Starting phenix.real_space_refine on Tue Jun 10 09:37:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxi_36702/06_2025/8jxi_36702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxi_36702/06_2025/8jxi_36702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxi_36702/06_2025/8jxi_36702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxi_36702/06_2025/8jxi_36702.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxi_36702/06_2025/8jxi_36702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxi_36702/06_2025/8jxi_36702.cif" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 129 5.16 5 C 7014 2.51 5 N 2002 2.21 5 O 2345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11506 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 895 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 9053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9053 Classifications: {'peptide': 1167} Link IDs: {'PTRANS': 57, 'TRANS': 1109} Chain breaks: 1 Chain: "B" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1124 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 152 Unusual residues: {' CA': 12, 'A2G': 8, 'NAG': 2} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Unusual residues: {' CA': 4, 'A2G': 1, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.83, per 1000 atoms: 0.59 Number of scatterers: 11506 At special positions: 0 Unit cell: (142.511, 129.812, 143.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 16 19.99 S 129 16.00 O 2345 8.00 N 2002 7.00 C 7014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 329 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 345 " distance=2.04 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 384 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 673 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 973 " - pdb=" SG CYS A 987 " distance=2.03 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS A 999 " - pdb=" SG CYS A1012 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1050 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1079 " distance=2.03 Simple disulfide: pdb=" SG CYS A1073 " - pdb=" SG CYS A1092 " distance=2.03 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS A1110 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1135 " distance=2.03 Simple disulfide: pdb=" SG CYS A1129 " - pdb=" SG CYS A1144 " distance=2.03 Simple disulfide: pdb=" SG CYS A1150 " - pdb=" SG CYS A1162 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1175 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1184 " distance=2.03 Simple disulfide: pdb=" SG CYS A1188 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1238 " - pdb=" SG CYS A1257 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.03 Simple disulfide: pdb=" SG CYS A1272 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1297 " distance=2.03 Simple disulfide: pdb=" SG CYS A1291 " - pdb=" SG CYS A1306 " distance=2.03 Simple disulfide: pdb=" SG CYS A3165 " - pdb=" SG CYS A3178 " distance=2.03 Simple disulfide: pdb=" SG CYS A3180 " - pdb=" SG CYS A3193 " distance=2.03 Simple disulfide: pdb=" SG CYS B2720 " - pdb=" SG CYS B2737 " distance=2.04 Simple disulfide: pdb=" SG CYS B2742 " - pdb=" SG CYS B2754 " distance=2.03 Simple disulfide: pdb=" SG CYS B2749 " - pdb=" SG CYS B2767 " distance=2.02 Simple disulfide: pdb=" SG CYS B2761 " - pdb=" SG CYS B2776 " distance=2.03 Simple disulfide: pdb=" SG CYS B2781 " - pdb=" SG CYS B2794 " distance=2.03 Simple disulfide: pdb=" SG CYS B2789 " - pdb=" SG CYS B2807 " distance=2.04 Simple disulfide: pdb=" SG CYS B2801 " - pdb=" SG CYS B2818 " distance=2.03 Simple disulfide: pdb=" SG CYS B2823 " - pdb=" SG CYS B2836 " distance=2.03 Simple disulfide: pdb=" SG CYS B2830 " - pdb=" SG CYS B2849 " distance=2.03 Simple disulfide: pdb=" SG CYS B2843 " - pdb=" SG CYS B2860 " 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=6, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " BETA1-3 " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A4701 " - " ASN A 340 " " NAG A4702 " - " ASN A1187 " " NAG B4701 " - " ASN B2782 " " NAG B4702 " - " ASN B2810 " " NAG D 1 " - " ASN A 462 " " NAG E 1 " - " ASN A 657 " " NAG F 1 " - " ASN A 865 " " NAG I 1 " - " ASN A1063 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 32 sheets defined 14.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'C' and resid 257 through 269 removed outlier: 4.144A pdb=" N SER C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 315 Processing helix chain 'C' and resid 316 through 358 removed outlier: 3.782A pdb=" N LEU C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.517A pdb=" N SER A 312 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.961A pdb=" N SER A 664 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN A 665 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN A 666 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 removed outlier: 4.062A pdb=" N GLY A 981 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1043 No H-bonds generated for 'chain 'A' and resid 1041 through 1043' Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1178 through 1182 Processing helix chain 'A' and resid 1205 through 1207 No H-bonds generated for 'chain 'A' and resid 1205 through 1207' Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.824A pdb=" N HIS A1264 " --> pdb=" O SER A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1290 No H-bonds generated for 'chain 'A' and resid 1288 through 1290' Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'B' and resid 2733 through 2738 removed outlier: 3.701A pdb=" N CYS B2737 " --> pdb=" O LEU B2733 " (cutoff:3.500A) Processing helix chain 'B' and resid 2758 through 2760 No H-bonds generated for 'chain 'B' and resid 2758 through 2760' Processing helix chain 'B' and resid 2770 through 2774 Processing helix chain 'B' and resid 2812 through 2817 removed outlier: 3.796A pdb=" N ASN B2817 " --> pdb=" O SER B2813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 417 removed outlier: 5.349A pdb=" N ILE A 415 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A 405 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 398 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY A 646 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.431A pdb=" N VAL A 447 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 468 through 474 removed outlier: 3.708A pdb=" N ASN A 470 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 490 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 511 through 516 removed outlier: 3.877A pdb=" N GLY A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 539 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ASP A 549 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 558 through 564 removed outlier: 4.145A pdb=" N GLY A 560 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 580 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 607 through 609 removed outlier: 6.581A pdb=" N VAL A 623 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.697A pdb=" N ALA A 717 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS A 958 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 742 through 748 removed outlier: 4.109A pdb=" N GLY A 744 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 764 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 791 removed outlier: 3.923A pdb=" N CYS A 787 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 807 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 827 through 833 removed outlier: 6.364A pdb=" N SER A 842 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 830 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 840 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 832 " --> pdb=" O TYR A 838 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A 838 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 850 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 871 through 877 removed outlier: 3.955A pdb=" N GLY A 873 " --> pdb=" O VAL A 886 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 915 through 921 removed outlier: 3.715A pdb=" N GLY A 917 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG A 937 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 948 " --> pdb=" O ARG A 937 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 986 through 990 Processing sheet with id=AC4, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id=AC5, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id=AC6, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id=AC7, first strand: chain 'A' and resid 1114 through 1116 Processing sheet with id=AC8, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 3.707A pdb=" N ARG A1161 " --> pdb=" O CYS A1157 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id=AD1, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id=AD2, first strand: chain 'A' and resid 1276 through 1278 Processing sheet with id=AD3, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id=AD4, first strand: chain 'B' and resid 2746 through 2748 Processing sheet with id=AD5, first strand: chain 'B' and resid 2829 through 2830 310 hydrogen bonds defined for protein. 753 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: 4.58 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3899 1.34 - 1.46: 2685 1.46 - 1.58: 5018 1.58 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 11749 Sorted by residual: bond pdb=" N CYS A 372 " pdb=" CA CYS A 372 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" N CYS A 384 " pdb=" CA CYS A 384 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.11e+00 bond pdb=" C SER A 738 " pdb=" N PRO A 739 " ideal model delta sigma weight residual 1.333 1.352 -0.019 7.80e-03 1.64e+04 5.93e+00 bond pdb=" N GLU A 373 " pdb=" CA GLU A 373 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.32e-02 5.74e+03 5.93e+00 bond pdb=" N GLU A 374 " pdb=" CA GLU A 374 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.54e+00 ... (remaining 11744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 15626 2.78 - 5.56: 260 5.56 - 8.34: 31 8.34 - 11.12: 4 11.12 - 13.89: 5 Bond angle restraints: 15926 Sorted by residual: angle pdb=" N PHE B2827 " pdb=" CA PHE B2827 " pdb=" C PHE B2827 " ideal model delta sigma weight residual 111.56 104.71 6.85 1.38e+00 5.25e-01 2.46e+01 angle pdb=" C2 A2G B4703 " pdb=" C1 A2G B4703 " pdb=" O5 A2G B4703 " ideal model delta sigma weight residual 111.38 125.27 -13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C2 A2G A4705 " pdb=" C1 A2G A4705 " pdb=" O5 A2G A4705 " ideal model delta sigma weight residual 111.38 124.48 -13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C GLU A 328 " pdb=" N CYS A 329 " pdb=" CA CYS A 329 " ideal model delta sigma weight residual 122.62 116.03 6.59 1.56e+00 4.11e-01 1.79e+01 angle pdb=" C2 A2G A4703 " pdb=" C1 A2G A4703 " pdb=" O5 A2G A4703 " ideal model delta sigma weight residual 111.38 123.79 -12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 15921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 6820 22.15 - 44.31: 542 44.31 - 66.46: 100 66.46 - 88.61: 29 88.61 - 110.76: 10 Dihedral angle restraints: 7501 sinusoidal: 3400 harmonic: 4101 Sorted by residual: dihedral pdb=" CB CYS A1272 " pdb=" SG CYS A1272 " pdb=" SG CYS A1284 " pdb=" CB CYS A1284 " ideal model delta sinusoidal sigma weight residual 93.00 172.70 -79.70 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 973 " pdb=" SG CYS A 973 " pdb=" SG CYS A 987 " pdb=" CB CYS A 987 " ideal model delta sinusoidal sigma weight residual 93.00 156.31 -63.31 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS A 351 " pdb=" SG CYS A 351 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -146.82 60.82 1 1.00e+01 1.00e-02 4.92e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1638 0.104 - 0.207: 98 0.207 - 0.311: 6 0.311 - 0.414: 1 0.414 - 0.518: 1 Chirality restraints: 1744 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O3 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.70e+02 chirality pdb=" C2 NAG B4702 " pdb=" C1 NAG B4702 " pdb=" C3 NAG B4702 " pdb=" N2 NAG B4702 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C2 A2G A4703 " pdb=" C1 A2G A4703 " pdb=" C3 A2G A4703 " pdb=" N2 A2G A4703 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1741 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.203 2.00e-02 2.50e+03 1.66e-01 3.47e+02 pdb=" C7 NAG F 2 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.268 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.153 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" C7 NAG I 1 " -0.047 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.199 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B4702 " 0.152 2.00e-02 2.50e+03 1.24e-01 1.91e+02 pdb=" C7 NAG B4702 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B4702 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG B4702 " -0.194 2.00e-02 2.50e+03 pdb=" O7 NAG B4702 " -0.028 2.00e-02 2.50e+03 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 345 2.68 - 3.24: 11860 3.24 - 3.79: 17921 3.79 - 4.35: 24388 4.35 - 4.90: 39481 Nonbonded interactions: 93995 Sorted by model distance: nonbonded pdb=" OG1 THR A1065 " pdb=" C1 A2G A4705 " model vdw 2.126 3.470 nonbonded pdb=" OD2 ASP B2731 " pdb="CA CA B4704 " model vdw 2.129 2.510 nonbonded pdb=" OD2 ASP A1097 " pdb="CA CA A4717 " model vdw 2.142 2.510 nonbonded pdb=" OD1 ASP B2721 " pdb="CA CA B4704 " model vdw 2.156 2.510 nonbonded pdb=" OD1 ASP A1087 " pdb="CA CA A4717 " model vdw 2.167 2.510 ... (remaining 93990 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 'D' selection = chain 'I' } ncs_group { reference = chain 'E' 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: 0.970 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.090 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.007 0.456 11826 Z= 0.579 Angle : 0.922 13.894 16086 Z= 0.472 Chirality : 0.056 0.518 1744 Planarity : 0.008 0.166 2108 Dihedral : 16.694 110.763 4704 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 2.07 % Allowed : 16.38 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1412 helix: 1.78 (0.47), residues: 112 sheet: -0.66 (0.29), residues: 281 loop : -0.53 (0.21), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 528 HIS 0.005 0.001 HIS A1276 PHE 0.033 0.002 PHE A1062 TYR 0.019 0.002 TYR A 219 ARG 0.011 0.001 ARG A 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 8) link_NAG-ASN : angle 4.54252 ( 24) link_ALPHA1-6 : bond 0.00831 ( 2) link_ALPHA1-6 : angle 1.24768 ( 6) link_BETA1-4 : bond 0.00459 ( 5) link_BETA1-4 : angle 2.77358 ( 15) link_ALPHA1-3 : bond 0.00476 ( 2) link_ALPHA1-3 : angle 1.31260 ( 6) hydrogen bonds : bond 0.20163 ( 310) hydrogen bonds : angle 8.29813 ( 753) SS BOND : bond 0.00318 ( 53) SS BOND : angle 1.44439 ( 106) link_BETA1-3 : bond 0.01727 ( 1) link_BETA1-3 : angle 8.85989 ( 3) covalent geometry : bond 0.00511 (11749) covalent geometry : angle 0.88946 (15926) Misc. bond : bond 0.23193 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.166 Fit side-chains REVERT: C 268 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.6006 (mp10) REVERT: A 359 GLN cc_start: 0.8293 (mt0) cc_final: 0.8014 (mt0) REVERT: A 496 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8469 (pm20) outliers start: 26 outliers final: 19 residues processed: 120 average time/residue: 0.2285 time to fit residues: 40.3834 Evaluate side-chains 111 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2835 ILE Chi-restraints excluded: chain B residue 2837 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 HIS C 323 ASN A 321 HIS A 382 GLN A 412 ASN A 444 GLN A 456 ASN A 639 GLN A 681 ASN A 895 HIS A 978 HIS A 985 HIS A 992 ASN A1058 GLN A1099 GLN A1254 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103926 restraints weight = 19092.273| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.47 r_work: 0.3129 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11826 Z= 0.159 Angle : 0.710 14.194 16086 Z= 0.356 Chirality : 0.049 0.357 1744 Planarity : 0.004 0.040 2108 Dihedral : 11.305 90.842 2127 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.97 % Allowed : 14.63 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1412 helix: 2.17 (0.46), residues: 106 sheet: -0.47 (0.29), residues: 278 loop : -0.49 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 528 HIS 0.003 0.001 HIS A 985 PHE 0.013 0.002 PHE B2778 TYR 0.016 0.002 TYR C 339 ARG 0.007 0.001 ARG A 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 8) link_NAG-ASN : angle 2.90826 ( 24) link_ALPHA1-6 : bond 0.01213 ( 2) link_ALPHA1-6 : angle 2.53623 ( 6) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 2.57647 ( 15) link_ALPHA1-3 : bond 0.00947 ( 2) link_ALPHA1-3 : angle 2.52484 ( 6) hydrogen bonds : bond 0.04490 ( 310) hydrogen bonds : angle 6.18622 ( 753) SS BOND : bond 0.00312 ( 53) SS BOND : angle 0.91751 ( 106) link_BETA1-3 : bond 0.03493 ( 1) link_BETA1-3 : angle 9.04226 ( 3) covalent geometry : bond 0.00353 (11749) covalent geometry : angle 0.68140 (15926) Misc. bond : bond 0.00091 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7971 (mpp80) cc_final: 0.7288 (mtt90) REVERT: C 268 GLN cc_start: 0.6021 (OUTLIER) cc_final: 0.5449 (mp10) REVERT: C 298 GLN cc_start: 0.8757 (mt0) cc_final: 0.8389 (mm-40) REVERT: C 347 ASP cc_start: 0.7459 (t0) cc_final: 0.7240 (t0) REVERT: A 308 MET cc_start: 0.4531 (OUTLIER) cc_final: 0.4016 (tpt) REVERT: A 359 GLN cc_start: 0.8233 (mt0) cc_final: 0.7784 (mt0) REVERT: A 496 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: A 631 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: A 3194 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7253 (ttp80) REVERT: A 3198 ASN cc_start: 0.8318 (t0) cc_final: 0.8095 (t0) REVERT: B 2808 HIS cc_start: 0.6097 (m90) cc_final: 0.5872 (m170) outliers start: 50 outliers final: 23 residues processed: 139 average time/residue: 0.2493 time to fit residues: 49.9746 Evaluate side-chains 117 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2795 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 108 optimal weight: 0.0270 chunk 107 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN A 645 HIS A1160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101433 restraints weight = 19454.418| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.29 r_work: 0.3143 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11826 Z= 0.132 Angle : 0.638 12.417 16086 Z= 0.321 Chirality : 0.047 0.343 1744 Planarity : 0.004 0.038 2108 Dihedral : 10.079 83.254 2115 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.05 % Allowed : 15.34 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1412 helix: 2.33 (0.47), residues: 106 sheet: -0.46 (0.30), residues: 265 loop : -0.50 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 528 HIS 0.004 0.001 HIS A 510 PHE 0.010 0.001 PHE A1071 TYR 0.011 0.001 TYR C 297 ARG 0.005 0.000 ARG C 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 8) link_NAG-ASN : angle 2.47217 ( 24) link_ALPHA1-6 : bond 0.01286 ( 2) link_ALPHA1-6 : angle 2.54060 ( 6) link_BETA1-4 : bond 0.00480 ( 5) link_BETA1-4 : angle 2.37848 ( 15) link_ALPHA1-3 : bond 0.01228 ( 2) link_ALPHA1-3 : angle 1.85889 ( 6) hydrogen bonds : bond 0.04017 ( 310) hydrogen bonds : angle 5.80560 ( 753) SS BOND : bond 0.00206 ( 53) SS BOND : angle 0.81499 ( 106) link_BETA1-3 : bond 0.02894 ( 1) link_BETA1-3 : angle 7.76791 ( 3) covalent geometry : bond 0.00291 (11749) covalent geometry : angle 0.61363 (15926) Misc. bond : bond 0.00060 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 ARG cc_start: 0.7731 (mpp80) cc_final: 0.7199 (mtt90) REVERT: C 268 GLN cc_start: 0.5867 (OUTLIER) cc_final: 0.5186 (mp10) REVERT: C 295 ASN cc_start: 0.8953 (p0) cc_final: 0.8655 (p0) REVERT: C 298 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8427 (mm-40) REVERT: A 321 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5054 (m-70) REVERT: A 359 GLN cc_start: 0.8152 (mt0) cc_final: 0.7527 (mt0) REVERT: A 496 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: A 631 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: A 1230 MET cc_start: 0.8170 (tpt) cc_final: 0.7718 (tpp) REVERT: A 3194 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7229 (ttp80) outliers start: 51 outliers final: 25 residues processed: 153 average time/residue: 0.2469 time to fit residues: 54.4531 Evaluate side-chains 124 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 3194 ARG Chi-restraints excluded: chain B residue 2769 ASP Chi-restraints excluded: chain B residue 2786 GLU Chi-restraints excluded: chain B residue 2788 THR Chi-restraints excluded: chain B residue 2797 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.3188 > 50: distance: 39 - 101: 28.594 distance: 42 - 98: 26.683 distance: 59 - 64: 30.003 distance: 64 - 65: 32.523 distance: 65 - 66: 57.471 distance: 65 - 68: 11.044 distance: 66 - 67: 58.533 distance: 66 - 75: 28.880 distance: 68 - 69: 39.095 distance: 69 - 70: 28.098 distance: 70 - 71: 29.411 distance: 71 - 72: 5.861 distance: 72 - 73: 21.572 distance: 72 - 74: 42.134 distance: 76 - 77: 42.826 distance: 77 - 78: 46.265 distance: 77 - 79: 57.873 distance: 79 - 80: 3.937 distance: 80 - 81: 52.522 distance: 81 - 82: 30.218 distance: 81 - 83: 49.738 distance: 83 - 84: 39.469 distance: 84 - 85: 7.964 distance: 84 - 87: 23.597 distance: 85 - 86: 7.272 distance: 85 - 92: 41.555 distance: 87 - 88: 28.402 distance: 88 - 89: 21.114 distance: 89 - 90: 5.096 distance: 89 - 91: 29.131 distance: 92 - 93: 27.886 distance: 93 - 94: 48.302 distance: 93 - 96: 26.253 distance: 94 - 95: 43.754 distance: 94 - 98: 33.996 distance: 96 - 97: 22.819 distance: 98 - 99: 49.145 distance: 99 - 100: 33.363 distance: 99 - 102: 8.500 distance: 100 - 101: 10.470 distance: 100 - 106: 31.680 distance: 102 - 103: 33.139 distance: 102 - 104: 37.136 distance: 103 - 105: 19.951 distance: 106 - 107: 17.632 distance: 106 - 112: 28.203 distance: 107 - 108: 49.288 distance: 107 - 110: 27.346 distance: 110 - 111: 10.818 distance: 111 - 112: 44.031 distance: 113 - 114: 30.828 distance: 114 - 115: 20.601 distance: 115 - 116: 17.976 distance: 115 - 117: 39.321 distance: 117 - 118: 13.724 distance: 118 - 119: 19.984 distance: 118 - 121: 40.931 distance: 119 - 120: 7.805 distance: 119 - 126: 14.340 distance: 121 - 122: 32.730 distance: 122 - 123: 21.475 distance: 123 - 124: 18.228 distance: 123 - 125: 28.551 distance: 126 - 127: 35.501 distance: 127 - 128: 20.936 distance: 127 - 130: 40.439 distance: 128 - 129: 11.713 distance: 128 - 140: 10.539 distance: 130 - 131: 19.864 distance: 131 - 132: 47.915 distance: 131 - 133: 23.535 distance: 132 - 134: 28.616 distance: 133 - 135: 19.306 distance: 133 - 136: 23.426 distance: 134 - 135: 31.828 distance: 135 - 137: 25.589 distance: 136 - 138: 19.712 distance: 137 - 139: 34.066 distance: 138 - 139: 18.102