Starting phenix.real_space_refine on Tue Feb 20 06:20:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7h_23713/02_2024/7m7h_23713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7h_23713/02_2024/7m7h_23713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7h_23713/02_2024/7m7h_23713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7h_23713/02_2024/7m7h_23713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7h_23713/02_2024/7m7h_23713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7h_23713/02_2024/7m7h_23713.pdb" } resolution = 4.1 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= 0.003 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 16869 2.51 5 N 4866 2.21 5 O 5217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27046 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 10513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 10513 Classifications: {'peptide': 1425} Link IDs: {'PTRANS': 76, 'TRANS': 1348} Chain breaks: 2 Chain: "A" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10319 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 74, 'TRANS': 1315} Chain: "C" 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: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 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: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Time building chain proxies: 13.81, per 1000 atoms: 0.51 Number of scatterers: 27046 At special positions: 0 Unit cell: (137, 159, 170, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 5217 8.00 N 4866 7.00 C 16869 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=2.01 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 - 3.50 Amino acid : False - 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: 10.72 Conformation dependent library (CDL) restraints added in 5.3 seconds 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6556 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 35 sheets defined 33.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'B' and resid 5 through 32 removed outlier: 3.525A pdb=" N ARG B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.631A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 136 removed outlier: 3.591A pdb=" N MET B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 182 through 192 removed outlier: 3.634A pdb=" N GLY B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 5.430A 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 222 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 312 through 328 removed outlier: 4.023A pdb=" N LEU B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.778A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 removed outlier: 4.366A pdb=" N ASN B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.620A pdb=" N VAL B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 499 removed outlier: 3.684A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 492 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 528 through 540 removed outlier: 3.559A pdb=" N LEU B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 585 through 595 Processing helix chain 'B' and resid 601 through 608 removed outlier: 3.643A pdb=" N PHE B 605 " --> pdb=" O GLU B 601 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 608 " --> pdb=" O PRO B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 623 through 645 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.687A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 686 removed outlier: 3.597A pdb=" N VAL B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.510A pdb=" N ARG B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 740 removed outlier: 4.164A pdb=" N VAL B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 759 through 762 Processing helix chain 'B' and resid 763 through 770 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 837 through 847 removed outlier: 4.122A pdb=" N ILE B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.586A pdb=" N HIS B 888 " --> pdb=" O TRP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 967 removed outlier: 4.149A pdb=" N THR B 963 " --> pdb=" O ASP B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 973 removed outlier: 4.439A pdb=" N SER B 971 " --> pdb=" O ALA B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 998 Processing helix chain 'B' and resid 1017 through 1020 Processing helix chain 'B' and resid 1021 through 1037 Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 4.070A pdb=" N LEU B1067 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP B1068 " --> pdb=" O HIS B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1106 removed outlier: 3.585A pdb=" N ALA B1097 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA B1101 " --> pdb=" O ALA B1097 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA B1102 " --> pdb=" O ARG B1098 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1164 removed outlier: 3.802A pdb=" N ILE B1156 " --> pdb=" O VAL B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1174 through 1178 Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'B' and resid 1204 through 1214 Processing helix chain 'B' and resid 1240 through 1263 removed outlier: 6.271A pdb=" N ALA B1250 " --> pdb=" O ARG B1246 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B1251 " --> pdb=" O ALA B1247 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B1254 " --> pdb=" O ALA B1250 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1305 removed outlier: 3.521A pdb=" N ASN B1292 " --> pdb=" O TYR B1288 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B1304 " --> pdb=" O GLN B1300 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1335 removed outlier: 3.689A pdb=" N ARG B1333 " --> pdb=" O ASP B1329 " (cutoff:3.500A) Processing helix chain 'B' and resid 1340 through 1354 removed outlier: 4.262A pdb=" N ARG B1346 " --> pdb=" O GLU B1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1428 Processing helix chain 'B' and resid 1448 through 1463 Processing helix chain 'B' and resid 1470 through 1475 Processing helix chain 'B' and resid 1477 through 1488 Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.566A pdb=" N ARG A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 removed outlier: 4.110A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.506A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 138 removed outlier: 3.623A pdb=" N LEU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.910A pdb=" N LEU A 144 " --> pdb=" O PRO A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 4.313A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.683A 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 244 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.661A pdb=" N ARG A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.550A pdb=" N GLY A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.513A pdb=" N GLU A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.288A pdb=" N ASN A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 386 through 398 removed outlier: 4.322A pdb=" N VAL A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.591A pdb=" N ARG A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.617A pdb=" N SER A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 3.661A pdb=" N ALA A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.866A pdb=" N PHE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 removed outlier: 3.848A pdb=" N GLU A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 645 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 657 through 667 removed outlier: 3.813A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.599A pdb=" N VAL A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.609A pdb=" N GLU A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.529A pdb=" N TRP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 Processing helix chain 'A' and resid 837 through 843 Processing helix chain 'A' and resid 864 through 879 removed outlier: 3.505A pdb=" N PHE A 868 " --> pdb=" O SER A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.809A pdb=" N VAL A 887 " --> pdb=" O ASP A 883 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 921 through 927 removed outlier: 4.071A pdb=" N VAL A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 967 removed outlier: 4.088A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 998 Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1021 through 1037 Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 4.038A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 3.564A pdb=" N ALA A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA A1102 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 3.926A pdb=" N ILE A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1180 through 1192 Processing helix chain 'A' and resid 1204 through 1215 Processing helix chain 'A' and resid 1240 through 1263 removed outlier: 6.094A pdb=" N ALA A1250 " --> pdb=" O ARG A1246 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1280 Processing helix chain 'A' and resid 1288 through 1305 removed outlier: 3.589A pdb=" N SER A1304 " --> pdb=" O GLN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1340 through 1354 removed outlier: 4.480A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1370 Processing helix chain 'A' and resid 1385 through 1390 removed outlier: 3.682A pdb=" N ARG A1389 " --> pdb=" O ASP A1386 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 69 removed outlier: 4.118A pdb=" N LYS C 69 " --> pdb=" O ALA C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.802A pdb=" N TYR D 208 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 209 " --> pdb=" O ALA D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 209' Processing helix chain 'E' and resid 66 through 69 removed outlier: 4.118A pdb=" N LYS E 69 " --> pdb=" O ALA E 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 66 through 69' Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.802A pdb=" N TYR F 208 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU F 209 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 210 " --> pdb=" O ASP F 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 205 through 210' Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 199 removed outlier: 7.953A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 272 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 42 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET B 274 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N MET B 40 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 276 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU B 294 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 455 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 296 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 336 " --> pdb=" O ARG B 437 " (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 367 through 369 removed outlier: 5.743A pdb=" N LEU B 367 " --> pdb=" O SER B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.560A pdb=" N PHE B 524 " --> pdb=" O TRP B 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 652 through 654 removed outlier: 6.704A pdb=" N VAL B 559 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 713 through 719 removed outlier: 5.189A pdb=" N ILE B 714 " --> pdb=" O ALA B 726 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ALA B 726 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER B 722 " --> pdb=" O ASN B 718 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 694 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 784 through 786 removed outlier: 4.811A pdb=" N PHE B 784 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 975 through 980 removed outlier: 3.898A pdb=" N ARG B 977 " --> pdb=" O TRP B 949 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 979 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 948 " --> pdb=" O GLY B1002 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU B1004 " --> pdb=" O THR B 948 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU B 950 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B1006 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA B 952 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA B1008 " --> pdb=" O ALA B 952 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU B1007 " --> pdb=" O VAL B1046 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLU B1048 " --> pdb=" O LEU B1007 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B1043 " --> pdb=" O GLY B1084 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B1086 " --> pdb=" O LEU B1043 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B1045 " --> pdb=" O VAL B1086 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B1088 " --> pdb=" O THR B1045 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR B1047 " --> pdb=" O VAL B1088 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1145 through 1146 Processing sheet with id=AB2, first strand: chain 'B' and resid 1168 through 1172 Processing sheet with id=AB3, first strand: chain 'B' and resid 1271 through 1273 Processing sheet with id=AB4, first strand: chain 'A' and resid 198 through 201 removed outlier: 3.514A pdb=" N VAL A 153 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 39 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU A 278 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VAL A 37 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG A 437 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP A 335 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLY A 370 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 337 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AB6, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AB7, first strand: chain 'A' and resid 649 through 654 removed outlier: 7.052A pdb=" N ALA A 558 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 652 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 560 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY A 654 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE A 562 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 559 " --> pdb=" O LEU A 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 695 through 697 removed outlier: 5.621A pdb=" N SER A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA A 726 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE A 714 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 975 through 980 removed outlier: 3.807A pdb=" N ARG A 977 " --> pdb=" O TRP A 949 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 979 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 948 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU A1004 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 950 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A1043 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A1086 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR A1045 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A1088 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR A1047 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A1112 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A1123 " --> pdb=" O GLN A1112 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1142 through 1143 removed outlier: 6.735A pdb=" N VAL A1143 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1171 " --> pdb=" O VAL A1143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1145 through 1146 removed outlier: 6.954A pdb=" N PHE A1225 " --> pdb=" O THR A1146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1271 through 1275 removed outlier: 6.467A pdb=" N LEU A1272 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP A1314 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER A1274 " --> pdb=" O TRP A1314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AC5, first strand: chain 'C' and resid 12 through 14 removed outlier: 4.297A pdb=" N GLY C 12 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET C 36 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 52 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.957A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 187 " --> pdb=" O CYS C 147 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 188 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.628A pdb=" N CYS C 203 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS C 207 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C 212 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 21 through 22 removed outlier: 3.717A pdb=" N PHE D 92 " --> pdb=" O CYS D 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 26 through 29 removed outlier: 6.633A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.688A pdb=" N ASN D 159 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 152 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 154 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 199 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR D 195 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AD3, first strand: chain 'E' and resid 12 through 14 removed outlier: 4.297A pdb=" N GLY E 12 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET E 36 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE E 52 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP E 38 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.957A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 187 " --> pdb=" O CYS E 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 188 " --> pdb=" O HIS E 171 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.667A pdb=" N CYS E 203 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS E 207 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR E 212 " --> pdb=" O HIS E 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 27 through 29 removed outlier: 3.702A pdb=" N GLY F 105 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP F 56 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.973A pdb=" N PHE F 92 " --> pdb=" O CYS F 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.688A pdb=" N ASN F 159 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA F 152 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 154 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 199 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR F 195 " --> pdb=" O ASN F 160 " (cutoff:3.500A) 985 hydrogen bonds defined for protein. 2787 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: 11.78 Time building geometry restraints manager: 11.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5196 1.33 - 1.45: 6909 1.45 - 1.58: 15338 1.58 - 1.71: 0 1.71 - 1.83: 146 Bond restraints: 27589 Sorted by residual: bond pdb=" CA SER B 208 " pdb=" CB SER B 208 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.58e-02 4.01e+03 1.31e+01 bond pdb=" CA SER B 200 " pdb=" CB SER B 200 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.53e-02 4.27e+03 1.30e+01 bond pdb=" CA SER F 112 " pdb=" CB SER F 112 " ideal model delta sigma weight residual 1.529 1.493 0.036 1.02e-02 9.61e+03 1.26e+01 bond pdb=" N VAL A1364 " pdb=" CA VAL A1364 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.27e-02 6.20e+03 1.10e+01 bond pdb=" CA SER B 207 " pdb=" CB SER B 207 " ideal model delta sigma weight residual 1.532 1.481 0.051 1.58e-02 4.01e+03 1.03e+01 ... (remaining 27584 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.50: 387 103.50 - 111.28: 11401 111.28 - 119.06: 11281 119.06 - 126.85: 14075 126.85 - 134.63: 397 Bond angle restraints: 37541 Sorted by residual: angle pdb=" C PRO B 197 " pdb=" CA PRO B 197 " pdb=" CB PRO B 197 " ideal model delta sigma weight residual 111.71 100.44 11.27 1.30e+00 5.92e-01 7.51e+01 angle pdb=" N PRO D 24 " pdb=" CA PRO D 24 " pdb=" C PRO D 24 " ideal model delta sigma weight residual 112.47 96.72 15.75 2.06e+00 2.36e-01 5.84e+01 angle pdb=" N THR A 838 " pdb=" CA THR A 838 " pdb=" C THR A 838 " ideal model delta sigma weight residual 113.18 104.32 8.86 1.21e+00 6.83e-01 5.37e+01 angle pdb=" N ALA B 650 " pdb=" CA ALA B 650 " pdb=" C ALA B 650 " ideal model delta sigma weight residual 113.12 104.85 8.27 1.25e+00 6.40e-01 4.37e+01 angle pdb=" N MET A 176 " pdb=" CA MET A 176 " pdb=" C MET A 176 " ideal model delta sigma weight residual 114.62 107.56 7.06 1.14e+00 7.69e-01 3.84e+01 ... (remaining 37536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14849 17.98 - 35.97: 1228 35.97 - 53.95: 286 53.95 - 71.94: 99 71.94 - 89.92: 26 Dihedral angle restraints: 16488 sinusoidal: 6241 harmonic: 10247 Sorted by residual: dihedral pdb=" CA THR F 115 " pdb=" C THR F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta harmonic sigma weight residual 0.00 42.98 -42.98 0 5.00e+00 4.00e-02 7.39e+01 dihedral pdb=" CA THR D 115 " pdb=" C THR D 115 " pdb=" N PRO D 116 " pdb=" CA PRO D 116 " ideal model delta harmonic sigma weight residual 0.00 42.22 -42.22 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA GLU C 155 " pdb=" C GLU C 155 " pdb=" N PRO C 156 " pdb=" CA PRO C 156 " ideal model delta harmonic sigma weight residual 180.00 141.83 38.17 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 16485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3737 0.078 - 0.155: 425 0.155 - 0.233: 63 0.233 - 0.311: 20 0.311 - 0.389: 4 Chirality restraints: 4249 Sorted by residual: chirality pdb=" CA VAL B 559 " pdb=" N VAL B 559 " pdb=" C VAL B 559 " pdb=" CB VAL B 559 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA VAL C 149 " pdb=" N VAL C 149 " pdb=" C VAL C 149 " pdb=" CB VAL C 149 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PRO D 24 " pdb=" N PRO D 24 " pdb=" C PRO D 24 " pdb=" CB PRO D 24 " both_signs ideal model delta sigma weight residual False 2.72 3.05 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 4246 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 642 " -0.018 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP A 642 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A 642 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 642 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 642 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 642 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 642 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 642 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 642 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 642 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 33 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO F 34 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 34 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 34 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 33 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO D 34 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 34 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 34 " -0.040 5.00e-02 4.00e+02 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2660 2.75 - 3.28: 28287 3.28 - 3.82: 49055 3.82 - 4.36: 59485 4.36 - 4.90: 97336 Nonbonded interactions: 236823 Sorted by model distance: nonbonded pdb=" O PRO B 835 " pdb=" OG1 THR B 838 " model vdw 2.208 2.440 nonbonded pdb=" O GLN B1301 " pdb=" OG SER B1304 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR B1230 " pdb=" O ALA B1247 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR A1230 " pdb=" O ALA A1247 " model vdw 2.231 2.440 nonbonded pdb=" NE2 GLN E 41 " pdb=" O ALA E 42 " model vdw 2.234 2.520 ... (remaining 236818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 912 or resid 938 through 1365 or resid 1367 thro \ ugh 1368 or resid 1371 through 1372 or resid 1374 or resid 1377 through 1379 or \ resid 1382 through 1383 or resid 1386 or resid 1388)) selection = (chain 'B' and (resid 1 through 1363 or resid 1420 through 1421 or resid 1448 or \ resid 1456 or resid 1459 or resid 1461 or resid 1463 or resid 1466 or resid 146 \ 8 through 1469 or resid 1473 through 1474 or resid 1477 or resid 1483)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 17 through 172 or resid 178 through 231)) selection = (chain 'F' and (resid 17 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: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.020 Extract box with map and model: 9.300 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 73.420 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.150 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 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 : 0.005 0.057 27589 Z= 0.312 Angle : 0.878 15.747 37541 Z= 0.553 Chirality : 0.055 0.389 4249 Planarity : 0.006 0.073 4974 Dihedral : 15.129 89.924 9908 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.68 % Allowed : 1.98 % Favored : 93.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.13), residues: 3605 helix: -1.15 (0.15), residues: 1077 sheet: -1.44 (0.21), residues: 583 loop : -1.85 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 642 HIS 0.006 0.001 HIS A1334 PHE 0.027 0.002 PHE A 244 TYR 0.017 0.001 TYR C 152 ARG 0.014 0.000 ARG B1435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 99 time to evaluate : 3.068 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.9024 (p) REVERT: B 163 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.9092 (mmt180) REVERT: B 577 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8610 (pp) REVERT: A 111 MET cc_start: 0.8177 (tmm) cc_final: 0.7635 (tmm) REVERT: A 126 MET cc_start: 0.8822 (mmm) cc_final: 0.8342 (mmm) REVERT: A 247 MET cc_start: 0.9145 (pmm) cc_final: 0.8617 (pmm) REVERT: A 688 MET cc_start: -0.3397 (mtt) cc_final: -0.3818 (mtm) REVERT: A 1053 THR cc_start: 0.7349 (OUTLIER) cc_final: 0.6555 (p) REVERT: A 1373 TYR cc_start: 0.6573 (t80) cc_final: 0.6145 (t80) REVERT: D 27 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8991 (tp) REVERT: D 110 MET cc_start: 0.8113 (tpp) cc_final: 0.7380 (tpt) REVERT: D 153 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8526 (m) REVERT: E 91 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8884 (mtmt) REVERT: F 20 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: F 21 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8614 (m) REVERT: F 102 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7871 (pm20) REVERT: F 115 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.7829 (p) outliers start: 130 outliers final: 14 residues processed: 216 average time/residue: 0.4531 time to fit residues: 149.8731 Evaluate side-chains 97 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 7.9990 chunk 273 optimal weight: 50.0000 chunk 151 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 172 optimal weight: 40.0000 chunk 210 optimal weight: 20.0000 chunk 327 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN B 322 GLN ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1349 GLN ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS A 340 HIS A 368 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 ASN ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 : 0.006 0.129 27589 Z= 0.391 Angle : 0.775 10.877 37541 Z= 0.394 Chirality : 0.043 0.181 4249 Planarity : 0.006 0.096 4974 Dihedral : 5.116 34.151 3961 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.36 % Allowed : 6.80 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3605 helix: -0.74 (0.15), residues: 1115 sheet: -1.63 (0.20), residues: 618 loop : -1.46 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 642 HIS 0.009 0.002 HIS A1334 PHE 0.022 0.003 PHE D 92 TYR 0.018 0.002 TYR E 98 ARG 0.025 0.001 ARG B 818 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9121 (mmm) cc_final: 0.8783 (mmm) REVERT: B 635 MET cc_start: 0.4668 (tpt) cc_final: 0.4360 (tpt) REVERT: B 665 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6435 (m) REVERT: B 1484 HIS cc_start: 0.8719 (t-170) cc_final: 0.8512 (t70) REVERT: A 176 MET cc_start: 0.9357 (ppp) cc_final: 0.9121 (ppp) REVERT: A 688 MET cc_start: -0.2479 (mtt) cc_final: -0.3064 (mtm) REVERT: A 694 MET cc_start: -0.5644 (ptt) cc_final: -0.5874 (ptt) REVERT: C 36 MET cc_start: 0.9187 (mmm) cc_final: 0.8962 (mmp) REVERT: D 20 MET cc_start: 0.9081 (mmp) cc_final: 0.8875 (mmm) REVERT: F 20 MET cc_start: 0.9067 (mmp) cc_final: 0.8817 (mmm) REVERT: F 102 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8559 (pm20) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 0.3991 time to fit residues: 63.2994 Evaluate side-chains 73 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.9980 chunk 101 optimal weight: 0.0870 chunk 272 optimal weight: 7.9990 chunk 223 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 328 optimal weight: 3.9990 chunk 354 optimal weight: 1.9990 chunk 292 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS A1350 ASN ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 169 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27589 Z= 0.188 Angle : 0.591 8.014 37541 Z= 0.300 Chirality : 0.042 0.179 4249 Planarity : 0.005 0.057 4974 Dihedral : 4.888 38.026 3961 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3605 helix: -0.35 (0.16), residues: 1109 sheet: -1.45 (0.20), residues: 629 loop : -1.33 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1137 HIS 0.005 0.001 HIS A 768 PHE 0.017 0.002 PHE A 244 TYR 0.019 0.001 TYR F 57 ARG 0.008 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9107 (mmm) cc_final: 0.8422 (mmm) REVERT: B 176 MET cc_start: 0.9544 (tmm) cc_final: 0.9303 (tmm) REVERT: B 228 MET cc_start: 0.9341 (tpt) cc_final: 0.8813 (tpp) REVERT: B 240 MET cc_start: 0.7647 (tmm) cc_final: 0.7369 (tmm) REVERT: A 176 MET cc_start: 0.9434 (ppp) cc_final: 0.9219 (ppp) REVERT: A 688 MET cc_start: -0.2794 (mtt) cc_final: -0.3343 (mtm) REVERT: A 694 MET cc_start: -0.5857 (ptt) cc_final: -0.6133 (ptt) REVERT: C 36 MET cc_start: 0.9091 (mmm) cc_final: 0.8841 (mmp) REVERT: D 20 MET cc_start: 0.9032 (mmp) cc_final: 0.8751 (mmm) REVERT: F 55 ASP cc_start: 0.8733 (t0) cc_final: 0.8408 (t0) REVERT: F 102 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8588 (pm20) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4011 time to fit residues: 56.7065 Evaluate side-chains 70 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 156 optimal weight: 0.0970 chunk 220 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN D 114 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27589 Z= 0.233 Angle : 0.599 7.562 37541 Z= 0.304 Chirality : 0.041 0.164 4249 Planarity : 0.005 0.057 4974 Dihedral : 4.760 34.005 3961 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3605 helix: -0.05 (0.16), residues: 1117 sheet: -1.45 (0.20), residues: 635 loop : -1.20 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 642 HIS 0.006 0.001 HIS A1334 PHE 0.017 0.002 PHE D 120 TYR 0.013 0.001 TYR A1288 ARG 0.006 0.000 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9095 (mmm) cc_final: 0.8414 (mmm) REVERT: B 176 MET cc_start: 0.9536 (tmm) cc_final: 0.9325 (tmm) REVERT: B 228 MET cc_start: 0.9365 (tpt) cc_final: 0.9123 (tpt) REVERT: B 1339 MET cc_start: -0.3411 (mmp) cc_final: -0.4044 (mmp) REVERT: A 126 MET cc_start: 0.9094 (mmp) cc_final: 0.8794 (mmm) REVERT: A 228 MET cc_start: 0.9473 (tpt) cc_final: 0.8965 (tpp) REVERT: A 688 MET cc_start: -0.2661 (mtt) cc_final: -0.3235 (mtm) REVERT: A 694 MET cc_start: -0.5860 (ptt) cc_final: -0.6148 (ptt) REVERT: A 1322 MET cc_start: 0.1148 (ttp) cc_final: -0.0127 (mtt) REVERT: C 36 MET cc_start: 0.9123 (mmm) cc_final: 0.8761 (mmm) REVERT: D 20 MET cc_start: 0.9094 (mmp) cc_final: 0.8860 (mmm) REVERT: D 110 MET cc_start: 0.8713 (mmm) cc_final: 0.8360 (mmm) REVERT: F 55 ASP cc_start: 0.8614 (t0) cc_final: 0.8190 (t0) REVERT: F 102 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8722 (pm20) REVERT: F 110 MET cc_start: 0.8110 (tpt) cc_final: 0.7545 (tpt) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.4185 time to fit residues: 57.7870 Evaluate side-chains 70 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 5 optimal weight: 0.0030 chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 241 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27589 Z= 0.297 Angle : 0.660 9.011 37541 Z= 0.335 Chirality : 0.042 0.184 4249 Planarity : 0.005 0.077 4974 Dihedral : 4.893 33.111 3961 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3605 helix: 0.24 (0.16), residues: 1117 sheet: -1.56 (0.20), residues: 618 loop : -1.15 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 642 HIS 0.006 0.002 HIS A 655 PHE 0.021 0.002 PHE D 92 TYR 0.019 0.002 TYR E 34 ARG 0.021 0.001 ARG A1332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9148 (mmm) cc_final: 0.8416 (mmm) REVERT: B 228 MET cc_start: 0.9357 (tpt) cc_final: 0.8945 (tpt) REVERT: B 635 MET cc_start: 0.4551 (tpt) cc_final: 0.4257 (tpt) REVERT: B 1339 MET cc_start: -0.2187 (mmp) cc_final: -0.2861 (mmp) REVERT: A 111 MET cc_start: 0.8189 (tmm) cc_final: 0.7943 (tmm) REVERT: A 228 MET cc_start: 0.9441 (tpt) cc_final: 0.9172 (mmm) REVERT: A 572 MET cc_start: 0.6041 (mmm) cc_final: 0.5760 (mmm) REVERT: A 688 MET cc_start: -0.2155 (mtt) cc_final: -0.2803 (mtm) REVERT: A 694 MET cc_start: -0.5703 (ptt) cc_final: -0.5995 (ptt) REVERT: A 1322 MET cc_start: 0.1385 (ttp) cc_final: 0.0016 (mtt) REVERT: C 36 MET cc_start: 0.9117 (mmm) cc_final: 0.8749 (mmm) REVERT: F 20 MET cc_start: 0.9123 (mmp) cc_final: 0.8876 (mmm) REVERT: F 55 ASP cc_start: 0.8476 (t0) cc_final: 0.8066 (t0) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.4241 time to fit residues: 57.2448 Evaluate side-chains 68 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 115 optimal weight: 50.0000 chunk 183 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN B 375 ASN B 555 GLN B 597 HIS ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS A 365 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 27589 Z= 0.394 Angle : 0.744 8.675 37541 Z= 0.376 Chirality : 0.044 0.206 4249 Planarity : 0.006 0.054 4974 Dihedral : 5.230 35.724 3961 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 33.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3605 helix: -0.01 (0.15), residues: 1119 sheet: -1.74 (0.20), residues: 636 loop : -1.21 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1137 HIS 0.008 0.002 HIS A 655 PHE 0.044 0.003 PHE D 92 TYR 0.024 0.002 TYR E 34 ARG 0.008 0.001 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9243 (mmm) cc_final: 0.8591 (mmm) REVERT: B 176 MET cc_start: 0.9430 (tmm) cc_final: 0.9226 (tmm) REVERT: B 228 MET cc_start: 0.9360 (tpt) cc_final: 0.9153 (tpt) REVERT: B 1339 MET cc_start: -0.1816 (mmp) cc_final: -0.2341 (mmp) REVERT: A 126 MET cc_start: 0.9332 (mmp) cc_final: 0.9113 (mmm) REVERT: A 228 MET cc_start: 0.9417 (tpt) cc_final: 0.9208 (mmm) REVERT: A 240 MET cc_start: 0.8949 (tpt) cc_final: 0.8653 (tpt) REVERT: A 631 MET cc_start: 0.7717 (mmp) cc_final: 0.7382 (mmm) REVERT: A 688 MET cc_start: -0.1510 (mtt) cc_final: -0.2159 (mtm) REVERT: A 694 MET cc_start: -0.5434 (ptt) cc_final: -0.5715 (ptt) REVERT: A 1322 MET cc_start: 0.1401 (ttp) cc_final: 0.0029 (mtt) REVERT: C 36 MET cc_start: 0.9098 (mmm) cc_final: 0.8791 (mmp) REVERT: C 87 MET cc_start: 0.8664 (mpp) cc_final: 0.8448 (mpp) REVERT: D 20 MET cc_start: 0.9170 (mmp) cc_final: 0.8879 (mmm) REVERT: E 87 MET cc_start: 0.9434 (mpp) cc_final: 0.9198 (mpp) REVERT: F 20 MET cc_start: 0.9176 (mmp) cc_final: 0.8943 (mmm) REVERT: F 55 ASP cc_start: 0.8599 (t0) cc_final: 0.8217 (t0) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.4083 time to fit residues: 52.4181 Evaluate side-chains 65 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 255 optimal weight: 0.1980 chunk 197 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 217 optimal weight: 40.0000 chunk 212 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27589 Z= 0.245 Angle : 0.617 9.421 37541 Z= 0.313 Chirality : 0.042 0.222 4249 Planarity : 0.005 0.062 4974 Dihedral : 5.031 41.970 3961 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3605 helix: 0.28 (0.16), residues: 1128 sheet: -1.75 (0.20), residues: 637 loop : -1.11 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 642 HIS 0.008 0.001 HIS A 405 PHE 0.027 0.002 PHE A 244 TYR 0.022 0.002 TYR E 34 ARG 0.009 0.000 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9313 (mmm) cc_final: 0.8609 (mmm) REVERT: B 228 MET cc_start: 0.9391 (tpt) cc_final: 0.9083 (tpt) REVERT: B 1339 MET cc_start: -0.1420 (mmp) cc_final: -0.2166 (mmp) REVERT: A 688 MET cc_start: -0.1548 (mtt) cc_final: -0.2244 (mtm) REVERT: A 694 MET cc_start: -0.5886 (ptt) cc_final: -0.6190 (ptt) REVERT: A 1322 MET cc_start: 0.1938 (ttp) cc_final: 0.0261 (mtt) REVERT: C 36 MET cc_start: 0.9016 (mmm) cc_final: 0.8668 (mmp) REVERT: C 87 MET cc_start: 0.8705 (mpp) cc_final: 0.8479 (mpp) REVERT: D 20 MET cc_start: 0.9188 (mmp) cc_final: 0.8971 (mmm) REVERT: E 87 MET cc_start: 0.9378 (mpp) cc_final: 0.9119 (mpp) REVERT: F 20 MET cc_start: 0.9108 (mmp) cc_final: 0.8877 (mmm) REVERT: F 55 ASP cc_start: 0.8629 (t0) cc_final: 0.8218 (t0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3828 time to fit residues: 48.8090 Evaluate side-chains 63 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 3.9990 chunk 138 optimal weight: 50.0000 chunk 207 optimal weight: 8.9990 chunk 104 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 67 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 273 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27589 Z= 0.289 Angle : 0.658 10.592 37541 Z= 0.332 Chirality : 0.042 0.265 4249 Planarity : 0.005 0.065 4974 Dihedral : 5.027 36.368 3961 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3605 helix: 0.35 (0.16), residues: 1126 sheet: -1.73 (0.20), residues: 627 loop : -1.12 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 642 HIS 0.008 0.001 HIS A 405 PHE 0.036 0.002 PHE A 244 TYR 0.015 0.002 TYR E 98 ARG 0.013 0.001 ARG A1332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9404 (mmm) cc_final: 0.8720 (mmp) REVERT: B 228 MET cc_start: 0.9376 (tpt) cc_final: 0.9080 (tpt) REVERT: B 1339 MET cc_start: -0.0871 (mmp) cc_final: -0.1599 (mmp) REVERT: A 240 MET cc_start: 0.9105 (tpt) cc_final: 0.8887 (tpp) REVERT: A 688 MET cc_start: -0.1404 (mtt) cc_final: -0.2102 (mtm) REVERT: A 694 MET cc_start: -0.5817 (ptt) cc_final: -0.6126 (ptt) REVERT: A 1322 MET cc_start: 0.1949 (ttp) cc_final: 0.0332 (mtt) REVERT: C 36 MET cc_start: 0.8931 (mmm) cc_final: 0.8609 (mmp) REVERT: C 87 MET cc_start: 0.8703 (mpp) cc_final: 0.8417 (mpp) REVERT: D 20 MET cc_start: 0.9172 (mmp) cc_final: 0.8952 (mmm) REVERT: E 87 MET cc_start: 0.9410 (mpp) cc_final: 0.9114 (mpp) REVERT: F 20 MET cc_start: 0.9162 (mmp) cc_final: 0.8933 (mmm) REVERT: F 55 ASP cc_start: 0.8533 (t0) cc_final: 0.8104 (t0) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.4040 time to fit residues: 49.4902 Evaluate side-chains 63 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 304 optimal weight: 0.6980 chunk 324 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 254 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 292 optimal weight: 0.3980 chunk 306 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN B 556 GLN B1032 GLN ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27589 Z= 0.192 Angle : 0.609 22.111 37541 Z= 0.304 Chirality : 0.042 0.223 4249 Planarity : 0.005 0.061 4974 Dihedral : 4.854 37.824 3961 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3605 helix: 0.48 (0.16), residues: 1123 sheet: -1.67 (0.20), residues: 605 loop : -1.07 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 642 HIS 0.005 0.001 HIS A 340 PHE 0.039 0.002 PHE A 244 TYR 0.013 0.001 TYR E 34 ARG 0.008 0.000 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9401 (mmm) cc_final: 0.8750 (mmp) REVERT: B 228 MET cc_start: 0.9391 (tpt) cc_final: 0.9173 (tpt) REVERT: B 635 MET cc_start: 0.4463 (tpt) cc_final: 0.4198 (tpt) REVERT: B 1339 MET cc_start: -0.0637 (mmp) cc_final: -0.1425 (mmp) REVERT: A 126 MET cc_start: 0.9432 (mmt) cc_final: 0.9155 (mmp) REVERT: A 240 MET cc_start: 0.9031 (tpt) cc_final: 0.8781 (tpp) REVERT: A 688 MET cc_start: -0.1430 (mtt) cc_final: -0.2194 (mtm) REVERT: A 694 MET cc_start: -0.5877 (ptt) cc_final: -0.6184 (ptt) REVERT: A 1322 MET cc_start: 0.2056 (ttp) cc_final: 0.0474 (mtt) REVERT: C 36 MET cc_start: 0.8830 (mmm) cc_final: 0.8559 (mmp) REVERT: C 87 MET cc_start: 0.8775 (mpp) cc_final: 0.8507 (mpp) REVERT: D 20 MET cc_start: 0.9166 (mmp) cc_final: 0.8956 (mmm) REVERT: E 87 MET cc_start: 0.9361 (mpp) cc_final: 0.9090 (mpp) REVERT: F 55 ASP cc_start: 0.8633 (t0) cc_final: 0.8212 (t70) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.4025 time to fit residues: 51.0724 Evaluate side-chains 64 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 2.9990 chunk 342 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 359 optimal weight: 0.0570 chunk 331 optimal weight: 8.9990 chunk 286 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27589 Z= 0.169 Angle : 0.575 10.687 37541 Z= 0.288 Chirality : 0.042 0.198 4249 Planarity : 0.005 0.056 4974 Dihedral : 4.672 36.257 3961 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.93 (0.14), residues: 3605 helix: 0.67 (0.16), residues: 1111 sheet: -1.65 (0.20), residues: 627 loop : -0.99 (0.15), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B1137 HIS 0.003 0.001 HIS A 340 PHE 0.034 0.002 PHE A 785 TYR 0.011 0.001 TYR A1288 ARG 0.007 0.000 ARG F 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9410 (mmm) cc_final: 0.8743 (mmp) REVERT: B 395 MET cc_start: 0.9249 (mtt) cc_final: 0.8920 (ttm) REVERT: B 1339 MET cc_start: -0.0506 (mmp) cc_final: -0.1320 (mmp) REVERT: B 1417 PHE cc_start: 0.8810 (t80) cc_final: 0.8460 (m-80) REVERT: A 126 MET cc_start: 0.9389 (mmt) cc_final: 0.9179 (mmp) REVERT: A 240 MET cc_start: 0.9047 (tpt) cc_final: 0.8823 (tpp) REVERT: A 631 MET cc_start: 0.7650 (mmp) cc_final: 0.7356 (mmm) REVERT: A 688 MET cc_start: -0.1463 (mtt) cc_final: -0.2230 (mtm) REVERT: A 694 MET cc_start: -0.5938 (ptt) cc_final: -0.6280 (ptt) REVERT: A 1322 MET cc_start: 0.2298 (ttp) cc_final: 0.0731 (mtt) REVERT: C 36 MET cc_start: 0.8812 (mmm) cc_final: 0.8565 (mmp) REVERT: C 87 MET cc_start: 0.8761 (mpp) cc_final: 0.8525 (mpp) REVERT: D 20 MET cc_start: 0.9125 (mmp) cc_final: 0.8908 (mmm) REVERT: E 87 MET cc_start: 0.9325 (mpp) cc_final: 0.9067 (mpp) REVERT: F 55 ASP cc_start: 0.8561 (t0) cc_final: 0.8140 (t70) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.4162 time to fit residues: 53.4975 Evaluate side-chains 64 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 264 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 286 optimal weight: 0.0370 chunk 120 optimal weight: 40.0000 chunk 294 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS A 123 GLN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.077536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.052058 restraints weight = 317212.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.050319 restraints weight = 253812.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.050496 restraints weight = 185844.547| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27589 Z= 0.191 Angle : 0.581 14.531 37541 Z= 0.291 Chirality : 0.042 0.200 4249 Planarity : 0.005 0.057 4974 Dihedral : 4.608 35.812 3961 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.84 (0.14), residues: 3605 helix: 0.79 (0.16), residues: 1102 sheet: -1.64 (0.20), residues: 620 loop : -0.95 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 642 HIS 0.004 0.001 HIS A 340 PHE 0.030 0.002 PHE A 244 TYR 0.013 0.001 TYR E 34 ARG 0.006 0.000 ARG F 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4234.78 seconds wall clock time: 79 minutes 50.57 seconds (4790.57 seconds total)