Starting phenix.real_space_refine on Wed Mar 4 22:00:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uxv_20933/03_2026/6uxv_20933.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uxv_20933/03_2026/6uxv_20933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uxv_20933/03_2026/6uxv_20933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uxv_20933/03_2026/6uxv_20933.map" model { file = "/net/cci-nas-00/data/ceres_data/6uxv_20933/03_2026/6uxv_20933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uxv_20933/03_2026/6uxv_20933.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 10539 2.51 5 N 2901 2.21 5 O 3160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16649 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1133 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain: "B" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3890 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain breaks: 6 Chain: "C" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2005 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1322 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 12, 'TRANS': 126} Chain: "F" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1583 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1435 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 6, 'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2085 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 3 Chain: "I" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 673 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "I" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 336 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 66} Unresolved non-hydrogen planarities: 66 Chain: "K" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 141 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 91 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 416 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'CIS': 1, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'UNK:plan-1': 82} Unresolved non-hydrogen planarities: 82 Chain: "N" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 151 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: O Time building chain proxies: 4.68, per 1000 atoms: 0.28 Number of scatterers: 16649 At special positions: 0 Unit cell: (137.76, 154.56, 151.2, 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 49 16.00 O 3160 8.00 N 2901 7.00 C 10539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 766.9 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 5 sheets defined 68.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 490 through 518 removed outlier: 3.585A pdb=" N ALA A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 557 Proline residue: A 540 - end of helix removed outlier: 3.785A pdb=" N GLN A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 597 removed outlier: 3.683A pdb=" N ALA A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 715 Processing helix chain 'B' and resid 717 through 734 removed outlier: 3.660A pdb=" N ASN B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 765 Processing helix chain 'B' and resid 792 through 805 removed outlier: 4.087A pdb=" N VAL B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 798 " --> pdb=" O LYS B 794 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B 805 " --> pdb=" O GLU B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 895 removed outlier: 3.770A pdb=" N LYS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 929 removed outlier: 3.729A pdb=" N LEU B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 941 through 957 removed outlier: 3.502A pdb=" N ILE B 957 " --> pdb=" O TRP B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 981 Processing helix chain 'B' and resid 989 through 1003 removed outlier: 4.135A pdb=" N ASP B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1046 removed outlier: 3.886A pdb=" N PHE B1038 " --> pdb=" O LYS B1034 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B1040 " --> pdb=" O GLN B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1061 Processing helix chain 'B' and resid 1079 through 1090 removed outlier: 3.749A pdb=" N LYS B1083 " --> pdb=" O HIS B1079 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B1086 " --> pdb=" O LYS B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1093 No H-bonds generated for 'chain 'B' and resid 1091 through 1093' Processing helix chain 'B' and resid 1105 through 1114 removed outlier: 3.774A pdb=" N VAL B1109 " --> pdb=" O LEU B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1137 removed outlier: 4.402A pdb=" N ILE B1133 " --> pdb=" O PRO B1129 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1149 removed outlier: 3.764A pdb=" N SER B1141 " --> pdb=" O SER B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1216 Processing helix chain 'B' and resid 1232 through 1259 Processing helix chain 'B' and resid 1263 through 1270 removed outlier: 3.927A pdb=" N LYS B1267 " --> pdb=" O PRO B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1278 through 1286 Processing helix chain 'B' and resid 1292 through 1314 removed outlier: 4.041A pdb=" N GLU B1314 " --> pdb=" O LEU B1310 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 450 Processing helix chain 'C' and resid 487 through 499 Processing helix chain 'C' and resid 510 through 522 Processing helix chain 'C' and resid 528 through 533 Processing helix chain 'C' and resid 571 through 580 removed outlier: 4.557A pdb=" N PHE C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 610 removed outlier: 4.139A pdb=" N THR C 591 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR C 604 " --> pdb=" O GLN C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 649 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 320 through 327 Processing helix chain 'D' and resid 328 through 332 removed outlier: 3.996A pdb=" N THR D 332 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 357 removed outlier: 3.880A pdb=" N ASN D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.507A pdb=" N SER D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 436 through 442 removed outlier: 4.152A pdb=" N LEU D 440 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 461 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 320 through 327 removed outlier: 3.707A pdb=" N VAL E 324 " --> pdb=" O HIS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 339 through 357 removed outlier: 3.948A pdb=" N ASN E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.642A pdb=" N ALA E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 388 Processing helix chain 'E' and resid 429 through 434 Processing helix chain 'F' and resid 528 through 542 Processing helix chain 'F' and resid 545 through 552 Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.592A pdb=" N PHE F 565 " --> pdb=" O CYS F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 624 Proline residue: F 620 - end of helix removed outlier: 4.072A pdb=" N GLN F 624 " --> pdb=" O PRO F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 647 removed outlier: 4.047A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 749 Processing helix chain 'F' and resid 766 through 780 Proline residue: F 777 - end of helix removed outlier: 4.306A pdb=" N LEU F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 541 removed outlier: 3.694A pdb=" N GLU G 541 " --> pdb=" O LYS G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 552 Processing helix chain 'G' and resid 557 through 567 Processing helix chain 'G' and resid 625 through 630 removed outlier: 3.760A pdb=" N ARG G 629 " --> pdb=" O SER G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 655 Proline residue: G 649 - end of helix removed outlier: 3.566A pdb=" N GLU G 655 " --> pdb=" O GLU G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 680 through 747 Processing helix chain 'G' and resid 764 through 779 Proline residue: G 777 - end of helix Processing helix chain 'H' and resid 82 through 114 removed outlier: 3.959A pdb=" N LEU H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR H 114 " --> pdb=" O GLN H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 117 No H-bonds generated for 'chain 'H' and resid 115 through 117' Processing helix chain 'H' and resid 311 through 318 Processing helix chain 'H' and resid 324 through 340 Processing helix chain 'H' and resid 382 through 387 Processing helix chain 'H' and resid 393 through 397 Processing helix chain 'H' and resid 403 through 410 Processing helix chain 'H' and resid 450 through 456 removed outlier: 4.563A pdb=" N ASN H 453 " --> pdb=" O LEU H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 510 Proline residue: H 478 - end of helix removed outlier: 3.950A pdb=" N ASP H 510 " --> pdb=" O LYS H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 529 removed outlier: 3.577A pdb=" N ALA H 514 " --> pdb=" O ASP H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 547 removed outlier: 4.074A pdb=" N ASN H 544 " --> pdb=" O VAL H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 562 removed outlier: 3.693A pdb=" N LEU H 553 " --> pdb=" O ASN H 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 560 " --> pdb=" O ASN H 556 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU H 561 " --> pdb=" O ILE H 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 86 Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 102 through 121 removed outlier: 3.645A pdb=" N ASN I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 147 removed outlier: 4.653A pdb=" N GLU I 139 " --> pdb=" O ARG I 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN I 147 " --> pdb=" O ARG I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 163 removed outlier: 4.000A pdb=" N UNK I 160 " --> pdb=" O UNK I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 175 Processing helix chain 'J' and resid 2 through 57 removed outlier: 3.987A pdb=" N UNK J 6 " --> pdb=" O UNK J 2 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N UNK J 11 " --> pdb=" O UNK J 7 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK J 19 " --> pdb=" O UNK J 15 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N UNK J 27 " --> pdb=" O UNK J 23 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N UNK J 56 " --> pdb=" O UNK J 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'L' and resid 9 through 19 Processing helix chain 'L' and resid 20 through 22 No H-bonds generated for 'chain 'L' and resid 20 through 22' Processing helix chain 'M' and resid 43 through 81 removed outlier: 3.806A pdb=" N UNK M 47 " --> pdb=" O UNK M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'O' and resid 7 through 17 Processing helix chain 'O' and resid 18 through 20 No H-bonds generated for 'chain 'O' and resid 18 through 20' Processing sheet with id=AA1, first strand: chain 'B' and resid 1006 through 1007 removed outlier: 4.134A pdb=" N GLN B1006 " --> pdb=" O ASN B1026 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 458 through 461 Processing sheet with id=AA3, first strand: chain 'C' and resid 543 through 552 removed outlier: 3.706A pdb=" N GLN C 556 " --> pdb=" O GLN C 654 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 654 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 411 through 412 removed outlier: 6.549A pdb=" N GLN D 411 " --> pdb=" O ILE E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 378 through 380 915 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5582 1.34 - 1.46: 2910 1.46 - 1.57: 8333 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 16906 Sorted by residual: bond pdb=" CA ASN H 544 " pdb=" C ASN H 544 " ideal model delta sigma weight residual 1.522 1.436 0.086 1.72e-02 3.38e+03 2.50e+01 bond pdb=" C GLU B1198 " pdb=" N ASN B1199 " ideal model delta sigma weight residual 1.332 1.280 0.052 1.29e-02 6.01e+03 1.59e+01 bond pdb=" CA VAL G 618 " pdb=" CB VAL G 618 " ideal model delta sigma weight residual 1.553 1.531 0.022 7.40e-03 1.83e+04 8.87e+00 bond pdb=" CA LEU B1061 " pdb=" C LEU B1061 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.38e-02 5.25e+03 6.46e+00 bond pdb=" CA ILE C 647 " pdb=" C ILE C 647 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.27e-02 6.20e+03 4.92e+00 ... (remaining 16901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 22498 2.69 - 5.38: 378 5.38 - 8.06: 35 8.06 - 10.75: 6 10.75 - 13.44: 2 Bond angle restraints: 22919 Sorted by residual: angle pdb=" C ARG C 640 " pdb=" N PRO C 641 " pdb=" CA PRO C 641 " ideal model delta sigma weight residual 119.84 133.28 -13.44 1.25e+00 6.40e-01 1.16e+02 angle pdb=" N PRO F 649 " pdb=" CA PRO F 649 " pdb=" CB PRO F 649 " ideal model delta sigma weight residual 103.35 110.58 -7.23 8.70e-01 1.32e+00 6.91e+01 angle pdb=" N PRO F 606 " pdb=" CA PRO F 606 " pdb=" CB PRO F 606 " ideal model delta sigma weight residual 103.25 111.64 -8.39 1.05e+00 9.07e-01 6.38e+01 angle pdb=" N PRO F 599 " pdb=" CA PRO F 599 " pdb=" CB PRO F 599 " ideal model delta sigma weight residual 103.19 110.37 -7.18 1.00e+00 1.00e+00 5.15e+01 angle pdb=" N PRO F 777 " pdb=" CA PRO F 777 " pdb=" CB PRO F 777 " ideal model delta sigma weight residual 103.52 110.16 -6.64 1.06e+00 8.90e-01 3.92e+01 ... (remaining 22914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9279 17.86 - 35.72: 890 35.72 - 53.58: 149 53.58 - 71.44: 31 71.44 - 89.30: 24 Dihedral angle restraints: 10373 sinusoidal: 3857 harmonic: 6516 Sorted by residual: dihedral pdb=" CA ASP B 776 " pdb=" C ASP B 776 " pdb=" N TYR B 777 " pdb=" CA TYR B 777 " ideal model delta harmonic sigma weight residual -180.00 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA ASP B 932 " pdb=" C ASP B 932 " pdb=" N ASN B 933 " pdb=" CA ASN B 933 " ideal model delta harmonic sigma weight residual 180.00 -148.55 -31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA TYR B 745 " pdb=" C TYR B 745 " pdb=" N PRO B 746 " pdb=" CA PRO B 746 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 10370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2325 0.065 - 0.129: 330 0.129 - 0.194: 20 0.194 - 0.259: 9 0.259 - 0.323: 1 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CA ILE G 570 " pdb=" N ILE G 570 " pdb=" C ILE G 570 " pdb=" CB ILE G 570 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PRO C 641 " pdb=" N PRO C 641 " pdb=" C PRO C 641 " pdb=" CB PRO C 641 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO F 599 " pdb=" N PRO F 599 " pdb=" C PRO F 599 " pdb=" CB PRO F 599 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2682 not shown) Planarity restraints: 2978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 646 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C LYS C 646 " 0.075 2.00e-02 2.50e+03 pdb=" O LYS C 646 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE C 647 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 640 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C ARG C 640 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG C 640 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO C 641 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 569 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C PRO G 569 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO G 569 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE G 570 " 0.013 2.00e-02 2.50e+03 ... (remaining 2975 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 37 2.21 - 2.88: 7747 2.88 - 3.55: 27650 3.55 - 4.23: 38440 4.23 - 4.90: 60449 Nonbonded interactions: 134323 Sorted by model distance: nonbonded pdb=" O ALA C 643 " pdb=" CG1 ILE C 647 " model vdw 1.532 3.440 nonbonded pdb=" O ALA C 643 " pdb=" CD1 ILE C 647 " model vdw 1.960 3.460 nonbonded pdb=" OD1 ASN I 110 " pdb=" OG SER I 113 " model vdw 2.040 3.040 nonbonded pdb=" O LEU H 78 " pdb=" OG SER H 81 " model vdw 2.080 3.040 nonbonded pdb=" O PRO E 308 " pdb=" OG SER E 311 " model vdw 2.110 3.040 ... (remaining 134318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'K' selection = (chain 'N' and resid 5 through 32) } ncs_group { reference = chain 'L' selection = chain 'O' } 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: 5.470 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.006 0.086 16906 Z= 0.314 Angle : 0.880 13.441 22919 Z= 0.509 Chirality : 0.046 0.323 2685 Planarity : 0.005 0.054 2978 Dihedral : 15.161 89.304 6079 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 29.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 17.68 % Favored : 82.05 % Rotamer: Outliers : 0.48 % Allowed : 10.52 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.06 (0.15), residues: 1872 helix: -2.55 (0.12), residues: 1039 sheet: -3.79 (0.63), residues: 28 loop : -4.49 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 926 TYR 0.021 0.002 TYR B1092 PHE 0.021 0.002 PHE G 681 TRP 0.016 0.002 TRP E 313 HIS 0.012 0.002 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00586 (16906) covalent geometry : angle 0.88032 (22919) hydrogen bonds : bond 0.16624 ( 915) hydrogen bonds : angle 7.19105 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 264 time to evaluate : 0.655 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: A 488 ILE cc_start: 0.7385 (mt) cc_final: 0.7017 (mm) REVERT: A 542 GLN cc_start: 0.8719 (pt0) cc_final: 0.8036 (pt0) REVERT: A 590 GLU cc_start: 0.9505 (tt0) cc_final: 0.9058 (tm-30) REVERT: B 755 LEU cc_start: 0.9459 (tp) cc_final: 0.9192 (tt) REVERT: B 772 ARG cc_start: 0.9085 (mpp-170) cc_final: 0.8663 (mtm-85) REVERT: B 938 MET cc_start: 0.8276 (tmm) cc_final: 0.7984 (tmm) REVERT: B 1298 GLN cc_start: 0.9602 (mm110) cc_final: 0.9209 (mm110) REVERT: C 575 PHE cc_start: 0.9072 (m-80) cc_final: 0.8753 (t80) REVERT: C 579 MET cc_start: 0.8978 (mpp) cc_final: 0.8685 (mmt) REVERT: D 412 TYR cc_start: 0.7352 (m-80) cc_final: 0.7128 (m-80) REVERT: D 433 GLN cc_start: 0.9528 (pm20) cc_final: 0.8848 (pp30) REVERT: E 344 MET cc_start: 0.9405 (ttm) cc_final: 0.8821 (tpp) REVERT: E 346 TYR cc_start: 0.9217 (m-80) cc_final: 0.8889 (m-80) REVERT: F 533 GLN cc_start: 0.9355 (tt0) cc_final: 0.9100 (tm-30) REVERT: F 717 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.9119 (mtt90) REVERT: F 726 ARG cc_start: 0.8549 (tpp-160) cc_final: 0.8109 (tpp-160) REVERT: G 711 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9126 (mm-30) REVERT: G 712 ARG cc_start: 0.8630 (tpt170) cc_final: 0.8418 (tpp80) REVERT: H 92 ARG cc_start: 0.9092 (mmp-170) cc_final: 0.8888 (mmm160) REVERT: H 105 ARG cc_start: 0.8587 (mmp-170) cc_final: 0.8208 (mmp-170) REVERT: H 541 ARG cc_start: 0.8508 (mtt90) cc_final: 0.8238 (mtt90) REVERT: I 96 ASP cc_start: 0.8798 (m-30) cc_final: 0.8398 (m-30) REVERT: I 109 LYS cc_start: 0.9575 (ttmt) cc_final: 0.9318 (tttt) REVERT: I 123 LEU cc_start: 0.9331 (mt) cc_final: 0.8956 (mp) outliers start: 8 outliers final: 3 residues processed: 272 average time/residue: 0.1660 time to fit residues: 64.7265 Evaluate side-chains 192 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS A 528 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS A 588 ASN B 718 ASN B 874 GLN ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 ASN ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 ASN B1053 ASN B1093 ASN B1104 ASN B1120 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1215 ASN B1243 GLN B1274 ASN B1284 GLN B1298 GLN B1300 GLN B1304 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS C 466 GLN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN ** C 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 394 GLN E 301 GLN E 352 ASN E 394 GLN E 411 GLN E 433 GLN F 552 ASN F 718 GLN G 533 GLN G 555 ASN G 567 GLN G 684 ASN G 725 GLN G 745 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 ASN ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 HIS H 493 ASN H 516 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.042953 restraints weight = 136014.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.044010 restraints weight = 88694.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.044771 restraints weight = 63662.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045325 restraints weight = 49218.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.045751 restraints weight = 40076.095| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16906 Z= 0.209 Angle : 0.761 13.149 22919 Z= 0.398 Chirality : 0.044 0.259 2685 Planarity : 0.005 0.053 2978 Dihedral : 6.271 39.583 2305 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.35 % Favored : 86.54 % Rotamer: Outliers : 0.18 % Allowed : 5.68 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.18), residues: 1872 helix: -0.65 (0.15), residues: 1057 sheet: -3.17 (0.68), residues: 28 loop : -3.77 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 143 TYR 0.024 0.002 TYR F 666 PHE 0.031 0.002 PHE H 112 TRP 0.016 0.002 TRP E 313 HIS 0.013 0.002 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00430 (16906) covalent geometry : angle 0.76138 (22919) hydrogen bonds : bond 0.05148 ( 915) hydrogen bonds : angle 5.23229 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 270 time to evaluate : 0.647 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.9218 (m-80) cc_final: 0.8841 (m-80) REVERT: A 572 ARG cc_start: 0.7512 (mtp85) cc_final: 0.7223 (mtp85) REVERT: A 590 GLU cc_start: 0.9454 (tt0) cc_final: 0.9007 (tm-30) REVERT: A 595 GLU cc_start: 0.9488 (tt0) cc_final: 0.9217 (mm-30) REVERT: B 721 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8529 (mm-30) REVERT: B 770 TYR cc_start: 0.8858 (m-10) cc_final: 0.8541 (m-10) REVERT: B 772 ARG cc_start: 0.8854 (mpp-170) cc_final: 0.8566 (mtm-85) REVERT: C 603 MET cc_start: 0.9497 (ptp) cc_final: 0.9219 (mmm) REVERT: D 368 ARG cc_start: 0.9267 (mtm110) cc_final: 0.8370 (mtm-85) REVERT: D 412 TYR cc_start: 0.7559 (m-80) cc_final: 0.5387 (m-80) REVERT: D 433 GLN cc_start: 0.9512 (pm20) cc_final: 0.8792 (pp30) REVERT: D 441 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9013 (tptt) REVERT: E 316 LEU cc_start: 0.9292 (pt) cc_final: 0.8976 (pt) REVERT: E 344 MET cc_start: 0.9557 (ttm) cc_final: 0.8918 (tpp) REVERT: E 346 TYR cc_start: 0.9341 (m-80) cc_final: 0.8909 (m-80) REVERT: E 400 LEU cc_start: 0.8481 (tp) cc_final: 0.8268 (tp) REVERT: F 533 GLN cc_start: 0.9378 (tt0) cc_final: 0.9092 (tm-30) REVERT: F 717 ARG cc_start: 0.9507 (mmm-85) cc_final: 0.9259 (ttm-80) REVERT: G 691 MET cc_start: 0.9434 (mmp) cc_final: 0.9204 (mmp) REVERT: G 693 LYS cc_start: 0.9629 (mtmm) cc_final: 0.9392 (mttt) REVERT: G 711 GLU cc_start: 0.9621 (mt-10) cc_final: 0.9120 (mm-30) REVERT: G 717 ARG cc_start: 0.8790 (ttm170) cc_final: 0.8534 (ttm170) REVERT: H 92 ARG cc_start: 0.9146 (mmp-170) cc_final: 0.8893 (mmm160) REVERT: H 93 ASN cc_start: 0.8624 (m110) cc_final: 0.8245 (m110) REVERT: H 105 ARG cc_start: 0.8760 (mmp-170) cc_final: 0.8406 (mmp-170) REVERT: H 308 MET cc_start: 0.9359 (ttm) cc_final: 0.9120 (ttt) REVERT: H 333 TYR cc_start: 0.8827 (t80) cc_final: 0.8605 (t80) REVERT: H 535 TYR cc_start: 0.9358 (m-80) cc_final: 0.9048 (m-10) REVERT: H 541 ARG cc_start: 0.8884 (mtt90) cc_final: 0.8505 (mpt90) REVERT: I 109 LYS cc_start: 0.9554 (ttmt) cc_final: 0.9342 (tttt) REVERT: I 123 LEU cc_start: 0.9466 (mt) cc_final: 0.9126 (mp) REVERT: I 146 MET cc_start: 0.8663 (ptp) cc_final: 0.8434 (tmm) outliers start: 3 outliers final: 0 residues processed: 272 average time/residue: 0.1563 time to fit residues: 61.3431 Evaluate side-chains 195 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 160 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 ASN B1006 GLN B1135 GLN B1216 ASN C 410 ASN C 429 GLN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 HIS H 313 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.053207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044759 restraints weight = 136582.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045901 restraints weight = 88587.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.046716 restraints weight = 63311.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047352 restraints weight = 48625.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047805 restraints weight = 39079.790| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16906 Z= 0.142 Angle : 0.678 14.040 22919 Z= 0.351 Chirality : 0.042 0.198 2685 Planarity : 0.005 0.054 2978 Dihedral : 5.783 35.817 2305 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.00 % Favored : 88.89 % Rotamer: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.20), residues: 1872 helix: 0.52 (0.16), residues: 1059 sheet: -2.48 (0.78), residues: 28 loop : -3.50 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 712 TYR 0.022 0.002 TYR F 666 PHE 0.041 0.002 PHE A 552 TRP 0.013 0.002 TRP G 546 HIS 0.010 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00294 (16906) covalent geometry : angle 0.67790 (22919) hydrogen bonds : bond 0.04716 ( 915) hydrogen bonds : angle 4.60889 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.519 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: 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: A 488 ILE cc_start: 0.7537 (mt) cc_final: 0.7122 (mm) REVERT: A 590 GLU cc_start: 0.9413 (tt0) cc_final: 0.8955 (tm-30) REVERT: A 595 GLU cc_start: 0.9474 (tt0) cc_final: 0.9100 (mm-30) REVERT: B 721 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 770 TYR cc_start: 0.8910 (m-10) cc_final: 0.8608 (m-10) REVERT: B 795 MET cc_start: 0.8565 (mmt) cc_final: 0.8342 (mmm) REVERT: B 1239 ILE cc_start: 0.9504 (tp) cc_final: 0.9097 (tt) REVERT: C 543 ARG cc_start: 0.8680 (mpp-170) cc_final: 0.8124 (mtm-85) REVERT: C 599 GLU cc_start: 0.9303 (tt0) cc_final: 0.8868 (pt0) REVERT: D 323 GLU cc_start: 0.9192 (pt0) cc_final: 0.8974 (pt0) REVERT: D 380 ARG cc_start: 0.9519 (mtm180) cc_final: 0.8897 (mtt90) REVERT: D 412 TYR cc_start: 0.6929 (m-80) cc_final: 0.6248 (m-80) REVERT: D 433 GLN cc_start: 0.9471 (pm20) cc_final: 0.8797 (pp30) REVERT: E 312 LYS cc_start: 0.8889 (tppp) cc_final: 0.8612 (tppp) REVERT: E 316 LEU cc_start: 0.9233 (pt) cc_final: 0.8909 (pt) REVERT: E 344 MET cc_start: 0.9552 (ttm) cc_final: 0.8920 (tpp) REVERT: E 346 TYR cc_start: 0.9311 (m-80) cc_final: 0.8842 (m-80) REVERT: E 366 THR cc_start: 0.9665 (m) cc_final: 0.9453 (m) REVERT: E 400 LEU cc_start: 0.8619 (tp) cc_final: 0.8396 (tp) REVERT: F 533 GLN cc_start: 0.9346 (tt0) cc_final: 0.9099 (tm-30) REVERT: F 666 TYR cc_start: 0.8988 (m-80) cc_final: 0.8719 (m-80) REVERT: F 679 MET cc_start: 0.8971 (mmt) cc_final: 0.8608 (mmp) REVERT: F 681 PHE cc_start: 0.9197 (m-80) cc_final: 0.8895 (m-80) REVERT: F 689 LEU cc_start: 0.9779 (mm) cc_final: 0.9167 (tp) REVERT: F 717 ARG cc_start: 0.9482 (mmm-85) cc_final: 0.9175 (mtp180) REVERT: F 725 GLN cc_start: 0.8891 (mm110) cc_final: 0.8489 (mm-40) REVERT: G 691 MET cc_start: 0.9430 (mmp) cc_final: 0.9227 (mmp) REVERT: G 711 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9053 (mm-30) REVERT: G 717 ARG cc_start: 0.8775 (ttm170) cc_final: 0.8468 (ttm170) REVERT: H 88 PHE cc_start: 0.9106 (m-80) cc_final: 0.8739 (m-10) REVERT: H 92 ARG cc_start: 0.8925 (mmp-170) cc_final: 0.8718 (mmp-170) REVERT: H 93 ASN cc_start: 0.8697 (m110) cc_final: 0.8161 (m110) REVERT: H 96 MET cc_start: 0.8717 (mmp) cc_final: 0.8449 (mmp) REVERT: H 104 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8954 (mt-10) REVERT: H 305 GLU cc_start: 0.5854 (mt-10) cc_final: 0.5259 (pm20) REVERT: H 326 HIS cc_start: 0.9380 (t-90) cc_final: 0.9044 (t-90) REVERT: H 535 TYR cc_start: 0.9302 (m-80) cc_final: 0.9074 (m-10) REVERT: H 541 ARG cc_start: 0.9044 (mtt90) cc_final: 0.8561 (mpt-90) REVERT: H 552 MET cc_start: 0.9399 (ttm) cc_final: 0.9178 (ptm) REVERT: I 85 LEU cc_start: 0.9264 (pp) cc_final: 0.9061 (pp) REVERT: I 86 ARG cc_start: 0.9242 (mpt-90) cc_final: 0.8779 (mtt-85) REVERT: I 96 ASP cc_start: 0.8554 (m-30) cc_final: 0.7810 (p0) REVERT: I 109 LYS cc_start: 0.9508 (ttmt) cc_final: 0.9216 (tttt) REVERT: I 123 LEU cc_start: 0.9423 (mt) cc_final: 0.9165 (mp) outliers start: 2 outliers final: 0 residues processed: 293 average time/residue: 0.1529 time to fit residues: 64.7195 Evaluate side-chains 223 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 HIS B1135 GLN C 429 GLN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 GLN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.044601 restraints weight = 137141.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.045707 restraints weight = 90013.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046499 restraints weight = 64706.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.047027 restraints weight = 49912.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047502 restraints weight = 41374.924| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16906 Z= 0.163 Angle : 0.689 15.465 22919 Z= 0.355 Chirality : 0.041 0.168 2685 Planarity : 0.005 0.057 2978 Dihedral : 5.647 34.580 2305 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.02 % Favored : 87.87 % Rotamer: Outliers : 0.12 % Allowed : 3.95 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.20), residues: 1872 helix: 0.74 (0.16), residues: 1063 sheet: -1.94 (0.74), residues: 35 loop : -3.46 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 554 TYR 0.042 0.002 TYR E 310 PHE 0.036 0.002 PHE H 112 TRP 0.012 0.002 TRP E 313 HIS 0.009 0.002 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00338 (16906) covalent geometry : angle 0.68915 (22919) hydrogen bonds : bond 0.04541 ( 915) hydrogen bonds : angle 4.54622 ( 2691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.677 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.7089 (mt) cc_final: 0.6712 (mm) REVERT: A 567 PHE cc_start: 0.8615 (m-10) cc_final: 0.6630 (m-10) REVERT: A 590 GLU cc_start: 0.9388 (tt0) cc_final: 0.8942 (tm-30) REVERT: A 595 GLU cc_start: 0.9462 (tt0) cc_final: 0.9062 (mm-30) REVERT: B 721 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 788 TYR cc_start: 0.7232 (m-80) cc_final: 0.6929 (m-80) REVERT: B 795 MET cc_start: 0.8600 (mmt) cc_final: 0.8363 (mmm) REVERT: B 987 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8441 (mm-30) REVERT: B 1239 ILE cc_start: 0.9517 (tp) cc_final: 0.9094 (tt) REVERT: C 492 VAL cc_start: 0.9751 (t) cc_final: 0.9432 (p) REVERT: C 543 ARG cc_start: 0.8837 (mpp-170) cc_final: 0.8272 (mtm-85) REVERT: C 599 GLU cc_start: 0.9189 (tt0) cc_final: 0.8852 (pt0) REVERT: D 323 GLU cc_start: 0.9512 (pt0) cc_final: 0.9011 (pt0) REVERT: D 433 GLN cc_start: 0.9435 (pm20) cc_final: 0.8804 (pp30) REVERT: E 313 TRP cc_start: 0.9366 (p-90) cc_final: 0.8279 (p-90) REVERT: E 316 LEU cc_start: 0.9168 (pt) cc_final: 0.8863 (pt) REVERT: E 344 MET cc_start: 0.9527 (ttm) cc_final: 0.9018 (tpp) REVERT: E 346 TYR cc_start: 0.9357 (m-80) cc_final: 0.8944 (m-80) REVERT: E 370 ASN cc_start: 0.9347 (m110) cc_final: 0.9102 (m110) REVERT: E 400 LEU cc_start: 0.8613 (tp) cc_final: 0.8403 (tp) REVERT: F 533 GLN cc_start: 0.9336 (tt0) cc_final: 0.9078 (tm-30) REVERT: F 666 TYR cc_start: 0.8987 (m-80) cc_final: 0.8711 (m-80) REVERT: F 681 PHE cc_start: 0.9261 (m-80) cc_final: 0.8858 (m-80) REVERT: F 717 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.9228 (ttm-80) REVERT: G 561 CYS cc_start: 0.9400 (m) cc_final: 0.9133 (m) REVERT: G 711 GLU cc_start: 0.9582 (mt-10) cc_final: 0.9073 (mm-30) REVERT: G 717 ARG cc_start: 0.8618 (ttm170) cc_final: 0.8327 (ttm170) REVERT: H 85 LEU cc_start: 0.9364 (mp) cc_final: 0.9143 (mp) REVERT: H 88 PHE cc_start: 0.9110 (m-80) cc_final: 0.8777 (m-10) REVERT: H 92 ARG cc_start: 0.9001 (mmp-170) cc_final: 0.8760 (mmm160) REVERT: H 93 ASN cc_start: 0.8714 (m110) cc_final: 0.8206 (m110) REVERT: H 104 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8884 (mt-10) REVERT: H 105 ARG cc_start: 0.8779 (mmp-170) cc_final: 0.8472 (mmp-170) REVERT: H 305 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5496 (pm20) REVERT: H 326 HIS cc_start: 0.9382 (t-90) cc_final: 0.9077 (t-90) REVERT: H 535 TYR cc_start: 0.9067 (m-80) cc_final: 0.8457 (m-80) REVERT: H 541 ARG cc_start: 0.9041 (mtt90) cc_final: 0.8650 (mpt-90) REVERT: H 554 ARG cc_start: 0.9223 (tpt170) cc_final: 0.8989 (tpt170) REVERT: I 85 LEU cc_start: 0.9246 (pp) cc_final: 0.9026 (pp) REVERT: I 86 ARG cc_start: 0.9244 (mpt-90) cc_final: 0.8803 (mtt-85) REVERT: I 109 LYS cc_start: 0.9454 (ttmt) cc_final: 0.9231 (tttt) REVERT: I 123 LEU cc_start: 0.9478 (mt) cc_final: 0.9225 (mp) REVERT: I 146 MET cc_start: 0.8646 (ptp) cc_final: 0.8346 (tmm) outliers start: 2 outliers final: 0 residues processed: 268 average time/residue: 0.1536 time to fit residues: 60.1544 Evaluate side-chains 210 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 168 optimal weight: 0.0470 chunk 206 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 chunk 89 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 ASN B1006 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 GLN F 690 GLN F 718 GLN ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.043710 restraints weight = 140568.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.044793 restraints weight = 91618.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.045571 restraints weight = 65956.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.046146 restraints weight = 51027.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046573 restraints weight = 41557.734| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16906 Z= 0.223 Angle : 0.736 14.756 22919 Z= 0.382 Chirality : 0.043 0.204 2685 Planarity : 0.005 0.064 2978 Dihedral : 5.806 34.393 2305 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.93 % Favored : 86.97 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1872 helix: 0.61 (0.16), residues: 1067 sheet: -2.16 (0.69), residues: 35 loop : -3.44 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 905 TYR 0.018 0.002 TYR C 446 PHE 0.022 0.002 PHE F 707 TRP 0.011 0.002 TRP D 388 HIS 0.010 0.002 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00453 (16906) covalent geometry : angle 0.73554 (22919) hydrogen bonds : bond 0.04525 ( 915) hydrogen bonds : angle 4.75282 ( 2691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.624 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.7075 (mt) cc_final: 0.6708 (mm) REVERT: A 542 GLN cc_start: 0.9382 (pt0) cc_final: 0.9001 (pt0) REVERT: A 590 GLU cc_start: 0.9393 (tt0) cc_final: 0.8953 (tm-30) REVERT: B 721 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8398 (mm-30) REVERT: B 757 MET cc_start: 0.8680 (mtt) cc_final: 0.8184 (mtt) REVERT: B 795 MET cc_start: 0.8588 (mmt) cc_final: 0.8326 (mmm) REVERT: B 987 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 1239 ILE cc_start: 0.9509 (tp) cc_final: 0.9096 (tt) REVERT: C 599 GLU cc_start: 0.9460 (tt0) cc_final: 0.9029 (pt0) REVERT: D 323 GLU cc_start: 0.9516 (pt0) cc_final: 0.9002 (pt0) REVERT: D 433 GLN cc_start: 0.9397 (pm20) cc_final: 0.8807 (pp30) REVERT: E 310 TYR cc_start: 0.9271 (p90) cc_final: 0.8935 (p90) REVERT: E 313 TRP cc_start: 0.9362 (p-90) cc_final: 0.8625 (p-90) REVERT: E 344 MET cc_start: 0.9533 (ttm) cc_final: 0.9078 (tpp) REVERT: E 366 THR cc_start: 0.9655 (m) cc_final: 0.9454 (m) REVERT: E 370 ASN cc_start: 0.9383 (m110) cc_final: 0.9121 (m110) REVERT: E 400 LEU cc_start: 0.8577 (tp) cc_final: 0.8350 (tp) REVERT: F 533 GLN cc_start: 0.9365 (tt0) cc_final: 0.9083 (tm-30) REVERT: F 666 TYR cc_start: 0.8995 (m-80) cc_final: 0.8691 (m-80) REVERT: F 681 PHE cc_start: 0.9191 (m-80) cc_final: 0.8877 (m-80) REVERT: F 717 ARG cc_start: 0.9488 (mmm-85) cc_final: 0.9217 (ttm-80) REVERT: F 718 GLN cc_start: 0.9579 (mm-40) cc_final: 0.9354 (mm-40) REVERT: G 561 CYS cc_start: 0.9441 (m) cc_final: 0.9152 (m) REVERT: G 691 MET cc_start: 0.9427 (mmp) cc_final: 0.8752 (mmm) REVERT: G 711 GLU cc_start: 0.9600 (mt-10) cc_final: 0.9120 (mm-30) REVERT: G 717 ARG cc_start: 0.8714 (ttm170) cc_final: 0.8383 (ttm170) REVERT: H 85 LEU cc_start: 0.9342 (mp) cc_final: 0.9111 (mp) REVERT: H 88 PHE cc_start: 0.9186 (m-80) cc_final: 0.8696 (m-10) REVERT: H 93 ASN cc_start: 0.8722 (m110) cc_final: 0.8210 (m110) REVERT: H 97 LYS cc_start: 0.9644 (mmtt) cc_final: 0.9330 (mmmm) REVERT: H 104 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9146 (mt-10) REVERT: H 305 GLU cc_start: 0.6083 (mt-10) cc_final: 0.5626 (pm20) REVERT: H 326 HIS cc_start: 0.9424 (t-90) cc_final: 0.9105 (t-90) REVERT: H 535 TYR cc_start: 0.9075 (m-80) cc_final: 0.8716 (m-10) REVERT: I 85 LEU cc_start: 0.9240 (pp) cc_final: 0.9024 (pp) REVERT: I 109 LYS cc_start: 0.9487 (ttmt) cc_final: 0.9235 (tttt) REVERT: I 123 LEU cc_start: 0.9480 (mt) cc_final: 0.9205 (mp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1539 time to fit residues: 56.2344 Evaluate side-chains 192 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 41 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 0.0370 chunk 147 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 ASN B 903 ASN B 927 ASN C 429 GLN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.045032 restraints weight = 133351.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.046217 restraints weight = 87225.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047063 restraints weight = 62517.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.047684 restraints weight = 48172.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.048074 restraints weight = 39025.651| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16906 Z= 0.129 Angle : 0.669 16.016 22919 Z= 0.339 Chirality : 0.041 0.164 2685 Planarity : 0.005 0.081 2978 Dihedral : 5.459 35.228 2305 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.74 % Favored : 89.21 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.20), residues: 1872 helix: 1.05 (0.16), residues: 1064 sheet: -2.30 (0.72), residues: 28 loop : -3.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 368 TYR 0.023 0.002 TYR A 586 PHE 0.028 0.002 PHE G 729 TRP 0.010 0.001 TRP G 546 HIS 0.009 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00270 (16906) covalent geometry : angle 0.66895 (22919) hydrogen bonds : bond 0.04359 ( 915) hydrogen bonds : angle 4.29929 ( 2691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.777 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: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.6883 (mt) cc_final: 0.6500 (mm) REVERT: A 534 TYR cc_start: 0.9022 (m-80) cc_final: 0.8713 (m-80) REVERT: A 542 GLN cc_start: 0.9382 (pt0) cc_final: 0.9121 (pt0) REVERT: A 560 LEU cc_start: 0.9339 (mt) cc_final: 0.9128 (mt) REVERT: A 567 PHE cc_start: 0.8677 (m-80) cc_final: 0.8188 (m-10) REVERT: A 590 GLU cc_start: 0.9369 (tt0) cc_final: 0.8940 (tm-30) REVERT: B 721 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8300 (mm-30) REVERT: B 787 TYR cc_start: 0.8444 (m-80) cc_final: 0.7936 (m-10) REVERT: B 795 MET cc_start: 0.8590 (mmt) cc_final: 0.8322 (mmm) REVERT: B 987 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8427 (mm-30) REVERT: C 492 VAL cc_start: 0.9768 (t) cc_final: 0.9474 (p) REVERT: C 496 LEU cc_start: 0.9727 (mt) cc_final: 0.9338 (pp) REVERT: C 599 GLU cc_start: 0.9395 (tt0) cc_final: 0.8860 (pt0) REVERT: D 368 ARG cc_start: 0.9226 (ptp90) cc_final: 0.9016 (ptt90) REVERT: D 433 GLN cc_start: 0.9415 (pm20) cc_final: 0.8833 (pp30) REVERT: E 313 TRP cc_start: 0.9167 (p-90) cc_final: 0.8197 (p-90) REVERT: E 316 LEU cc_start: 0.9050 (pt) cc_final: 0.8760 (pt) REVERT: E 344 MET cc_start: 0.9505 (ttm) cc_final: 0.8993 (tpp) REVERT: E 366 THR cc_start: 0.9662 (m) cc_final: 0.9447 (m) REVERT: E 370 ASN cc_start: 0.9362 (m110) cc_final: 0.9122 (m110) REVERT: E 380 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8586 (ttp-110) REVERT: F 666 TYR cc_start: 0.8992 (m-80) cc_final: 0.8710 (m-80) REVERT: F 681 PHE cc_start: 0.9182 (m-80) cc_final: 0.8846 (m-80) REVERT: F 691 MET cc_start: 0.9394 (mmp) cc_final: 0.8947 (mtp) REVERT: F 717 ARG cc_start: 0.9486 (mmm-85) cc_final: 0.9222 (mtp180) REVERT: F 718 GLN cc_start: 0.9538 (mm-40) cc_final: 0.9156 (pp30) REVERT: F 725 GLN cc_start: 0.8864 (mm110) cc_final: 0.8421 (mm-40) REVERT: G 561 CYS cc_start: 0.9393 (m) cc_final: 0.9144 (m) REVERT: G 691 MET cc_start: 0.9425 (mmp) cc_final: 0.8802 (mmm) REVERT: G 693 LYS cc_start: 0.9587 (mtmm) cc_final: 0.9333 (mttt) REVERT: G 711 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9075 (mm-30) REVERT: G 717 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8336 (ttm170) REVERT: H 85 LEU cc_start: 0.9346 (mp) cc_final: 0.9101 (mp) REVERT: H 88 PHE cc_start: 0.9135 (m-80) cc_final: 0.8695 (m-10) REVERT: H 93 ASN cc_start: 0.8714 (m110) cc_final: 0.8232 (m110) REVERT: H 97 LYS cc_start: 0.9641 (mmtt) cc_final: 0.9337 (mmmm) REVERT: H 104 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8673 (mt-10) REVERT: H 105 ARG cc_start: 0.8788 (mmp-170) cc_final: 0.8422 (mmp-170) REVERT: H 305 GLU cc_start: 0.5891 (mt-10) cc_final: 0.5602 (pm20) REVERT: H 326 HIS cc_start: 0.9380 (t-90) cc_final: 0.9065 (t-90) REVERT: H 535 TYR cc_start: 0.9003 (m-80) cc_final: 0.8756 (m-10) REVERT: H 541 ARG cc_start: 0.9007 (mtt90) cc_final: 0.8744 (mpt-90) REVERT: I 85 LEU cc_start: 0.9184 (pp) cc_final: 0.8963 (pp) REVERT: I 109 LYS cc_start: 0.9414 (ttmt) cc_final: 0.9199 (tttt) REVERT: I 146 MET cc_start: 0.8620 (ptp) cc_final: 0.8372 (tmm) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1470 time to fit residues: 59.7526 Evaluate side-chains 208 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 13 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 0.0170 chunk 155 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN B 927 ASN C 429 GLN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.045364 restraints weight = 133509.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.046497 restraints weight = 87977.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.047342 restraints weight = 63701.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.047868 restraints weight = 49170.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.048379 restraints weight = 40875.874| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16906 Z= 0.130 Angle : 0.667 14.512 22919 Z= 0.339 Chirality : 0.041 0.219 2685 Planarity : 0.005 0.090 2978 Dihedral : 5.340 34.973 2305 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.74 % Favored : 89.21 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1872 helix: 1.19 (0.16), residues: 1062 sheet: -2.21 (0.73), residues: 28 loop : -3.12 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 881 TYR 0.051 0.002 TYR D 412 PHE 0.032 0.002 PHE H 112 TRP 0.010 0.001 TRP B1032 HIS 0.009 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00280 (16906) covalent geometry : angle 0.66731 (22919) hydrogen bonds : bond 0.04317 ( 915) hydrogen bonds : angle 4.21836 ( 2691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.424 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 ILE cc_start: 0.8617 (pt) cc_final: 0.8052 (mm) REVERT: A 488 ILE cc_start: 0.6718 (mt) cc_final: 0.6296 (mm) REVERT: A 542 GLN cc_start: 0.9390 (pt0) cc_final: 0.9044 (pt0) REVERT: A 567 PHE cc_start: 0.8369 (m-80) cc_final: 0.7468 (m-10) REVERT: A 590 GLU cc_start: 0.9334 (tt0) cc_final: 0.8911 (tm-30) REVERT: B 721 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8260 (mm-30) REVERT: B 723 ASN cc_start: 0.8706 (m110) cc_final: 0.8499 (m110) REVERT: B 787 TYR cc_start: 0.8397 (m-80) cc_final: 0.7966 (m-10) REVERT: B 795 MET cc_start: 0.8577 (mmt) cc_final: 0.8300 (mmm) REVERT: B 1239 ILE cc_start: 0.9467 (tp) cc_final: 0.9030 (tt) REVERT: C 492 VAL cc_start: 0.9757 (t) cc_final: 0.9464 (p) REVERT: C 496 LEU cc_start: 0.9734 (mt) cc_final: 0.9344 (pp) REVERT: C 547 LYS cc_start: 0.9302 (ttmm) cc_final: 0.8965 (mtpp) REVERT: C 599 GLU cc_start: 0.9227 (tt0) cc_final: 0.8877 (pt0) REVERT: D 323 GLU cc_start: 0.9626 (pt0) cc_final: 0.9345 (pt0) REVERT: D 433 GLN cc_start: 0.9422 (pm20) cc_final: 0.8849 (pp30) REVERT: E 341 GLU cc_start: 0.9424 (mp0) cc_final: 0.9220 (mp0) REVERT: E 344 MET cc_start: 0.9479 (ttm) cc_final: 0.9001 (tpp) REVERT: E 380 ARG cc_start: 0.9138 (mtm-85) cc_final: 0.8607 (ttp-110) REVERT: F 666 TYR cc_start: 0.8981 (m-80) cc_final: 0.8667 (m-80) REVERT: F 681 PHE cc_start: 0.9170 (m-80) cc_final: 0.8863 (m-80) REVERT: F 717 ARG cc_start: 0.9455 (mmm-85) cc_final: 0.9143 (ttm-80) REVERT: F 718 GLN cc_start: 0.9556 (mm-40) cc_final: 0.9158 (pp30) REVERT: G 561 CYS cc_start: 0.9400 (m) cc_final: 0.9150 (m) REVERT: G 691 MET cc_start: 0.9451 (mmp) cc_final: 0.8727 (mmm) REVERT: G 711 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9085 (mm-30) REVERT: G 717 ARG cc_start: 0.8706 (ttm170) cc_final: 0.8343 (ttm170) REVERT: H 85 LEU cc_start: 0.9367 (mp) cc_final: 0.9117 (mp) REVERT: H 88 PHE cc_start: 0.9154 (m-80) cc_final: 0.8693 (m-10) REVERT: H 93 ASN cc_start: 0.8747 (m110) cc_final: 0.8278 (m110) REVERT: H 97 LYS cc_start: 0.9658 (mmtt) cc_final: 0.9350 (mmmm) REVERT: H 104 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8383 (mt-10) REVERT: H 105 ARG cc_start: 0.8800 (mmp-170) cc_final: 0.8425 (mmp-170) REVERT: H 305 GLU cc_start: 0.5884 (mt-10) cc_final: 0.5601 (pm20) REVERT: H 326 HIS cc_start: 0.9376 (t-90) cc_final: 0.9088 (t-90) REVERT: H 535 TYR cc_start: 0.8969 (m-80) cc_final: 0.8699 (m-10) REVERT: H 542 ARG cc_start: 0.8774 (ppt170) cc_final: 0.7976 (tmm160) REVERT: I 85 LEU cc_start: 0.9132 (pp) cc_final: 0.8902 (pp) REVERT: I 116 ASP cc_start: 0.8055 (t0) cc_final: 0.7844 (t0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1446 time to fit residues: 57.1043 Evaluate side-chains 197 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 55 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN B 927 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 HIS ** G 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044885 restraints weight = 136271.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045963 restraints weight = 89998.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046774 restraints weight = 65777.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047287 restraints weight = 50845.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.047762 restraints weight = 42266.466| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 16906 Z= 0.159 Angle : 0.688 15.015 22919 Z= 0.351 Chirality : 0.042 0.186 2685 Planarity : 0.005 0.065 2978 Dihedral : 5.362 35.360 2305 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.16 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1872 helix: 1.16 (0.16), residues: 1069 sheet: -2.34 (0.72), residues: 28 loop : -3.17 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 881 TYR 0.025 0.002 TYR D 456 PHE 0.030 0.002 PHE G 729 TRP 0.011 0.001 TRP D 388 HIS 0.009 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00343 (16906) covalent geometry : angle 0.68780 (22919) hydrogen bonds : bond 0.04251 ( 915) hydrogen bonds : angle 4.32739 ( 2691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.694 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 ILE cc_start: 0.8619 (pt) cc_final: 0.8050 (mm) REVERT: A 488 ILE cc_start: 0.6615 (mt) cc_final: 0.6189 (mm) REVERT: A 542 GLN cc_start: 0.9398 (pt0) cc_final: 0.9197 (pt0) REVERT: A 567 PHE cc_start: 0.7794 (m-80) cc_final: 0.7175 (m-80) REVERT: A 590 GLU cc_start: 0.9350 (tt0) cc_final: 0.8927 (tm-30) REVERT: B 721 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 723 ASN cc_start: 0.8858 (m110) cc_final: 0.8430 (m110) REVERT: B 787 TYR cc_start: 0.8517 (m-80) cc_final: 0.8031 (m-10) REVERT: B 795 MET cc_start: 0.8633 (mmt) cc_final: 0.8355 (mmm) REVERT: B 890 LYS cc_start: 0.9479 (pptt) cc_final: 0.9265 (pptt) REVERT: B 938 MET cc_start: 0.7611 (ppp) cc_final: 0.6818 (ppp) REVERT: B 987 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8338 (mm-30) REVERT: C 492 VAL cc_start: 0.9753 (t) cc_final: 0.9462 (p) REVERT: C 496 LEU cc_start: 0.9727 (mt) cc_final: 0.9355 (pp) REVERT: C 547 LYS cc_start: 0.9310 (ttmm) cc_final: 0.8960 (mtpp) REVERT: C 599 GLU cc_start: 0.9294 (tt0) cc_final: 0.8873 (pt0) REVERT: D 323 GLU cc_start: 0.9620 (pt0) cc_final: 0.9376 (pt0) REVERT: D 433 GLN cc_start: 0.9425 (pm20) cc_final: 0.8843 (pp30) REVERT: E 341 GLU cc_start: 0.9422 (mp0) cc_final: 0.9192 (mp0) REVERT: E 380 ARG cc_start: 0.9154 (mtm-85) cc_final: 0.8556 (ttp-110) REVERT: E 426 GLU cc_start: 0.8062 (mp0) cc_final: 0.7586 (mp0) REVERT: F 666 TYR cc_start: 0.8991 (m-80) cc_final: 0.8659 (m-80) REVERT: F 681 PHE cc_start: 0.9171 (m-80) cc_final: 0.8909 (m-80) REVERT: F 691 MET cc_start: 0.9292 (mmp) cc_final: 0.8852 (mtp) REVERT: F 717 ARG cc_start: 0.9429 (mmm-85) cc_final: 0.9135 (ttm-80) REVERT: F 718 GLN cc_start: 0.9570 (mm-40) cc_final: 0.9189 (pp30) REVERT: G 561 CYS cc_start: 0.9390 (m) cc_final: 0.9093 (m) REVERT: G 693 LYS cc_start: 0.9598 (mtmm) cc_final: 0.9363 (mttt) REVERT: G 711 GLU cc_start: 0.9600 (mt-10) cc_final: 0.9087 (mm-30) REVERT: G 717 ARG cc_start: 0.8744 (ttm170) cc_final: 0.8365 (ttm170) REVERT: G 726 ARG cc_start: 0.9568 (mtp-110) cc_final: 0.9216 (ttt180) REVERT: H 85 LEU cc_start: 0.9371 (mp) cc_final: 0.9113 (mp) REVERT: H 88 PHE cc_start: 0.9202 (m-80) cc_final: 0.8747 (m-10) REVERT: H 93 ASN cc_start: 0.8814 (m110) cc_final: 0.8279 (m110) REVERT: H 96 MET cc_start: 0.8674 (mmp) cc_final: 0.8408 (mmp) REVERT: H 104 GLU cc_start: 0.9317 (mt-10) cc_final: 0.9057 (mt-10) REVERT: H 305 GLU cc_start: 0.6043 (mt-10) cc_final: 0.5753 (pm20) REVERT: H 326 HIS cc_start: 0.9400 (t-90) cc_final: 0.9065 (t-90) REVERT: H 535 TYR cc_start: 0.8994 (m-80) cc_final: 0.8626 (m-10) REVERT: H 541 ARG cc_start: 0.8907 (mtt90) cc_final: 0.8601 (mpt-90) REVERT: H 542 ARG cc_start: 0.8884 (ppt170) cc_final: 0.7977 (tmm160) REVERT: I 85 LEU cc_start: 0.9194 (pp) cc_final: 0.8984 (pp) REVERT: I 116 ASP cc_start: 0.8111 (t0) cc_final: 0.7903 (t0) REVERT: I 146 MET cc_start: 0.8560 (ptp) cc_final: 0.8330 (tmm) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1526 time to fit residues: 57.2223 Evaluate side-chains 194 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.052251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.044361 restraints weight = 137897.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045420 restraints weight = 91516.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.046124 restraints weight = 66564.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046735 restraints weight = 52212.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047123 restraints weight = 42246.618| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 16906 Z= 0.198 Angle : 0.733 14.678 22919 Z= 0.377 Chirality : 0.043 0.236 2685 Planarity : 0.005 0.068 2978 Dihedral : 5.531 37.618 2305 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.34 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.20), residues: 1872 helix: 1.01 (0.16), residues: 1068 sheet: -2.35 (0.72), residues: 28 loop : -3.21 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 881 TYR 0.036 0.002 TYR A 534 PHE 0.033 0.002 PHE H 112 TRP 0.014 0.001 TRP D 388 HIS 0.009 0.002 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00417 (16906) covalent geometry : angle 0.73344 (22919) hydrogen bonds : bond 0.04309 ( 915) hydrogen bonds : angle 4.49351 ( 2691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.548 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 ILE cc_start: 0.8602 (pt) cc_final: 0.8016 (mm) REVERT: A 488 ILE cc_start: 0.6685 (mt) cc_final: 0.6275 (mm) REVERT: A 542 GLN cc_start: 0.9471 (pt0) cc_final: 0.9149 (pt0) REVERT: A 553 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8986 (tt0) REVERT: A 590 GLU cc_start: 0.9299 (tt0) cc_final: 0.8830 (tm-30) REVERT: B 721 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 723 ASN cc_start: 0.8906 (m110) cc_final: 0.8569 (m110) REVERT: B 787 TYR cc_start: 0.8680 (m-80) cc_final: 0.8286 (m-10) REVERT: B 795 MET cc_start: 0.8637 (mmt) cc_final: 0.8342 (mmm) REVERT: B 890 LYS cc_start: 0.9423 (pptt) cc_final: 0.9192 (pptt) REVERT: B 987 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8327 (mm-30) REVERT: C 492 VAL cc_start: 0.9763 (t) cc_final: 0.9500 (p) REVERT: C 496 LEU cc_start: 0.9735 (mt) cc_final: 0.9485 (tp) REVERT: C 547 LYS cc_start: 0.9305 (ttmm) cc_final: 0.8842 (mtpp) REVERT: C 599 GLU cc_start: 0.9351 (tt0) cc_final: 0.8886 (pt0) REVERT: D 323 GLU cc_start: 0.9601 (pt0) cc_final: 0.9378 (pt0) REVERT: D 368 ARG cc_start: 0.8948 (ptp90) cc_final: 0.8730 (ptt-90) REVERT: D 412 TYR cc_start: 0.7855 (m-80) cc_final: 0.7155 (m-80) REVERT: D 433 GLN cc_start: 0.9449 (pm20) cc_final: 0.8864 (pp30) REVERT: E 313 TRP cc_start: 0.9315 (p-90) cc_final: 0.8344 (p-90) REVERT: E 320 HIS cc_start: 0.9090 (t-90) cc_final: 0.7893 (t-90) REVERT: E 341 GLU cc_start: 0.9418 (mp0) cc_final: 0.9172 (mp0) REVERT: E 366 THR cc_start: 0.9649 (m) cc_final: 0.9445 (m) REVERT: E 370 ASN cc_start: 0.9423 (m110) cc_final: 0.9102 (m110) REVERT: F 666 TYR cc_start: 0.8985 (m-80) cc_final: 0.8673 (m-80) REVERT: F 681 PHE cc_start: 0.9149 (m-80) cc_final: 0.8896 (m-80) REVERT: F 691 MET cc_start: 0.9318 (mmp) cc_final: 0.8849 (mtp) REVERT: F 717 ARG cc_start: 0.9428 (mmm-85) cc_final: 0.9124 (ttm-80) REVERT: F 718 GLN cc_start: 0.9584 (mm-40) cc_final: 0.9379 (mm-40) REVERT: G 561 CYS cc_start: 0.9430 (m) cc_final: 0.9130 (m) REVERT: G 693 LYS cc_start: 0.9613 (mtmm) cc_final: 0.9409 (mttt) REVERT: G 711 GLU cc_start: 0.9606 (mt-10) cc_final: 0.9120 (mm-30) REVERT: G 717 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8374 (ttm170) REVERT: G 726 ARG cc_start: 0.9495 (mtp-110) cc_final: 0.9095 (ttt180) REVERT: H 85 LEU cc_start: 0.9341 (mp) cc_final: 0.9070 (mp) REVERT: H 88 PHE cc_start: 0.9150 (m-80) cc_final: 0.8665 (m-10) REVERT: H 93 ASN cc_start: 0.8816 (m110) cc_final: 0.8325 (m110) REVERT: H 104 GLU cc_start: 0.9380 (mt-10) cc_final: 0.9124 (mt-10) REVERT: H 326 HIS cc_start: 0.9437 (t-90) cc_final: 0.9117 (t-90) REVERT: H 542 ARG cc_start: 0.8886 (ppt170) cc_final: 0.8006 (tmm160) REVERT: I 85 LEU cc_start: 0.9230 (pp) cc_final: 0.8980 (pp) REVERT: I 86 ARG cc_start: 0.9179 (mpt-90) cc_final: 0.8783 (mtt-85) REVERT: I 146 MET cc_start: 0.8612 (ptp) cc_final: 0.8410 (tmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1384 time to fit residues: 51.5028 Evaluate side-chains 194 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 209 optimal weight: 10.0000 chunk 167 optimal weight: 0.0270 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN B 927 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.053434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045289 restraints weight = 134420.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046391 restraints weight = 88465.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047235 restraints weight = 63807.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047827 restraints weight = 49440.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048240 restraints weight = 40032.452| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16906 Z= 0.137 Angle : 0.696 13.822 22919 Z= 0.353 Chirality : 0.042 0.174 2685 Planarity : 0.005 0.071 2978 Dihedral : 5.375 36.882 2305 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.47 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1872 helix: 1.14 (0.16), residues: 1069 sheet: -2.02 (0.77), residues: 28 loop : -3.13 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 936 TYR 0.029 0.002 TYR A 534 PHE 0.026 0.002 PHE G 729 TRP 0.052 0.002 TRP B1032 HIS 0.007 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00298 (16906) covalent geometry : angle 0.69633 (22919) hydrogen bonds : bond 0.04225 ( 915) hydrogen bonds : angle 4.28434 ( 2691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.568 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 ILE cc_start: 0.8587 (pt) cc_final: 0.8009 (mm) REVERT: A 488 ILE cc_start: 0.6423 (mt) cc_final: 0.5978 (mm) REVERT: A 542 GLN cc_start: 0.9424 (pt0) cc_final: 0.9126 (pt0) REVERT: A 590 GLU cc_start: 0.9284 (tt0) cc_final: 0.8819 (tm-30) REVERT: B 721 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 787 TYR cc_start: 0.8624 (m-80) cc_final: 0.8234 (m-10) REVERT: B 795 MET cc_start: 0.8535 (mmt) cc_final: 0.8230 (mmm) REVERT: B 890 LYS cc_start: 0.9419 (pptt) cc_final: 0.9169 (pptt) REVERT: B 941 ASN cc_start: 0.8938 (t0) cc_final: 0.8700 (t0) REVERT: B 987 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8159 (mm-30) REVERT: B 1142 GLN cc_start: 0.9243 (tp-100) cc_final: 0.9007 (tp-100) REVERT: B 1197 GLU cc_start: 0.7949 (mp0) cc_final: 0.7333 (mp0) REVERT: C 492 VAL cc_start: 0.9741 (t) cc_final: 0.9450 (p) REVERT: C 496 LEU cc_start: 0.9714 (mt) cc_final: 0.9348 (pp) REVERT: D 323 GLU cc_start: 0.9583 (pt0) cc_final: 0.9302 (pt0) REVERT: D 412 TYR cc_start: 0.7867 (m-80) cc_final: 0.7203 (m-80) REVERT: D 433 GLN cc_start: 0.9429 (pm20) cc_final: 0.8854 (pp30) REVERT: E 320 HIS cc_start: 0.8960 (t-90) cc_final: 0.8336 (t-170) REVERT: E 341 GLU cc_start: 0.9395 (mp0) cc_final: 0.9183 (mp0) REVERT: E 344 MET cc_start: 0.9531 (tpt) cc_final: 0.8595 (tpp) REVERT: E 380 ARG cc_start: 0.9161 (mtm-85) cc_final: 0.8498 (ttp-110) REVERT: E 426 GLU cc_start: 0.8217 (mp0) cc_final: 0.8000 (mp0) REVERT: F 666 TYR cc_start: 0.8971 (m-80) cc_final: 0.8652 (m-80) REVERT: F 681 PHE cc_start: 0.9142 (m-80) cc_final: 0.8917 (m-80) REVERT: F 691 MET cc_start: 0.9279 (mmp) cc_final: 0.8823 (mtp) REVERT: F 717 ARG cc_start: 0.9415 (mmm-85) cc_final: 0.9089 (ttm-80) REVERT: F 725 GLN cc_start: 0.9013 (mm110) cc_final: 0.8591 (mm-40) REVERT: G 561 CYS cc_start: 0.9399 (m) cc_final: 0.9090 (m) REVERT: G 693 LYS cc_start: 0.9599 (mtmm) cc_final: 0.9394 (mttt) REVERT: G 711 GLU cc_start: 0.9581 (mt-10) cc_final: 0.9082 (mm-30) REVERT: G 717 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8288 (ttm170) REVERT: H 85 LEU cc_start: 0.9340 (mp) cc_final: 0.9063 (mp) REVERT: H 88 PHE cc_start: 0.9145 (m-80) cc_final: 0.8700 (m-10) REVERT: H 93 ASN cc_start: 0.8811 (m110) cc_final: 0.8284 (m110) REVERT: H 96 MET cc_start: 0.8747 (mmp) cc_final: 0.8452 (mmp) REVERT: H 97 LYS cc_start: 0.9648 (mmtt) cc_final: 0.9355 (mmmm) REVERT: H 104 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9051 (mt-10) REVERT: H 326 HIS cc_start: 0.9396 (t-90) cc_final: 0.9068 (t-90) REVERT: H 542 ARG cc_start: 0.8773 (ppt170) cc_final: 0.8015 (tmm160) REVERT: I 85 LEU cc_start: 0.9172 (pp) cc_final: 0.8922 (pp) REVERT: I 86 ARG cc_start: 0.9148 (mpt-90) cc_final: 0.8730 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1390 time to fit residues: 55.0054 Evaluate side-chains 203 residues out of total 1802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN B 927 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN C 560 GLN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN I 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045877 restraints weight = 133192.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046959 restraints weight = 89129.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.047788 restraints weight = 64839.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.048403 restraints weight = 50461.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048749 restraints weight = 40854.588| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16906 Z= 0.134 Angle : 0.698 13.842 22919 Z= 0.356 Chirality : 0.042 0.221 2685 Planarity : 0.007 0.206 2978 Dihedral : 5.305 36.224 2305 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.58 % Favored : 89.37 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1872 helix: 1.16 (0.16), residues: 1071 sheet: -2.11 (0.74), residues: 28 loop : -3.07 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 368 TYR 0.026 0.002 TYR E 310 PHE 0.031 0.002 PHE A 567 TRP 0.044 0.002 TRP B1032 HIS 0.008 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00290 (16906) covalent geometry : angle 0.69795 (22919) hydrogen bonds : bond 0.04270 ( 915) hydrogen bonds : angle 4.24209 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.38 seconds wall clock time: 45 minutes 8.80 seconds (2708.80 seconds total)