Starting phenix.real_space_refine on Thu Jun 19 04:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjn_41305/06_2025/8tjn_41305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjn_41305/06_2025/8tjn_41305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tjn_41305/06_2025/8tjn_41305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjn_41305/06_2025/8tjn_41305.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjn_41305/06_2025/8tjn_41305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjn_41305/06_2025/8tjn_41305.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 P 1 5.49 5 S 77 5.16 5 C 13698 2.51 5 N 3910 2.21 5 O 4217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21903 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 883, 6556 Classifications: {'peptide': 883} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 830} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'4HH:plan-3': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 9300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1257, 9300 Classifications: {'peptide': 1257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 68, 'TRANS': 1188} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1450 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1565 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1493 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 181} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 14.28, per 1000 atoms: 0.65 Number of scatterers: 21903 At special positions: 0 Unit cell: (112.2, 176, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 1 15.00 O 4217 8.00 N 3910 7.00 C 13698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 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: 5.43 Conformation dependent library (CDL) restraints added in 2.9 seconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5300 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 29 sheets defined 33.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.550A pdb=" N GLU B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 120 through 138 removed outlier: 4.105A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.671A pdb=" N LEU B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.945A pdb=" N GLY B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 312 through 327 removed outlier: 3.913A pdb=" N GLN B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 4.272A pdb=" N ILE B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.826A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 4.057A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.546A pdb=" N LEU B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 530 through 542 Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.507A pdb=" N ALA B 573 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 574 " --> pdb=" O GLY B 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 570 through 574' Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 587 through 599 Proline residue: B 596 - end of helix Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 624 through 645 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 657 through 667 removed outlier: 4.477A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 679 removed outlier: 4.025A pdb=" N ARG B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 837 through 848 removed outlier: 3.802A pdb=" N ILE B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 removed outlier: 3.919A pdb=" N PHE B 868 " --> pdb=" O SER B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.738A pdb=" N VAL B 887 " --> pdb=" O ASP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1428 Processing helix chain 'B' and resid 1448 through 1464 removed outlier: 3.550A pdb=" N GLU B1454 " --> pdb=" O LEU B1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1475 Processing helix chain 'B' and resid 1477 through 1487 Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.685A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 removed outlier: 3.567A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.890A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.518A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 312 through 328 removed outlier: 4.342A pdb=" N GLN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.990A pdb=" N ILE A 334 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.758A pdb=" N ILE A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.785A pdb=" N SER A 374 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.562A pdb=" N THR A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.660A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 580 through 595 removed outlier: 3.517A pdb=" N CYS A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.939A pdb=" N PHE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 645 Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 670 through 683 Processing helix chain 'A' and resid 812 through 824 Processing helix chain 'A' and resid 836 through 847 removed outlier: 4.278A pdb=" N ALA A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.792A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.596A pdb=" N ALA A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1078 Processing helix chain 'A' and resid 1093 through 1100 removed outlier: 3.884A pdb=" N HIS A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1151 through 1164 Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1182 through 1192 Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1240 through 1248 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.916A pdb=" N VAL A1252 " --> pdb=" O SER A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1305 removed outlier: 4.134A pdb=" N GLY A1291 " --> pdb=" O GLY A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1340 through 1354 removed outlier: 3.565A pdb=" N ALA A1344 " --> pdb=" O PRO A1340 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A1345 " --> pdb=" O PRO A1341 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 Processing helix chain 'A' and resid 1385 through 1390 removed outlier: 4.258A pdb=" N ARG A1390 " --> pdb=" O ASP A1387 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.540A pdb=" N SER D 193 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.029A pdb=" N LEU B 367 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 370 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 336 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 296 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 455 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU B 294 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 276 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N MET B 40 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET B 274 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N CYS B 42 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA B 272 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 200 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 200 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 151 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 201 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 153 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 227 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 231 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 272 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N CYS A 42 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET A 274 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET A 40 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 276 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 370 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AA5, first strand: chain 'B' and resid 649 through 654 removed outlier: 6.403A pdb=" N ALA B 558 " --> pdb=" O PRO B 649 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 651 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 653 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 559 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 784 through 786 removed outlier: 4.233A pdb=" N PHE B 784 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.604A pdb=" N GLU A 427 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 561 removed outlier: 6.373A pdb=" N VAL A 559 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 828 " --> pdb=" O ILE A 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1120 through 1127 removed outlier: 4.289A pdb=" N VAL A1120 " --> pdb=" O THR A 937 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 935 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA A1313 " --> pdb=" O VAL A1361 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER A1274 " --> pdb=" O TRP A1314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 974 through 977 removed outlier: 6.494A pdb=" N GLY A 947 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 977 " --> pdb=" O GLY A 947 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP A 949 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR A 948 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A1002 " --> pdb=" O THR A 948 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1169 through 1170 removed outlier: 6.934A pdb=" N THR A1142 " --> pdb=" O ALA A1223 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE A1225 " --> pdb=" O THR A1142 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A1144 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A1222 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL A1271 " --> pdb=" O SER A1222 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A1224 " --> pdb=" O VAL A1271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 25 Processing sheet with id=AB5, first strand: chain 'C' and resid 62 through 63 removed outlier: 5.235A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C 36 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 96 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.716A pdb=" N THR C 158 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.694A pdb=" N ASP D 127 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 57 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 70 " --> pdb=" O ASN D 74 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN D 74 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB9, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AC1, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.001A pdb=" N LYS D 167 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 219 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 218 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 227 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AC3, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC4, first strand: chain 'E' and resid 47 through 52 removed outlier: 6.793A pdb=" N TRP E 38 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE E 52 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET E 36 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 149 through 152 removed outlier: 6.255A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 184 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 176 " --> pdb=" O SER E 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AC7, first strand: chain 'F' and resid 28 through 29 Processing sheet with id=AC8, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AC9, first strand: chain 'F' and resid 66 through 69 removed outlier: 5.535A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE F 69 " --> pdb=" O TRP F 56 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 138 through 140 removed outlier: 3.748A pdb=" N LEU F 157 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE F 140 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL F 155 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN F 182 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 167 through 168 removed outlier: 3.563A pdb=" N LYS F 167 " --> pdb=" O THR F 219 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 219 " --> pdb=" O LYS F 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 809 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.70 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7501 1.34 - 1.46: 4963 1.46 - 1.58: 9766 1.58 - 1.70: 2 1.70 - 1.82: 120 Bond restraints: 22352 Sorted by residual: bond pdb=" N VAL B 684 " pdb=" CA VAL B 684 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.35e+00 bond pdb=" N ILE B 685 " pdb=" CA ILE B 685 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N LEU B 837 " pdb=" CA LEU B 837 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.52e-02 4.33e+03 3.82e+00 bond pdb=" CA VAL D 154 " pdb=" CB VAL D 154 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.60e+00 bond pdb=" CA VAL B 684 " pdb=" C VAL B 684 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.27e-02 6.20e+03 1.59e+00 ... (remaining 22347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 30034 2.37 - 4.74: 322 4.74 - 7.10: 34 7.10 - 9.47: 13 9.47 - 11.84: 4 Bond angle restraints: 30407 Sorted by residual: angle pdb=" CA LYS B1414 " pdb=" CB LYS B1414 " pdb=" CG LYS B1414 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 angle pdb=" C PRO C 154 " pdb=" N GLU C 155 " pdb=" CA GLU C 155 " ideal model delta sigma weight residual 121.80 132.60 -10.80 2.44e+00 1.68e-01 1.96e+01 angle pdb=" CB MET A1339 " pdb=" CG MET A1339 " pdb=" SD MET A1339 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA MET A1339 " pdb=" CB MET A1339 " pdb=" CG MET A1339 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA GLU F 102 " pdb=" CB GLU F 102 " pdb=" CG GLU F 102 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.40e+01 ... (remaining 30402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11691 17.81 - 35.62: 1239 35.62 - 53.43: 309 53.43 - 71.24: 58 71.24 - 89.05: 32 Dihedral angle restraints: 13329 sinusoidal: 5051 harmonic: 8278 Sorted by residual: dihedral pdb=" CB CYS F 39 " pdb=" SG CYS F 39 " pdb=" SG CYS F 109 " pdb=" CB CYS F 109 " ideal model delta sinusoidal sigma weight residual -86.00 -161.91 75.91 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS D 156 " pdb=" SG CYS D 156 " pdb=" SG CYS D 216 " pdb=" CB CYS D 216 " ideal model delta sinusoidal sigma weight residual 93.00 29.39 63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS F 156 " pdb=" SG CYS F 156 " pdb=" SG CYS F 216 " pdb=" CB CYS F 216 " ideal model delta sinusoidal sigma weight residual -86.00 -149.21 63.21 1 1.00e+01 1.00e-02 5.27e+01 ... (remaining 13326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3133 0.075 - 0.150: 294 0.150 - 0.224: 5 0.224 - 0.299: 1 0.299 - 0.374: 1 Chirality restraints: 3434 Sorted by residual: chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CB VAL C 118 " pdb=" CA VAL C 118 " pdb=" CG1 VAL C 118 " pdb=" CG2 VAL C 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 685 " pdb=" N ILE B 685 " pdb=" C ILE B 685 " pdb=" CB ILE B 685 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 3431 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 81 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO B 82 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1339 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A1340 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1340 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1340 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 120 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B 121 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.028 5.00e-02 4.00e+02 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1987 2.74 - 3.28: 22494 3.28 - 3.82: 36565 3.82 - 4.36: 40094 4.36 - 4.90: 69413 Nonbonded interactions: 170553 Sorted by model distance: nonbonded pdb=" OG1 THR C 92 " pdb=" OE1 GLU C 93 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR E 92 " pdb=" OE1 GLU E 93 " model vdw 2.200 3.040 nonbonded pdb=" OE1 GLU D 217 " pdb=" OG1 THR D 228 " model vdw 2.202 3.040 nonbonded pdb=" O LEU B 175 " pdb=" OG1 THR B 179 " model vdw 2.224 3.040 nonbonded pdb=" O PRO B1468 " pdb=" OG1 THR B1471 " model vdw 2.230 3.040 ... (remaining 170548 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 'C' selection = (chain 'E' and (resid 3 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 126 or resid 147 through 220)) } ncs_group { reference = (chain 'D' and (resid 17 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 143 or resid 154 through 172 or re \ sid 178 through 231)) selection = (chain 'F' and (resid 17 through 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB )) or resid 190 through 209 or resid 215 through 231)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 10.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 51.960 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.120 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 : 0.003 0.046 22360 Z= 0.121 Angle : 0.599 11.841 30423 Z= 0.305 Chirality : 0.041 0.374 3434 Planarity : 0.004 0.055 4009 Dihedral : 16.133 89.049 8005 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.67 % Favored : 92.95 % Rotamer: Outliers : 1.55 % Allowed : 21.28 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.52 (0.16), residues: 2892 helix: 1.69 (0.19), residues: 865 sheet: -0.70 (0.22), residues: 563 loop : -1.51 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 569 HIS 0.003 0.001 HIS D 220 PHE 0.016 0.001 PHE B 605 TYR 0.012 0.001 TYR F 70 ARG 0.005 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.19627 ( 809) hydrogen bonds : angle 6.95791 ( 2259) SS BOND : bond 0.00158 ( 8) SS BOND : angle 0.54218 ( 16) covalent geometry : bond 0.00258 (22352) covalent geometry : angle 0.59886 (30407) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8588 (tpp) cc_final: 0.8315 (tpp) REVERT: B 685 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6853 (pt) REVERT: A 274 MET cc_start: 0.8892 (tpp) cc_final: 0.8280 (tpt) REVERT: A 572 MET cc_start: 0.7818 (mpp) cc_final: 0.7229 (mpp) REVERT: A 631 MET cc_start: 0.7948 (mmt) cc_final: 0.7307 (mmt) REVERT: A 635 MET cc_start: 0.9424 (mtp) cc_final: 0.9185 (mmm) REVERT: A 990 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7798 (pt) REVERT: A 1322 MET cc_start: 0.5186 (ptt) cc_final: 0.3776 (pmm) REVERT: D 40 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8471 (ttp80) REVERT: F 20 MET cc_start: 0.9518 (pp-130) cc_final: 0.8980 (ppp) REVERT: F 110 MET cc_start: 0.8660 (tpp) cc_final: 0.8301 (tpp) outliers start: 35 outliers final: 28 residues processed: 86 average time/residue: 0.3670 time to fit residues: 51.8486 Evaluate side-chains 80 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 1456 ARG Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1134 ASP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 264 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS A 597 HIS A 628 GLN A 657 GLN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN F 159 ASN F 182 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.044543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.026176 restraints weight = 218913.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.026587 restraints weight = 140888.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.026882 restraints weight = 108917.821| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22360 Z= 0.171 Angle : 0.593 11.300 30423 Z= 0.302 Chirality : 0.041 0.230 3434 Planarity : 0.004 0.054 4009 Dihedral : 5.352 69.867 3245 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.71 % Favored : 91.98 % Rotamer: Outliers : 2.92 % Allowed : 19.25 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2892 helix: 1.67 (0.18), residues: 893 sheet: -0.61 (0.22), residues: 572 loop : -1.60 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.004 0.001 HIS A1334 PHE 0.015 0.001 PHE B 605 TYR 0.013 0.001 TYR F 70 ARG 0.004 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 809) hydrogen bonds : angle 5.18832 ( 2259) SS BOND : bond 0.00488 ( 8) SS BOND : angle 0.94470 ( 16) covalent geometry : bond 0.00377 (22352) covalent geometry : angle 0.59240 (30407) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 50 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 MET cc_start: 0.9098 (tmm) cc_final: 0.8889 (ptm) REVERT: B 609 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: A 111 MET cc_start: 0.8132 (ptm) cc_final: 0.7796 (ptm) REVERT: A 572 MET cc_start: 0.7844 (mpp) cc_final: 0.7415 (mpp) REVERT: A 631 MET cc_start: 0.7758 (mmt) cc_final: 0.7316 (mmt) REVERT: A 990 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7595 (pt) REVERT: A 1322 MET cc_start: 0.5791 (ptt) cc_final: 0.4317 (pmm) REVERT: D 110 MET cc_start: 0.9305 (mmm) cc_final: 0.8647 (tpt) REVERT: E 145 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7957 (tm) REVERT: F 20 MET cc_start: 0.9370 (pp-130) cc_final: 0.8970 (ppp) REVERT: F 71 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8932 (pp) REVERT: F 159 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.8908 (t0) outliers start: 66 outliers final: 37 residues processed: 116 average time/residue: 0.3328 time to fit residues: 63.2287 Evaluate side-chains 92 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 50 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 158 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 183 optimal weight: 0.0870 chunk 201 optimal weight: 6.9990 chunk 244 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.044463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.026074 restraints weight = 218266.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.026460 restraints weight = 140294.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.026786 restraints weight = 108768.839| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22360 Z= 0.154 Angle : 0.568 11.285 30423 Z= 0.288 Chirality : 0.041 0.214 3434 Planarity : 0.004 0.053 4009 Dihedral : 5.056 70.865 3224 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.40 % Favored : 92.32 % Rotamer: Outliers : 3.32 % Allowed : 19.65 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2892 helix: 1.68 (0.18), residues: 896 sheet: -0.59 (0.22), residues: 550 loop : -1.63 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 PHE 0.014 0.001 PHE A 97 TYR 0.014 0.001 TYR F 70 ARG 0.003 0.000 ARG A1098 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 809) hydrogen bonds : angle 4.89861 ( 2259) SS BOND : bond 0.00450 ( 8) SS BOND : angle 0.88198 ( 16) covalent geometry : bond 0.00346 (22352) covalent geometry : angle 0.56822 (30407) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 50 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 609 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: A 111 MET cc_start: 0.8192 (ptm) cc_final: 0.7794 (ptm) REVERT: A 240 MET cc_start: 0.9091 (mmm) cc_final: 0.8717 (mmm) REVERT: A 247 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8594 (pmm) REVERT: A 309 SER cc_start: 0.9543 (OUTLIER) cc_final: 0.9181 (p) REVERT: A 520 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8680 (m-70) REVERT: A 572 MET cc_start: 0.7877 (mpp) cc_final: 0.7422 (mpp) REVERT: A 631 MET cc_start: 0.7875 (mmt) cc_final: 0.7326 (mmt) REVERT: A 990 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7530 (pt) REVERT: A 1322 MET cc_start: 0.5860 (ptt) cc_final: 0.4387 (pmm) REVERT: D 110 MET cc_start: 0.9288 (mmm) cc_final: 0.8652 (tpt) REVERT: E 145 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8009 (tm) REVERT: F 20 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9023 (ppp) outliers start: 75 outliers final: 43 residues processed: 121 average time/residue: 0.3418 time to fit residues: 68.1388 Evaluate side-chains 98 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 48 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 273 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 197 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 282 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN E 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.044234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.025719 restraints weight = 222077.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.026130 restraints weight = 143189.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.026360 restraints weight = 111993.308| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22360 Z= 0.194 Angle : 0.602 11.411 30423 Z= 0.303 Chirality : 0.041 0.151 3434 Planarity : 0.004 0.052 4009 Dihedral : 5.162 73.049 3218 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 4.03 % Allowed : 19.51 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.59 (0.16), residues: 2892 helix: 1.66 (0.18), residues: 896 sheet: -0.68 (0.22), residues: 551 loop : -1.66 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 PHE 0.013 0.001 PHE A 868 TYR 0.012 0.001 TYR F 70 ARG 0.004 0.000 ARG B1456 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 809) hydrogen bonds : angle 4.78577 ( 2259) SS BOND : bond 0.00427 ( 8) SS BOND : angle 1.14606 ( 16) covalent geometry : bond 0.00432 (22352) covalent geometry : angle 0.60135 (30407) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 49 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8535 (mmt-90) REVERT: B 176 MET cc_start: 0.8698 (tpp) cc_final: 0.8459 (tpp) REVERT: B 391 MET cc_start: 0.9650 (OUTLIER) cc_final: 0.8751 (mpp) REVERT: A 111 MET cc_start: 0.8365 (ptm) cc_final: 0.8142 (ptt) REVERT: A 240 MET cc_start: 0.9079 (mmm) cc_final: 0.8835 (mmm) REVERT: A 247 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8612 (pmm) REVERT: A 309 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9180 (p) REVERT: A 520 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.8621 (m170) REVERT: A 572 MET cc_start: 0.7850 (mpp) cc_final: 0.7362 (mpp) REVERT: A 588 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8618 (mmp80) REVERT: A 631 MET cc_start: 0.7779 (mmt) cc_final: 0.7305 (mmt) REVERT: A 990 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7356 (pt) REVERT: A 1322 MET cc_start: 0.6018 (ptt) cc_final: 0.4515 (pmm) REVERT: E 145 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7897 (tm) REVERT: F 20 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8963 (ppp) REVERT: F 71 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8982 (pp) outliers start: 91 outliers final: 57 residues processed: 134 average time/residue: 0.3187 time to fit residues: 69.2748 Evaluate side-chains 116 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 49 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 196 optimal weight: 30.0000 chunk 211 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1292 ASN ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.044356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.025968 restraints weight = 220126.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.026454 restraints weight = 141492.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.026749 restraints weight = 108483.221| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22360 Z= 0.132 Angle : 0.562 11.453 30423 Z= 0.282 Chirality : 0.041 0.337 3434 Planarity : 0.004 0.052 4009 Dihedral : 5.045 75.055 3218 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.95 % Favored : 92.74 % Rotamer: Outliers : 3.23 % Allowed : 20.66 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2892 helix: 1.78 (0.18), residues: 895 sheet: -0.68 (0.22), residues: 562 loop : -1.66 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 949 HIS 0.005 0.001 HIS A1334 PHE 0.012 0.001 PHE A 868 TYR 0.014 0.001 TYR F 70 ARG 0.003 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 809) hydrogen bonds : angle 4.56428 ( 2259) SS BOND : bond 0.00384 ( 8) SS BOND : angle 0.81482 ( 16) covalent geometry : bond 0.00300 (22352) covalent geometry : angle 0.56182 (30407) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 49 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.8724 (mpp) REVERT: A 240 MET cc_start: 0.9003 (mmm) cc_final: 0.8718 (mmm) REVERT: A 247 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8528 (pmm) REVERT: A 309 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.9166 (p) REVERT: A 520 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.8615 (m170) REVERT: A 572 MET cc_start: 0.7797 (mpp) cc_final: 0.7252 (mpp) REVERT: A 588 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8606 (mmp80) REVERT: A 631 MET cc_start: 0.7788 (mmt) cc_final: 0.7483 (mmm) REVERT: A 990 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7071 (pt) REVERT: A 1322 MET cc_start: 0.6087 (ptt) cc_final: 0.4613 (pmm) REVERT: E 145 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7777 (tm) REVERT: F 20 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9004 (ppp) outliers start: 73 outliers final: 47 residues processed: 119 average time/residue: 0.3078 time to fit residues: 60.1701 Evaluate side-chains 103 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 48 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 182 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 645 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN E 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.044042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.025401 restraints weight = 217753.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.025858 restraints weight = 143754.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.026131 restraints weight = 110806.353| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 22360 Z= 0.241 Angle : 0.646 11.767 30423 Z= 0.324 Chirality : 0.042 0.225 3434 Planarity : 0.004 0.050 4009 Dihedral : 5.291 77.757 3214 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.92 % Favored : 90.73 % Rotamer: Outliers : 3.72 % Allowed : 20.62 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.70 (0.16), residues: 2892 helix: 1.60 (0.18), residues: 897 sheet: -0.86 (0.22), residues: 570 loop : -1.70 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 55 HIS 0.006 0.001 HIS A1334 PHE 0.013 0.002 PHE A 868 TYR 0.013 0.002 TYR F 195 ARG 0.005 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 809) hydrogen bonds : angle 4.82868 ( 2259) SS BOND : bond 0.00375 ( 8) SS BOND : angle 1.08394 ( 16) covalent geometry : bond 0.00533 (22352) covalent geometry : angle 0.64598 (30407) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 48 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8656 (mmt-90) REVERT: B 391 MET cc_start: 0.9616 (OUTLIER) cc_final: 0.8762 (mpp) REVERT: A 240 MET cc_start: 0.9091 (mmm) cc_final: 0.8824 (mmm) REVERT: A 247 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8632 (pmm) REVERT: A 309 SER cc_start: 0.9547 (OUTLIER) cc_final: 0.9179 (p) REVERT: A 520 HIS cc_start: 0.9009 (OUTLIER) cc_final: 0.8608 (m170) REVERT: A 572 MET cc_start: 0.7798 (mpp) cc_final: 0.7244 (mpp) REVERT: A 588 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8627 (mmp80) REVERT: A 631 MET cc_start: 0.7887 (mmt) cc_final: 0.7423 (mmm) REVERT: A 990 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7056 (pt) REVERT: A 1322 MET cc_start: 0.6300 (ptt) cc_final: 0.4688 (pmm) REVERT: D 40 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8507 (ttp80) REVERT: E 145 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7876 (tm) REVERT: F 71 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8959 (pp) outliers start: 84 outliers final: 56 residues processed: 127 average time/residue: 0.3656 time to fit residues: 74.1314 Evaluate side-chains 113 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 47 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 84 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 272 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 137 optimal weight: 0.0270 chunk 148 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN A1292 ASN ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.044248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.026032 restraints weight = 220252.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.026465 restraints weight = 141949.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.026766 restraints weight = 108580.468| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22360 Z= 0.116 Angle : 0.575 11.797 30423 Z= 0.286 Chirality : 0.041 0.293 3434 Planarity : 0.004 0.051 4009 Dihedral : 5.069 79.507 3214 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.74 % Favored : 92.91 % Rotamer: Outliers : 3.27 % Allowed : 21.33 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.58 (0.16), residues: 2892 helix: 1.73 (0.18), residues: 896 sheet: -0.78 (0.22), residues: 560 loop : -1.64 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 55 HIS 0.006 0.001 HIS B 645 PHE 0.014 0.001 PHE C 173 TYR 0.013 0.001 TYR F 70 ARG 0.003 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 809) hydrogen bonds : angle 4.50567 ( 2259) SS BOND : bond 0.00375 ( 8) SS BOND : angle 0.83342 ( 16) covalent geometry : bond 0.00265 (22352) covalent geometry : angle 0.57460 (30407) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 48 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9592 (OUTLIER) cc_final: 0.8794 (mpp) REVERT: A 240 MET cc_start: 0.9044 (mmm) cc_final: 0.8761 (mmm) REVERT: A 309 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.9176 (p) REVERT: A 520 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8602 (m170) REVERT: A 572 MET cc_start: 0.7388 (mpp) cc_final: 0.7176 (mmm) REVERT: A 588 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8625 (mmp80) REVERT: A 631 MET cc_start: 0.7905 (mmt) cc_final: 0.7234 (mmt) REVERT: A 990 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6788 (pt) REVERT: A 1322 MET cc_start: 0.6526 (ptt) cc_final: 0.5000 (pmm) REVERT: D 40 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8440 (ttp80) REVERT: E 145 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7796 (tm) outliers start: 74 outliers final: 55 residues processed: 119 average time/residue: 0.3646 time to fit residues: 68.6887 Evaluate side-chains 110 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 48 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 83 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.044218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.025951 restraints weight = 220243.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.026385 restraints weight = 141852.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.026692 restraints weight = 110305.988| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22360 Z= 0.132 Angle : 0.573 11.968 30423 Z= 0.284 Chirality : 0.040 0.192 3434 Planarity : 0.004 0.051 4009 Dihedral : 5.019 82.187 3213 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.05 % Rotamer: Outliers : 3.01 % Allowed : 21.59 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2892 helix: 1.78 (0.18), residues: 896 sheet: -0.77 (0.22), residues: 561 loop : -1.62 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 55 HIS 0.005 0.001 HIS B 645 PHE 0.012 0.001 PHE C 173 TYR 0.012 0.001 TYR F 70 ARG 0.003 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 809) hydrogen bonds : angle 4.44299 ( 2259) SS BOND : bond 0.00376 ( 8) SS BOND : angle 0.79822 ( 16) covalent geometry : bond 0.00302 (22352) covalent geometry : angle 0.57332 (30407) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 48 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9611 (OUTLIER) cc_final: 0.8785 (mpp) REVERT: A 240 MET cc_start: 0.9003 (mmm) cc_final: 0.8720 (mmm) REVERT: A 274 MET cc_start: 0.8845 (tpp) cc_final: 0.8103 (tpt) REVERT: A 309 SER cc_start: 0.9543 (OUTLIER) cc_final: 0.9184 (p) REVERT: A 572 MET cc_start: 0.7304 (mpp) cc_final: 0.7099 (mmm) REVERT: A 588 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8619 (mmp80) REVERT: A 631 MET cc_start: 0.7958 (mmt) cc_final: 0.7253 (mmt) REVERT: A 990 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6981 (pt) REVERT: A 1322 MET cc_start: 0.6400 (ptt) cc_final: 0.4892 (pmm) REVERT: D 40 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8409 (ttp80) REVERT: E 145 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7893 (tm) REVERT: F 110 MET cc_start: 0.8637 (tpp) cc_final: 0.8360 (tpp) outliers start: 68 outliers final: 58 residues processed: 114 average time/residue: 0.4052 time to fit residues: 74.0458 Evaluate side-chains 112 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 48 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 32 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 26 optimal weight: 0.0020 chunk 155 optimal weight: 10.0000 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.044005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.025546 restraints weight = 219607.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.025992 restraints weight = 143453.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026236 restraints weight = 109858.371| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22360 Z= 0.221 Angle : 0.637 12.252 30423 Z= 0.316 Chirality : 0.041 0.176 3434 Planarity : 0.004 0.050 4009 Dihedral : 5.259 86.485 3213 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.64 % Favored : 91.01 % Rotamer: Outliers : 3.05 % Allowed : 21.99 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.63 (0.16), residues: 2892 helix: 1.69 (0.18), residues: 896 sheet: -0.83 (0.22), residues: 550 loop : -1.68 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1314 HIS 0.007 0.001 HIS B 340 PHE 0.012 0.002 PHE C 173 TYR 0.013 0.001 TYR F 195 ARG 0.004 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 809) hydrogen bonds : angle 4.67213 ( 2259) SS BOND : bond 0.00345 ( 8) SS BOND : angle 1.02101 ( 16) covalent geometry : bond 0.00491 (22352) covalent geometry : angle 0.63696 (30407) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 46 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9606 (OUTLIER) cc_final: 0.8805 (mpp) REVERT: B 672 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: A 240 MET cc_start: 0.9008 (mmm) cc_final: 0.8722 (mmm) REVERT: A 309 SER cc_start: 0.9555 (OUTLIER) cc_final: 0.9197 (p) REVERT: A 572 MET cc_start: 0.7225 (mpp) cc_final: 0.7000 (mmm) REVERT: A 588 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8603 (mmp80) REVERT: A 631 MET cc_start: 0.7929 (mmt) cc_final: 0.7215 (mmt) REVERT: A 990 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6324 (pt) REVERT: A 1322 MET cc_start: 0.6573 (ptt) cc_final: 0.5102 (pmm) REVERT: D 40 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8507 (ttp80) REVERT: E 145 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7887 (tm) outliers start: 69 outliers final: 56 residues processed: 113 average time/residue: 0.4350 time to fit residues: 78.0551 Evaluate side-chains 109 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 46 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 149 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.044007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.025691 restraints weight = 220512.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.026072 restraints weight = 142468.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.026353 restraints weight = 110187.129| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22360 Z= 0.189 Angle : 0.608 12.038 30423 Z= 0.302 Chirality : 0.041 0.167 3434 Planarity : 0.004 0.050 4009 Dihedral : 5.242 88.828 3213 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.95 % Favored : 91.70 % Rotamer: Outliers : 2.96 % Allowed : 22.04 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.62 (0.16), residues: 2892 helix: 1.75 (0.18), residues: 895 sheet: -0.88 (0.22), residues: 549 loop : -1.67 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 55 HIS 0.006 0.001 HIS B 340 PHE 0.012 0.001 PHE C 173 TYR 0.013 0.001 TYR F 70 ARG 0.003 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 809) hydrogen bonds : angle 4.57964 ( 2259) SS BOND : bond 0.00394 ( 8) SS BOND : angle 0.95091 ( 16) covalent geometry : bond 0.00422 (22352) covalent geometry : angle 0.60742 (30407) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 47 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9622 (OUTLIER) cc_final: 0.8761 (mpp) REVERT: B 672 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: A 240 MET cc_start: 0.8952 (mmm) cc_final: 0.8676 (mmm) REVERT: A 309 SER cc_start: 0.9555 (OUTLIER) cc_final: 0.9199 (p) REVERT: A 520 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8681 (m170) REVERT: A 588 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8625 (mmp80) REVERT: A 631 MET cc_start: 0.7906 (mmt) cc_final: 0.7259 (mmt) REVERT: A 990 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6502 (pt) REVERT: A 1322 MET cc_start: 0.6502 (ptt) cc_final: 0.5088 (pmm) REVERT: D 40 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8430 (ttp80) REVERT: E 145 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7952 (tm) outliers start: 67 outliers final: 55 residues processed: 112 average time/residue: 0.4545 time to fit residues: 84.0440 Evaluate side-chains 109 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 46 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 241 optimal weight: 0.8980 chunk 277 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 245 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.044277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.026233 restraints weight = 220291.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.026631 restraints weight = 139643.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.026931 restraints weight = 107589.956| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22360 Z= 0.106 Angle : 0.578 12.069 30423 Z= 0.284 Chirality : 0.041 0.165 3434 Planarity : 0.004 0.050 4009 Dihedral : 5.062 86.445 3213 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.09 % Favored : 92.57 % Rotamer: Outliers : 2.83 % Allowed : 22.08 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.52 (0.16), residues: 2892 helix: 1.83 (0.18), residues: 893 sheet: -0.84 (0.22), residues: 559 loop : -1.60 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.005 0.001 HIS B 645 PHE 0.012 0.001 PHE B 600 TYR 0.014 0.001 TYR F 70 ARG 0.006 0.000 ARG B1458 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 809) hydrogen bonds : angle 4.38250 ( 2259) SS BOND : bond 0.00380 ( 8) SS BOND : angle 0.74478 ( 16) covalent geometry : bond 0.00247 (22352) covalent geometry : angle 0.57752 (30407) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8331.70 seconds wall clock time: 146 minutes 48.39 seconds (8808.39 seconds total)