 107.23 118.04 -10.81 1.67e+00 3.59e-01 4.19e+01 angle pdb=" N LEU A1089 " pdb=" CA LEU A1089 " pdb=" C LEU A1089 " ideal model delta sigma weight residual 111.36 106.02 5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" CA TYR A 312 " pdb=" CB TYR A 312 " pdb=" CG TYR A 312 " ideal model delta sigma weight residual 113.90 122.61 -8.71 1.80e+00 3.09e-01 2.34e+01 angle pdb=" N PHE A 947 " pdb=" CA PHE A 947 " pdb=" C PHE A 947 " ideal model delta sigma weight residual 113.19 118.86 -5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" N LEU B 136 " pdb=" CA LEU B 136 " pdb=" C LEU B 136 " ideal model delta sigma weight residual 109.79 116.91 -7.12 1.56e+00 4.11e-01 2.08e+01 ... (remaining 17290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 7008 25.83 - 51.65: 449 51.65 - 77.48: 38 77.48 - 103.31: 11 103.31 - 129.14: 2 Dihedral angle restraints: 7508 sinusoidal: 2943 harmonic: 4565 Sorted by residual: dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PHE A 92 " pdb=" CA PHE A 92 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN A 911 " pdb=" C GLN A 911 " pdb=" N GLU A 912 " pdb=" CA GLU A 912 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL A 869 " pdb=" C VAL A 869 " pdb=" N SER A 870 " pdb=" CA SER A 870 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 7505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1565 0.081 - 0.161: 353 0.161 - 0.242: 40 0.242 - 0.322: 10 0.322 - 0.403: 6 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C17 CLR A1304 " pdb=" C13 CLR A1304 " pdb=" C16 CLR A1304 " pdb=" C20 CLR A1304 " both_signs ideal model delta sigma weight residual False 2.55 2.96 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C17 CLR A1307 " pdb=" C13 CLR A1307 " pdb=" C16 CLR A1307 " pdb=" C20 CLR A1307 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C17 CLR A1305 " pdb=" C13 CLR A1305 " pdb=" C16 CLR A1305 " pdb=" C20 CLR A1305 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 1971 not shown) Planarity restraints: 2157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1132 " -0.025 2.00e-02 2.50e+03 1.88e-02 7.04e+00 pdb=" CG TYR A1132 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A1132 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A1132 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A1132 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A1132 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A1132 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1132 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 792 " -0.030 2.00e-02 2.50e+03 1.94e-02 6.62e+00 pdb=" CG PHE A 792 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 792 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 792 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 792 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 792 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 792 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 99 " 0.024 2.00e-02 2.50e+03 1.81e-02 5.72e+00 pdb=" CG PHE B 99 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 99 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 99 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 99 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 99 " 0.009 2.00e-02 2.50e+03 ... (remaining 2154 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 379 2.64 - 3.21: 12895 3.21 - 3.77: 18794 3.77 - 4.34: 25209 4.34 - 4.90: 40597 Nonbonded interactions: 97874 Sorted by model distance: nonbonded pdb=" O ASN A 332 " pdb=" ND2 ASN A 332 " model vdw 2.078 3.120 nonbonded pdb=" OG SER A 476 " pdb=" OE1 GLN A 477 " model vdw 2.090 3.040 nonbonded pdb=" O SER A 69 " pdb=" OG SER A 69 " model vdw 2.110 3.040 nonbonded pdb=" N GLN A 272 " pdb=" OE1 GLN A 272 " model vdw 2.180 3.120 nonbonded pdb=" O SER B 31 " pdb=" OG SER B 31 " model vdw 2.189 3.040 ... (remaining 97869 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.30 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: 7.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.015 0.117 12752 Z= 0.675 Angle : 1.289 11.748 17303 Z= 0.686 Chirality : 0.070 0.403 1974 Planarity : 0.006 0.053 2157 Dihedral : 16.721 129.137 4574 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.49 % Favored : 84.32 % Rotamer: Outliers : 2.44 % Allowed : 13.98 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.15), residues: 1577 helix: -3.16 (0.13), residues: 712 sheet: -3.13 (0.28), residues: 227 loop : -3.81 (0.18), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1221 TYR 0.044 0.003 TYR A1132 PHE 0.040 0.004 PHE B 99 TRP 0.031 0.004 TRP A 802 HIS 0.017 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.01519 / 0.68 (12748) covalent geometry : angle 1.28887 / 0.69 (17295) SS BOND : bond 0.00515 / 0.22 ( 4) SS BOND : angle 1.51536 / 0.86 ( 8) hydrogen bonds : bond 0.19862 / 12.89 ( 625) hydrogen bonds : angle 8.41184 / 6.06 ( 1806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 190 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 383 ARG cc_start: 0.7644 (mtp180) cc_final: 0.6440 (ttp80) REVERT: A 553 ILE cc_start: 0.8832 (mp) cc_final: 0.8605 (mp) REVERT: A 875 MET cc_start: 0.3854 (mmm) cc_final: 0.3645 (tmm) REVERT: A 884 ARG cc_start: 0.5732 (tpp-160) cc_final: 0.5349 (mtt180) REVERT: A 947 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8581 (t80) REVERT: B 139 ASN cc_start: 0.6873 (m-40) cc_final: 0.5916 (p0) REVERT: C 196 TYR cc_start: 0.7303 (m-80) cc_final: 0.6851 (m-80) REVERT: C 230 LYS cc_start: 0.7344 (ttpp) cc_final: 0.7136 (tttp) outliers start: 32 outliers final: 20 residues processed: 188 average time/residue: 0.1174 time to fit residues: 32.1005 Evaluate side-chains 130 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 132 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 HIS A 298 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 752 ASN A 823 GLN A 837 GLN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS A1104 ASN A1214 GLN B 39 GLN C 42 GLN C 191 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125256 restraints weight = 35373.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122649 restraints weight = 22652.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125040 restraints weight = 16106.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125665 restraints weight = 11291.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125996 restraints weight = 10409.583| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12752 Z= 0.166 Angle : 0.719 8.496 17303 Z= 0.374 Chirality : 0.044 0.224 1974 Planarity : 0.004 0.039 2157 Dihedral : 10.383 128.127 1840 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.06 % Allowed : 17.42 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.18), residues: 1577 helix: -1.14 (0.17), residues: 745 sheet: -2.70 (0.28), residues: 254 loop : -3.30 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 109 TYR 0.027 0.002 TYR A 249 PHE 0.030 0.002 PHE A 728 TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS A1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (12748) covalent geometry : angle 0.71871 / 0.37 (17295) SS BOND : bond 0.00213 / 0.10 ( 4) SS BOND : angle 1.20202 / 0.67 ( 8) hydrogen bonds : bond 0.07108 / 4.66 ( 625) hydrogen bonds : angle 5.70302 / 4.12 ( 1806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.553 Fit side-chains REVERT: A 119 TYR cc_start: 0.7829 (m-80) cc_final: 0.7526 (m-80) REVERT: A 218 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 383 ARG cc_start: 0.7670 (mtp180) cc_final: 0.6377 (ttp80) REVERT: A 537 GLN cc_start: 0.5714 (mt0) cc_final: 0.5248 (mt0) REVERT: A 553 ILE cc_start: 0.8669 (mp) cc_final: 0.8441 (mp) REVERT: A 875 MET cc_start: 0.3914 (mmm) cc_final: 0.3577 (tmm) REVERT: A 884 ARG cc_start: 0.5706 (tpp-160) cc_final: 0.5266 (mtm180) REVERT: A 901 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 947 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8687 (t80) REVERT: B 139 ASN cc_start: 0.6771 (m-40) cc_final: 0.6070 (p0) REVERT: C 196 TYR cc_start: 0.6867 (m-80) cc_final: 0.6337 (m-80) outliers start: 40 outliers final: 25 residues processed: 179 average time/residue: 0.0959 time to fit residues: 26.1356 Evaluate side-chains 146 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 171 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 121 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 332 ASN A 349 GLN A 841 ASN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134273 restraints weight = 33721.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136820 restraints weight = 42722.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139185 restraints weight = 16787.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140961 restraints weight = 10349.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141628 restraints weight = 7957.259| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12752 Z= 0.149 Angle : 0.624 7.219 17303 Z= 0.325 Chirality : 0.041 0.242 1974 Planarity : 0.004 0.038 2157 Dihedral : 9.467 124.612 1822 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.51 % Allowed : 20.17 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.20), residues: 1577 helix: -0.05 (0.18), residues: 741 sheet: -2.19 (0.29), residues: 246 loop : -2.87 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.028 0.002 TYR A 919 PHE 0.020 0.002 PHE C 142 TRP 0.015 0.002 TRP A 234 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (12748) covalent geometry : angle 0.62374 / 0.33 (17295) SS BOND : bond 0.00129 / 0.06 ( 4) SS BOND : angle 0.78255 / 0.45 ( 8) hydrogen bonds : bond 0.06211 / 4.04 ( 625) hydrogen bonds : angle 5.11101 / 3.71 ( 1806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.475 Fit side-chains REVERT: A 383 ARG cc_start: 0.7519 (mtp180) cc_final: 0.6512 (ttp-170) REVERT: A 553 ILE cc_start: 0.8813 (mp) cc_final: 0.8566 (mp) REVERT: A 556 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6370 (mt) REVERT: A 769 PHE cc_start: 0.8805 (m-80) cc_final: 0.8584 (m-80) REVERT: A 884 ARG cc_start: 0.5292 (tpp-160) cc_final: 0.5076 (mtm180) REVERT: A 914 LYS cc_start: 0.8077 (pttt) cc_final: 0.7674 (tptt) REVERT: A 947 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8821 (t80) REVERT: A 1036 PHE cc_start: 0.7461 (m-80) cc_final: 0.7224 (m-80) REVERT: A 1129 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8424 (t0) REVERT: B 139 ASN cc_start: 0.6549 (m-40) cc_final: 0.6010 (p0) REVERT: C 196 TYR cc_start: 0.7002 (m-80) cc_final: 0.6551 (m-80) outliers start: 46 outliers final: 36 residues processed: 176 average time/residue: 0.1041 time to fit residues: 27.5673 Evaluate side-chains 158 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 915 PHE Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.648 > 50: distance: 40 - 54: 3.720 distance: 44 - 60: 20.460 distance: 54 - 55: 8.658 distance: 55 - 56: 11.477 distance: 55 - 58: 3.202 distance: 56 - 57: 11.854 distance: 56 - 60: 20.212 distance: 58 - 59: 15.693 distance: 60 - 61: 6.868 distance: 61 - 62: 19.017 distance: 61 - 64: 26.046 distance: 62 - 63: 33.090 distance: 62 - 66: 15.959 distance: 64 - 65: 9.594 distance: 66 - 67: 10.314 distance: 67 - 68: 9.244 distance: 67 - 70: 20.270 distance: 68 - 69: 30.982 distance: 68 - 77: 25.587 distance: 70 - 71: 14.889 distance: 71 - 72: 18.166 distance: 71 - 73: 15.119 distance: 73 - 75: 5.224 distance: 77 - 78: 22.626 distance: 78 - 79: 22.650 distance: 78 - 81: 14.338 distance: 79 - 80: 19.767 distance: 79 - 82: 16.217 distance: 82 - 83: 17.094 distance: 82 - 88: 15.042 distance: 83 - 84: 10.112 distance: 83 - 86: 14.279 distance: 84 - 85: 8.639 distance: 84 - 89: 21.351 distance: 86 - 87: 20.486 distance: 87 - 88: 42.462 distance: 89 - 90: 4.656 distance: 90 - 91: 11.634 distance: 90 - 93: 3.947 distance: 91 - 92: 12.885 distance: 91 - 97: 11.946 distance: 92 - 114: 26.168 distance: 93 - 94: 6.466 distance: 94 - 95: 8.765 distance: 94 - 96: 8.909 distance: 97 - 98: 5.227 distance: 98 - 99: 13.360 distance: 98 - 101: 7.821 distance: 99 - 100: 20.384 distance: 99 - 109: 19.881 distance: 100 - 123: 23.771 distance: 101 - 102: 4.999 distance: 102 - 103: 3.787 distance: 103 - 105: 4.446 distance: 104 - 106: 3.282 distance: 105 - 107: 3.755 distance: 106 - 107: 3.420 distance: 109 - 110: 12.478 distance: 110 - 111: 10.657 distance: 110 - 113: 9.880 distance: 111 - 112: 20.976 distance: 111 - 114: 12.912 distance: 114 - 115: 6.027 distance: 115 - 116: 17.208 distance: 115 - 118: 14.098 distance: 116 - 117: 44.384 distance: 116 - 123: 17.741 distance: 118 - 119: 13.537 distance: 119 - 120: 10.780 distance: 120 - 121: 5.005 distance: 121 - 122: 3.186 distance: 123 - 124: 8.498 distance: 124 - 125: 17.099 distance: 124 - 127: 15.388 distance: 125 - 126: 17.913 distance: 125 - 128: 13.242