Starting phenix.real_space_refine on Thu Mar 5 20:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b7u_12087/03_2026/7b7u_12087.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b7u_12087/03_2026/7b7u_12087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b7u_12087/03_2026/7b7u_12087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b7u_12087/03_2026/7b7u_12087.map" model { file = "/net/cci-nas-00/data/ceres_data/7b7u_12087/03_2026/7b7u_12087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b7u_12087/03_2026/7b7u_12087.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 141 5.16 5 C 15884 2.51 5 N 4348 2.21 5 O 4712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s 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: 25091 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7861 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 946} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7842 Classifications: {'peptide': 979} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 930} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "H" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1184 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 938 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16397 SG CYS C 88 40.985 88.513 142.364 1.00114.25 S ATOM 16410 SG CYS C 90 38.602 91.009 140.990 1.00119.54 S ATOM 16445 SG CYS C 94 41.220 92.364 142.775 1.00 99.65 S ATOM 16467 SG CYS C 97 42.338 90.988 139.579 1.00 94.16 S ATOM 21350 SG CYS I 17 66.159 106.394 21.911 1.00108.76 S ATOM 21374 SG CYS I 20 64.121 106.696 23.374 1.00109.59 S ATOM 21535 SG CYS I 39 63.184 103.526 23.421 1.00111.06 S ATOM 22175 SG CYS I 119 96.180 109.723 52.714 1.00134.62 S ATOM 22285 SG CYS J 7 66.344 93.932 120.737 1.00 64.67 S ATOM 22309 SG CYS J 10 67.759 91.447 123.050 1.00 66.09 S ATOM 22573 SG CYS J 44 69.319 91.559 119.582 1.00 70.54 S ATOM 22579 SG CYS J 45 69.842 94.514 121.802 1.00 69.76 S ATOM 23725 SG CYS L 19 36.018 123.021 108.484 1.00135.06 S ATOM 23744 SG CYS L 22 36.828 125.865 110.773 1.00138.37 S ATOM 23861 SG CYS L 36 33.339 125.596 109.172 1.00145.51 S ATOM 23887 SG CYS L 39 36.500 126.651 107.218 1.00147.04 S ATOM 24490 SG CYS M 100 41.688 62.017 17.595 1.00148.98 S ATOM 24527 SG CYS M 105 39.498 61.049 14.778 1.00145.27 S ATOM 24780 SG CYS M 136 43.353 61.527 14.350 1.00151.29 S ATOM 24811 SG CYS M 140 40.971 64.556 14.847 1.00154.25 S Time building chain proxies: 5.22, per 1000 atoms: 0.21 Number of scatterers: 25091 At special positions: 0 Unit cell: (111.3, 154.35, 158.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 141 16.00 O 4712 8.00 N 4348 7.00 C 15884 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: 1.75 Conformation dependent library (CDL) restraints added in 894.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 701 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 100 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 105 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 140 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 136 " Number of angles added : 24 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5942 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 36 sheets defined 40.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 382 through 388 removed outlier: 3.625A pdb=" N MET A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 541 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.912A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.038A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.095A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.660A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 723 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.686A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.785A pdb=" N SER A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.623A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 920 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.050A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 3.864A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.161A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 removed outlier: 3.579A pdb=" N MET A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1160 removed outlier: 3.679A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.645A pdb=" N GLU A1198 " --> pdb=" O ASN A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1293 Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.682A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.541A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A1405 " --> pdb=" O LEU A1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.982A pdb=" N VAL B 59 " --> pdb=" O GLN B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 269 through 277 removed outlier: 3.510A pdb=" N GLY B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.998A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 423 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 450 removed outlier: 4.027A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 552 through 556 removed outlier: 4.032A pdb=" N ILE B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.546A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.727A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 4.026A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 731 removed outlier: 3.754A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 3.890A pdb=" N TYR B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 968 through 972 removed outlier: 3.563A pdb=" N ILE B 972 " --> pdb=" O PRO B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.797A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1054 through 1060 removed outlier: 4.412A pdb=" N HIS B1060 " --> pdb=" O ASP B1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.538A pdb=" N ALA C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.856A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.590A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.549A pdb=" N ARG E 52 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.732A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.116A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 134 removed outlier: 4.465A pdb=" N GLY H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.994A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.558A pdb=" N HIS J 52 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.072A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.528A pdb=" N ALA K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 67 removed outlier: 3.860A pdb=" N GLU M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 79 Processing helix chain 'M' and resid 80 through 82 No H-bonds generated for 'chain 'M' and resid 80 through 82' Processing helix chain 'M' and resid 83 through 97 Processing helix chain 'M' and resid 137 through 150 removed outlier: 3.997A pdb=" N GLN M 150 " --> pdb=" O PHE M 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.664A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.699A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.163A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA6, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA8, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AA9, first strand: chain 'A' and resid 1140 through 1141 Processing sheet with id=AB1, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 3.539A pdb=" N ILE A1175 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.775A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.449A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.682A pdb=" N GLN B 468 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AB7, first strand: chain 'B' and resid 204 through 208 removed outlier: 4.069A pdb=" N THR B 204 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG B 222 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC1, first strand: chain 'B' and resid 572 through 577 removed outlier: 5.456A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.624A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.624A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 909 " --> pdb=" O MET L 44 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET L 44 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.935A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 828 through 829 Processing sheet with id=AC7, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AC8, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.680A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.505A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD2, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.929A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AD4, first strand: chain 'F' and resid 105 through 107 Processing sheet with id=AD5, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.827A pdb=" N ASP I 29 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AD7, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AD8, first strand: chain 'L' and resid 16 through 17 Processing sheet with id=AD9, first strand: chain 'M' and resid 118 through 120 removed outlier: 3.988A pdb=" N UNK N 193 " --> pdb=" O ASP M 128 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 2970 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: 7.40 Time building geometry restraints manager: 2.25 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: 8346 1.34 - 1.46: 4330 1.46 - 1.58: 12656 1.58 - 1.69: 0 1.69 - 1.81: 221 Bond restraints: 25553 Sorted by residual: bond pdb=" C ALA E 122 " pdb=" N PRO E 123 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.27e+00 bond pdb=" CA PHE B 713 " pdb=" CB PHE B 713 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.38e+00 bond pdb=" CA VAL B 59 " pdb=" CB VAL B 59 " ideal model delta sigma weight residual 1.531 1.542 -0.011 1.11e-02 8.12e+03 1.06e+00 bond pdb=" N LYS M 114 " pdb=" CA LYS M 114 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.02e+00 bond pdb=" C ARG E 52 " pdb=" N PRO E 53 " ideal model delta sigma weight residual 1.334 1.356 -0.023 2.34e-02 1.83e+03 9.32e-01 ... (remaining 25548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 34077 2.17 - 4.34: 401 4.34 - 6.50: 44 6.50 - 8.67: 5 8.67 - 10.84: 3 Bond angle restraints: 34530 Sorted by residual: angle pdb=" N PRO H 82 " pdb=" CA PRO H 82 " pdb=" CB PRO H 82 " ideal model delta sigma weight residual 103.33 109.86 -6.53 1.10e+00 8.26e-01 3.53e+01 angle pdb=" CB ARG L 42 " pdb=" CG ARG L 42 " pdb=" CD ARG L 42 " ideal model delta sigma weight residual 111.30 120.51 -9.21 2.30e+00 1.89e-01 1.60e+01 angle pdb=" CA ARG B 230 " pdb=" CB ARG B 230 " pdb=" CG ARG B 230 " ideal model delta sigma weight residual 114.10 121.96 -7.86 2.00e+00 2.50e-01 1.55e+01 angle pdb=" N ILE B 866 " pdb=" CA ILE B 866 " pdb=" C ILE B 866 " ideal model delta sigma weight residual 113.42 109.48 3.94 1.17e+00 7.31e-01 1.13e+01 angle pdb=" C ASN A 722 " pdb=" N ASN A 723 " pdb=" CA ASN A 723 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 ... (remaining 34525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 14159 17.60 - 35.20: 1253 35.20 - 52.80: 207 52.80 - 70.40: 25 70.40 - 88.00: 17 Dihedral angle restraints: 15661 sinusoidal: 6495 harmonic: 9166 Sorted by residual: dihedral pdb=" CA GLU A 724 " pdb=" C GLU A 724 " pdb=" N LEU A 725 " pdb=" CA LEU A 725 " ideal model delta harmonic sigma weight residual 180.00 147.44 32.56 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA ARG E 52 " pdb=" C ARG E 52 " pdb=" N PRO E 53 " pdb=" CA PRO E 53 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA MET A 660 " pdb=" C MET A 660 " pdb=" N GLY A 661 " pdb=" CA GLY A 661 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 15658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2960 0.046 - 0.091: 658 0.091 - 0.137: 253 0.137 - 0.183: 11 0.183 - 0.228: 1 Chirality restraints: 3883 Sorted by residual: chirality pdb=" CA PRO H 82 " pdb=" N PRO H 82 " pdb=" C PRO H 82 " pdb=" CB PRO H 82 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A1130 " pdb=" CA ILE A1130 " pdb=" CG1 ILE A1130 " pdb=" CG2 ILE A1130 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA MET A 660 " pdb=" N MET A 660 " pdb=" C MET A 660 " pdb=" CB MET A 660 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 3880 not shown) Planarity restraints: 4462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 116 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO I 117 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO I 117 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 117 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 550 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C MET B 550 " -0.029 2.00e-02 2.50e+03 pdb=" O MET B 550 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 551 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 956 " 0.011 2.00e-02 2.50e+03 1.18e-02 2.42e+00 pdb=" CG PHE A 956 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 956 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 956 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 956 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 956 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 956 " 0.000 2.00e-02 2.50e+03 ... (remaining 4459 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 280 2.59 - 3.17: 21296 3.17 - 3.74: 41108 3.74 - 4.32: 55861 4.32 - 4.90: 93112 Nonbonded interactions: 211657 Sorted by model distance: nonbonded pdb=" CA CYS I 119 " pdb="ZN ZN I 202 " model vdw 2.012 2.128 nonbonded pdb=" OH TYR J 21 " pdb=" OE2 GLU J 31 " model vdw 2.055 3.040 nonbonded pdb=" OG SER K 82 " pdb=" OE1 GLU K 85 " model vdw 2.114 3.040 nonbonded pdb=" OG1 THR K 77 " pdb=" O TYR K 81 " model vdw 2.120 3.040 nonbonded pdb=" O ILE B 867 " pdb=" OG SER B 893 " model vdw 2.214 3.040 ... (remaining 211652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.230 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.002 0.029 25573 Z= 0.124 Angle : 0.608 13.142 34554 Z= 0.339 Chirality : 0.044 0.228 3883 Planarity : 0.003 0.046 4462 Dihedral : 13.412 87.998 9719 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.52 (0.16), residues: 3056 helix: 1.71 (0.17), residues: 1064 sheet: 0.02 (0.23), residues: 493 loop : -0.51 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 42 TYR 0.013 0.001 TYR H 97 PHE 0.027 0.001 PHE A 956 TRP 0.020 0.001 TRP A1192 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00245 (25553) covalent geometry : angle 0.59259 (34530) hydrogen bonds : bond 0.14140 ( 1061) hydrogen bonds : angle 5.62806 ( 2970) metal coordination : bond 0.00681 ( 20) metal coordination : angle 5.13848 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 372 time to evaluate : 0.865 Fit side-chains REVERT: A 457 ILE cc_start: 0.9094 (pt) cc_final: 0.8800 (pp) REVERT: A 956 PHE cc_start: 0.5764 (m-80) cc_final: 0.5341 (m-80) REVERT: F 59 LYS cc_start: 0.8614 (mppt) cc_final: 0.8211 (pmtt) REVERT: F 80 MET cc_start: 0.4410 (mmp) cc_final: 0.4100 (mmp) REVERT: F 90 LEU cc_start: 0.9121 (mm) cc_final: 0.8748 (mm) REVERT: F 106 ILE cc_start: 0.9406 (mt) cc_final: 0.9155 (pp) REVERT: F 107 ARG cc_start: 0.6535 (pmt170) cc_final: 0.6276 (pmt-80) REVERT: I 64 GLU cc_start: 0.8387 (tp30) cc_final: 0.8172 (tp30) REVERT: I 88 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8338 (pttm) REVERT: K 39 ASP cc_start: 0.7284 (p0) cc_final: 0.6904 (p0) REVERT: M 88 SER cc_start: 0.9131 (m) cc_final: 0.8409 (p) REVERT: M 92 ASP cc_start: 0.9194 (m-30) cc_final: 0.8734 (m-30) REVERT: M 93 GLU cc_start: 0.8807 (mp0) cc_final: 0.8406 (mp0) REVERT: M 112 VAL cc_start: 0.8639 (t) cc_final: 0.8395 (p) outliers start: 2 outliers final: 1 residues processed: 373 average time/residue: 0.6902 time to fit residues: 294.1244 Evaluate side-chains 268 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN B 370 HIS ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 582 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN E 95 GLN E 98 ASN E 107 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS I 32 ASN I 45 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.066533 restraints weight = 65521.196| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.14 r_work: 0.3024 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25573 Z= 0.144 Angle : 0.626 13.974 34554 Z= 0.316 Chirality : 0.045 0.184 3883 Planarity : 0.004 0.044 4462 Dihedral : 4.244 62.532 3424 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.37 % Allowed : 10.38 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.51 (0.16), residues: 3056 helix: 1.61 (0.16), residues: 1101 sheet: 0.04 (0.23), residues: 491 loop : -0.50 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 69 TYR 0.022 0.001 TYR L 17 PHE 0.018 0.001 PHE M 147 TRP 0.013 0.001 TRP B 548 HIS 0.004 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00328 (25553) covalent geometry : angle 0.61489 (34530) hydrogen bonds : bond 0.04009 ( 1061) hydrogen bonds : angle 4.78434 ( 2970) metal coordination : bond 0.00824 ( 20) metal coordination : angle 4.49401 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7441 (pmt-80) REVERT: A 457 ILE cc_start: 0.9177 (pt) cc_final: 0.8868 (pp) REVERT: A 561 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: B 108 MET cc_start: 0.8689 (ttm) cc_final: 0.8479 (ttt) REVERT: B 169 ARG cc_start: 0.9144 (mtp-110) cc_final: 0.8863 (ttp80) REVERT: B 798 ARG cc_start: 0.8806 (tpp80) cc_final: 0.7762 (tpp80) REVERT: B 805 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: B 908 MET cc_start: 0.8190 (ttp) cc_final: 0.7957 (ttp) REVERT: B 931 ILE cc_start: 0.8666 (pt) cc_final: 0.8441 (pp) REVERT: B 976 MET cc_start: 0.7953 (ptp) cc_final: 0.7480 (mtp) REVERT: B 995 GLU cc_start: 0.8477 (pm20) cc_final: 0.8100 (pm20) REVERT: C 172 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8441 (mm-30) REVERT: F 59 LYS cc_start: 0.8664 (mppt) cc_final: 0.8210 (pmtt) REVERT: F 80 MET cc_start: 0.4331 (mmp) cc_final: 0.4122 (mpt) REVERT: F 90 LEU cc_start: 0.8941 (mm) cc_final: 0.8437 (mm) REVERT: F 94 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8646 (mpp) REVERT: F 106 ILE cc_start: 0.9483 (mt) cc_final: 0.9165 (pp) REVERT: F 107 ARG cc_start: 0.6815 (pmt170) cc_final: 0.6229 (pmt-80) REVERT: I 23 MET cc_start: 0.8334 (ttp) cc_final: 0.8129 (ttp) REVERT: I 88 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8291 (pttm) REVERT: K 97 GLU cc_start: 0.8959 (tp30) cc_final: 0.8479 (tp30) REVERT: L 18 ILE cc_start: 0.9030 (tt) cc_final: 0.8322 (tp) REVERT: L 50 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8795 (mmpt) REVERT: M 73 GLU cc_start: 0.9106 (tp30) cc_final: 0.8704 (tm-30) REVERT: M 89 ASP cc_start: 0.8915 (m-30) cc_final: 0.8686 (m-30) REVERT: M 92 ASP cc_start: 0.9326 (m-30) cc_final: 0.8907 (m-30) REVERT: M 112 VAL cc_start: 0.8698 (t) cc_final: 0.8440 (p) outliers start: 38 outliers final: 6 residues processed: 307 average time/residue: 0.6667 time to fit residues: 235.9240 Evaluate side-chains 270 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 260 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain K residue 48 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 240 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN C 60 HIS C 260 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 45 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061920 restraints weight = 65282.914| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.12 r_work: 0.2906 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25573 Z= 0.234 Angle : 0.654 10.743 34554 Z= 0.334 Chirality : 0.047 0.186 3883 Planarity : 0.004 0.049 4462 Dihedral : 4.423 30.555 3422 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.17 % Allowed : 13.12 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.38 (0.16), residues: 3056 helix: 1.46 (0.16), residues: 1104 sheet: -0.11 (0.22), residues: 525 loop : -0.53 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 126 TYR 0.024 0.002 TYR F 115 PHE 0.022 0.002 PHE C 63 TRP 0.014 0.002 TRP B 27 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00542 (25553) covalent geometry : angle 0.64516 (34530) hydrogen bonds : bond 0.03895 ( 1061) hydrogen bonds : angle 4.66388 ( 2970) metal coordination : bond 0.01272 ( 20) metal coordination : angle 4.11844 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 285 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.6848 (pmt-80) REVERT: A 457 ILE cc_start: 0.9278 (pt) cc_final: 0.8972 (pp) REVERT: A 470 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5255 (ttt) REVERT: A 1135 LYS cc_start: 0.9022 (mppt) cc_final: 0.8813 (mppt) REVERT: A 1262 MET cc_start: 0.9350 (mmm) cc_final: 0.9108 (mpp) REVERT: B 108 MET cc_start: 0.8757 (ttm) cc_final: 0.8527 (ttp) REVERT: B 169 ARG cc_start: 0.9151 (mtp-110) cc_final: 0.8871 (ttp80) REVERT: B 546 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: C 27 ASP cc_start: 0.8190 (p0) cc_final: 0.7718 (p0) REVERT: C 172 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8583 (mm-30) REVERT: E 121 MET cc_start: 0.8101 (ppp) cc_final: 0.7718 (ppp) REVERT: F 59 LYS cc_start: 0.8831 (mppt) cc_final: 0.8478 (pmtt) REVERT: F 90 LEU cc_start: 0.9055 (mm) cc_final: 0.8463 (mm) REVERT: F 94 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8541 (mpp) REVERT: F 100 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8818 (mmm-85) REVERT: F 107 ARG cc_start: 0.7207 (pmt170) cc_final: 0.5737 (pmt-80) REVERT: F 109 TYR cc_start: 0.8772 (m-10) cc_final: 0.6710 (p90) REVERT: F 115 TYR cc_start: 0.8865 (p90) cc_final: 0.8417 (m-10) REVERT: F 116 GLU cc_start: 0.7946 (tt0) cc_final: 0.7674 (tt0) REVERT: H 55 LYS cc_start: 0.9338 (tppt) cc_final: 0.9000 (mmmm) REVERT: H 130 ASN cc_start: 0.9015 (p0) cc_final: 0.8316 (p0) REVERT: I 54 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8029 (p90) REVERT: I 64 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8340 (mm-30) REVERT: I 88 LYS cc_start: 0.9086 (ttpp) cc_final: 0.8426 (pttm) REVERT: K 8 GLU cc_start: 0.8066 (pm20) cc_final: 0.7820 (pm20) REVERT: K 48 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8977 (t) REVERT: K 97 GLU cc_start: 0.8987 (tp30) cc_final: 0.8678 (tp30) REVERT: M 73 GLU cc_start: 0.9091 (tp30) cc_final: 0.8677 (tm-30) REVERT: M 92 ASP cc_start: 0.9340 (m-30) cc_final: 0.8916 (m-30) REVERT: M 112 VAL cc_start: 0.8491 (t) cc_final: 0.8268 (p) REVERT: M 146 PHE cc_start: 0.9042 (t80) cc_final: 0.8739 (t80) outliers start: 60 outliers final: 19 residues processed: 313 average time/residue: 0.6798 time to fit residues: 243.8762 Evaluate side-chains 273 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 81 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 227 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 212 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN C 260 GLN I 32 ASN I 45 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063841 restraints weight = 65099.999| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.11 r_work: 0.2957 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25573 Z= 0.127 Angle : 0.598 13.290 34554 Z= 0.301 Chirality : 0.044 0.242 3883 Planarity : 0.004 0.050 4462 Dihedral : 4.262 30.040 3422 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.95 % Allowed : 15.94 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.43 (0.16), residues: 3056 helix: 1.63 (0.16), residues: 1087 sheet: -0.11 (0.23), residues: 521 loop : -0.56 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 62 TYR 0.022 0.001 TYR L 17 PHE 0.017 0.001 PHE B 805 TRP 0.012 0.001 TRP B 27 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00291 (25553) covalent geometry : angle 0.59094 (34530) hydrogen bonds : bond 0.03381 ( 1061) hydrogen bonds : angle 4.50721 ( 2970) metal coordination : bond 0.00818 ( 20) metal coordination : angle 3.64380 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 0.877 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: A 364 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6954 (pmt-80) REVERT: A 457 ILE cc_start: 0.9268 (pt) cc_final: 0.8963 (pp) REVERT: A 1015 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8628 (mp0) REVERT: A 1262 MET cc_start: 0.9397 (mmm) cc_final: 0.9126 (mpp) REVERT: A 1309 MET cc_start: 0.9062 (ttp) cc_final: 0.8704 (ttt) REVERT: B 108 MET cc_start: 0.8726 (ttm) cc_final: 0.8509 (ttp) REVERT: B 169 ARG cc_start: 0.9139 (mtp-110) cc_final: 0.8893 (ttp80) REVERT: B 500 GLN cc_start: 0.9113 (mt0) cc_final: 0.8888 (mt0) REVERT: B 546 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: B 976 MET cc_start: 0.8062 (ptp) cc_final: 0.7599 (mtm) REVERT: C 172 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8560 (mm-30) REVERT: E 121 MET cc_start: 0.8135 (ppp) cc_final: 0.7416 (ppp) REVERT: F 59 LYS cc_start: 0.8769 (mppt) cc_final: 0.8428 (pmtt) REVERT: F 90 LEU cc_start: 0.9032 (mm) cc_final: 0.8419 (mm) REVERT: F 94 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8579 (mpp) REVERT: F 101 LYS cc_start: 0.8838 (mttp) cc_final: 0.8587 (pttt) REVERT: F 107 ARG cc_start: 0.6770 (pmt170) cc_final: 0.5686 (pmt-80) REVERT: H 55 LYS cc_start: 0.9309 (tppt) cc_final: 0.8693 (mmtm) REVERT: H 111 ARG cc_start: 0.8804 (tpm170) cc_final: 0.8563 (mmm-85) REVERT: I 54 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7805 (p90) REVERT: I 88 LYS cc_start: 0.9010 (ttpp) cc_final: 0.8577 (tmmt) REVERT: M 73 GLU cc_start: 0.9055 (tp30) cc_final: 0.8682 (tm-30) REVERT: M 88 SER cc_start: 0.9235 (m) cc_final: 0.8437 (p) REVERT: M 89 ASP cc_start: 0.9104 (m-30) cc_final: 0.8671 (m-30) REVERT: M 92 ASP cc_start: 0.9338 (m-30) cc_final: 0.8914 (m-30) REVERT: M 112 VAL cc_start: 0.8690 (t) cc_final: 0.8451 (p) REVERT: M 146 PHE cc_start: 0.8975 (t80) cc_final: 0.8671 (t80) outliers start: 54 outliers final: 21 residues processed: 310 average time/residue: 0.6705 time to fit residues: 239.0217 Evaluate side-chains 286 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 81 PHE Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 186 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 0.0170 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN I 32 ASN I 45 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 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 = 0.3546 r_free = 0.3546 target = 0.083297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062452 restraints weight = 65260.182| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.12 r_work: 0.2921 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25573 Z= 0.173 Angle : 0.619 12.930 34554 Z= 0.312 Chirality : 0.045 0.303 3883 Planarity : 0.004 0.049 4462 Dihedral : 4.274 29.523 3422 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.46 % Allowed : 16.85 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 3056 helix: 1.60 (0.16), residues: 1089 sheet: -0.11 (0.23), residues: 503 loop : -0.55 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 798 TYR 0.011 0.001 TYR J 43 PHE 0.020 0.001 PHE K 13 TRP 0.015 0.001 TRP B 548 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00403 (25553) covalent geometry : angle 0.61153 (34530) hydrogen bonds : bond 0.03468 ( 1061) hydrogen bonds : angle 4.52556 ( 2970) metal coordination : bond 0.01076 ( 20) metal coordination : angle 3.61888 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 267 time to evaluate : 0.981 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: A 364 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6907 (pmt-80) REVERT: A 457 ILE cc_start: 0.9274 (pt) cc_final: 0.8963 (pp) REVERT: A 561 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.8524 (mtm) REVERT: A 861 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8573 (mm-40) REVERT: A 896 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8063 (tt) REVERT: A 1262 MET cc_start: 0.9396 (mmm) cc_final: 0.9117 (mpp) REVERT: A 1309 MET cc_start: 0.9078 (ttp) cc_final: 0.8766 (ttt) REVERT: B 265 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: B 386 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8636 (m-30) REVERT: B 497 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7970 (ptpp) REVERT: B 546 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: B 550 MET cc_start: 0.9040 (tpt) cc_final: 0.8569 (tpt) REVERT: B 798 ARG cc_start: 0.8775 (tpp80) cc_final: 0.8099 (tpp80) REVERT: B 976 MET cc_start: 0.8329 (ptp) cc_final: 0.7905 (mtp) REVERT: C 172 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8596 (mm-30) REVERT: E 121 MET cc_start: 0.8192 (ppp) cc_final: 0.7454 (ppp) REVERT: F 59 LYS cc_start: 0.8797 (mppt) cc_final: 0.8490 (pmtt) REVERT: F 94 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8621 (mpp) REVERT: F 107 ARG cc_start: 0.6689 (pmt170) cc_final: 0.5676 (pmt-80) REVERT: H 55 LYS cc_start: 0.9403 (tppt) cc_final: 0.9141 (mmtm) REVERT: H 111 ARG cc_start: 0.8801 (tpm170) cc_final: 0.8511 (mmm-85) REVERT: I 54 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7758 (p90) REVERT: I 56 ASN cc_start: 0.9202 (t0) cc_final: 0.8975 (t0) REVERT: I 88 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8606 (tmmt) REVERT: K 85 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: L 15 MET cc_start: 0.6011 (tmm) cc_final: 0.5725 (tmm) REVERT: M 61 ILE cc_start: 0.9450 (mp) cc_final: 0.9207 (OUTLIER) REVERT: M 73 GLU cc_start: 0.9043 (tp30) cc_final: 0.8669 (tm-30) REVERT: M 88 SER cc_start: 0.9252 (m) cc_final: 0.8450 (p) REVERT: M 92 ASP cc_start: 0.9351 (m-30) cc_final: 0.8939 (m-30) REVERT: M 112 VAL cc_start: 0.8512 (t) cc_final: 0.8281 (p) REVERT: M 146 PHE cc_start: 0.8942 (t80) cc_final: 0.8654 (t80) outliers start: 68 outliers final: 29 residues processed: 312 average time/residue: 0.6449 time to fit residues: 232.8277 Evaluate side-chains 294 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 138 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 139 optimal weight: 0.2980 chunk 303 optimal weight: 20.0000 chunk 297 optimal weight: 0.7980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS H 130 ASN I 32 ASN I 45 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 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 = 0.3502 r_free = 0.3502 target = 0.081106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.060175 restraints weight = 65937.980| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.09 r_work: 0.2864 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25573 Z= 0.253 Angle : 0.671 12.291 34554 Z= 0.340 Chirality : 0.047 0.285 3883 Planarity : 0.004 0.048 4462 Dihedral : 4.513 27.774 3422 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.71 % Allowed : 17.68 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 3056 helix: 1.44 (0.16), residues: 1096 sheet: -0.15 (0.23), residues: 501 loop : -0.56 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 33 TYR 0.025 0.001 TYR F 115 PHE 0.027 0.002 PHE C 63 TRP 0.012 0.002 TRP B 548 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00587 (25553) covalent geometry : angle 0.66297 (34530) hydrogen bonds : bond 0.03773 ( 1061) hydrogen bonds : angle 4.63069 ( 2970) metal coordination : bond 0.01268 ( 20) metal coordination : angle 4.02896 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 261 time to evaluate : 1.013 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: A 457 ILE cc_start: 0.9257 (pt) cc_final: 0.8953 (pp) REVERT: A 561 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.8616 (mtm) REVERT: A 861 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8521 (mm-40) REVERT: A 865 ILE cc_start: 0.9423 (tt) cc_final: 0.8939 (pp) REVERT: A 1262 MET cc_start: 0.9444 (mmm) cc_final: 0.9184 (mpp) REVERT: A 1309 MET cc_start: 0.9104 (ttp) cc_final: 0.8800 (ttt) REVERT: B 550 MET cc_start: 0.9101 (tpt) cc_final: 0.8403 (tpt) REVERT: B 798 ARG cc_start: 0.8867 (tpp80) cc_final: 0.7875 (tpp80) REVERT: B 976 MET cc_start: 0.8487 (ptp) cc_final: 0.8097 (mtp) REVERT: C 27 ASP cc_start: 0.8137 (p0) cc_final: 0.7665 (p0) REVERT: C 172 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8803 (mm-30) REVERT: E 121 MET cc_start: 0.8304 (ppp) cc_final: 0.7673 (ppp) REVERT: F 59 LYS cc_start: 0.8768 (mppt) cc_final: 0.8540 (pmtt) REVERT: F 94 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8610 (mpp) REVERT: F 107 ARG cc_start: 0.6796 (pmt170) cc_final: 0.5823 (pmt-80) REVERT: H 55 LYS cc_start: 0.9422 (tppt) cc_final: 0.9195 (tppt) REVERT: H 111 ARG cc_start: 0.8814 (tpm170) cc_final: 0.8553 (mmm-85) REVERT: I 54 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.7487 (p90) REVERT: I 56 ASN cc_start: 0.9199 (t0) cc_final: 0.8958 (t0) REVERT: I 88 LYS cc_start: 0.9156 (ttpp) cc_final: 0.8757 (tmmt) REVERT: I 92 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8440 (mppt) REVERT: I 93 GLU cc_start: 0.8905 (tt0) cc_final: 0.8614 (tt0) REVERT: I 108 MET cc_start: 0.8795 (tpt) cc_final: 0.8549 (tpt) REVERT: K 8 GLU cc_start: 0.8065 (pm20) cc_final: 0.7808 (pm20) REVERT: K 48 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.8996 (t) REVERT: K 85 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: M 73 GLU cc_start: 0.9014 (tp30) cc_final: 0.8675 (tm-30) REVERT: M 88 SER cc_start: 0.9274 (m) cc_final: 0.8485 (p) REVERT: M 89 ASP cc_start: 0.9136 (m-30) cc_final: 0.8704 (m-30) REVERT: M 92 ASP cc_start: 0.9363 (m-30) cc_final: 0.8968 (m-30) REVERT: M 112 VAL cc_start: 0.8615 (t) cc_final: 0.8365 (p) REVERT: M 146 PHE cc_start: 0.9037 (t80) cc_final: 0.8690 (t80) outliers start: 75 outliers final: 35 residues processed: 313 average time/residue: 0.6436 time to fit residues: 232.9669 Evaluate side-chains 293 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1292 MET Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 286 optimal weight: 0.9990 chunk 245 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 224 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 45 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.082502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061953 restraints weight = 65813.386| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.07 r_work: 0.2899 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25573 Z= 0.143 Angle : 0.644 14.427 34554 Z= 0.323 Chirality : 0.045 0.351 3883 Planarity : 0.004 0.048 4462 Dihedral : 4.381 27.642 3422 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.10 % Allowed : 19.02 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 3056 helix: 1.58 (0.16), residues: 1079 sheet: -0.21 (0.23), residues: 504 loop : -0.54 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 33 TYR 0.011 0.001 TYR J 43 PHE 0.019 0.001 PHE K 13 TRP 0.013 0.001 TRP B 27 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00334 (25553) covalent geometry : angle 0.63710 (34530) hydrogen bonds : bond 0.03433 ( 1061) hydrogen bonds : angle 4.54523 ( 2970) metal coordination : bond 0.00842 ( 20) metal coordination : angle 3.59036 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 1.066 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: A 457 ILE cc_start: 0.9208 (pt) cc_final: 0.8896 (pp) REVERT: A 561 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.8580 (mtm) REVERT: A 861 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8476 (mm-40) REVERT: A 865 ILE cc_start: 0.9399 (tt) cc_final: 0.8921 (pp) REVERT: A 872 MET cc_start: 0.8328 (ttm) cc_final: 0.8074 (mmm) REVERT: A 1286 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8148 (mtp-110) REVERT: A 1309 MET cc_start: 0.8948 (ttp) cc_final: 0.8692 (ttt) REVERT: A 1337 GLU cc_start: 0.8568 (mp0) cc_final: 0.8240 (mp0) REVERT: B 198 GLU cc_start: 0.8093 (tt0) cc_final: 0.7672 (tt0) REVERT: B 546 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: B 673 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.8973 (m) REVERT: B 798 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8065 (tpp80) REVERT: B 976 MET cc_start: 0.8344 (ptp) cc_final: 0.7859 (mtp) REVERT: C 27 ASP cc_start: 0.8234 (p0) cc_final: 0.7750 (p0) REVERT: C 172 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8695 (mm-30) REVERT: E 94 MET cc_start: 0.8704 (mtp) cc_final: 0.8271 (mtp) REVERT: E 121 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7585 (ppp) REVERT: F 94 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: F 107 ARG cc_start: 0.6775 (pmt170) cc_final: 0.5844 (pmt-80) REVERT: H 55 LYS cc_start: 0.9402 (tppt) cc_final: 0.9187 (tppt) REVERT: H 111 ARG cc_start: 0.8794 (tpm170) cc_final: 0.8534 (mmm-85) REVERT: I 54 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7608 (p90) REVERT: I 56 ASN cc_start: 0.9194 (t0) cc_final: 0.8991 (t0) REVERT: I 88 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8680 (tmmt) REVERT: I 92 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8406 (mppt) REVERT: I 93 GLU cc_start: 0.8949 (tt0) cc_final: 0.8658 (tt0) REVERT: I 108 MET cc_start: 0.8844 (tpt) cc_final: 0.8522 (tpt) REVERT: K 8 GLU cc_start: 0.7922 (pm20) cc_final: 0.7621 (pm20) REVERT: K 48 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8963 (t) REVERT: K 85 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: M 88 SER cc_start: 0.9240 (m) cc_final: 0.8448 (p) REVERT: M 89 ASP cc_start: 0.9142 (m-30) cc_final: 0.8735 (m-30) REVERT: M 92 ASP cc_start: 0.9359 (m-30) cc_final: 0.9007 (m-30) REVERT: M 112 VAL cc_start: 0.8570 (t) cc_final: 0.8326 (p) REVERT: M 141 TYR cc_start: 0.9111 (t80) cc_final: 0.8475 (t80) REVERT: M 146 PHE cc_start: 0.8999 (t80) cc_final: 0.8652 (t80) outliers start: 58 outliers final: 32 residues processed: 299 average time/residue: 0.6838 time to fit residues: 234.9564 Evaluate side-chains 297 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 161 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 281 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 45 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.081626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060842 restraints weight = 65697.153| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.08 r_work: 0.2873 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25573 Z= 0.197 Angle : 0.668 13.951 34554 Z= 0.336 Chirality : 0.046 0.338 3883 Planarity : 0.004 0.047 4462 Dihedral : 4.431 26.129 3422 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.46 % Allowed : 19.31 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 3056 helix: 1.50 (0.16), residues: 1086 sheet: -0.17 (0.23), residues: 498 loop : -0.49 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 202 TYR 0.024 0.001 TYR F 115 PHE 0.019 0.001 PHE C 63 TRP 0.012 0.001 TRP B 27 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00462 (25553) covalent geometry : angle 0.66132 (34530) hydrogen bonds : bond 0.03563 ( 1061) hydrogen bonds : angle 4.56381 ( 2970) metal coordination : bond 0.01026 ( 20) metal coordination : angle 3.60156 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 0.913 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: A 457 ILE cc_start: 0.9255 (pt) cc_final: 0.8944 (pp) REVERT: A 561 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: A 872 MET cc_start: 0.8340 (ttm) cc_final: 0.8093 (mmm) REVERT: A 1286 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8209 (mtp-110) REVERT: A 1309 MET cc_start: 0.8982 (ttp) cc_final: 0.8726 (ttt) REVERT: A 1337 GLU cc_start: 0.8559 (mp0) cc_final: 0.8253 (mp0) REVERT: B 546 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: B 673 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9022 (m) REVERT: B 798 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8088 (tpp80) REVERT: B 976 MET cc_start: 0.8343 (ptp) cc_final: 0.7899 (mtp) REVERT: C 27 ASP cc_start: 0.8256 (p0) cc_final: 0.7762 (p0) REVERT: C 172 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8793 (mm-30) REVERT: E 94 MET cc_start: 0.8683 (mtp) cc_final: 0.8241 (mtp) REVERT: E 121 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7679 (ppp) REVERT: F 94 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8567 (mpp) REVERT: F 107 ARG cc_start: 0.6846 (pmt170) cc_final: 0.5835 (pmt-80) REVERT: H 55 LYS cc_start: 0.9406 (tppt) cc_final: 0.9182 (tppt) REVERT: H 111 ARG cc_start: 0.8793 (tpm170) cc_final: 0.8539 (mmm-85) REVERT: I 54 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7670 (p90) REVERT: I 56 ASN cc_start: 0.9208 (t0) cc_final: 0.8995 (t0) REVERT: I 88 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8703 (tmmt) REVERT: I 92 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8470 (mppt) REVERT: I 93 GLU cc_start: 0.8961 (tt0) cc_final: 0.8687 (tt0) REVERT: I 108 MET cc_start: 0.8867 (tpt) cc_final: 0.8558 (tpt) REVERT: K 8 GLU cc_start: 0.8013 (pm20) cc_final: 0.7685 (pm20) REVERT: K 48 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.8973 (t) REVERT: K 85 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: L 50 LYS cc_start: 0.9279 (mmmm) cc_final: 0.9055 (mmpt) REVERT: M 73 GLU cc_start: 0.9028 (tp30) cc_final: 0.8583 (tm-30) REVERT: M 88 SER cc_start: 0.9267 (m) cc_final: 0.8474 (p) REVERT: M 89 ASP cc_start: 0.9160 (m-30) cc_final: 0.8784 (m-30) REVERT: M 92 ASP cc_start: 0.9375 (m-30) cc_final: 0.9032 (m-30) REVERT: M 112 VAL cc_start: 0.8599 (t) cc_final: 0.8349 (p) REVERT: M 146 PHE cc_start: 0.8984 (t80) cc_final: 0.8665 (t80) outliers start: 68 outliers final: 34 residues processed: 301 average time/residue: 0.6520 time to fit residues: 226.3866 Evaluate side-chains 297 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 301 optimal weight: 0.5980 chunk 278 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 468 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 45 GLN ** K 2 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 = 0.3540 r_free = 0.3540 target = 0.083256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062535 restraints weight = 65873.272| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.11 r_work: 0.2920 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25573 Z= 0.127 Angle : 0.661 14.124 34554 Z= 0.330 Chirality : 0.045 0.311 3883 Planarity : 0.004 0.047 4462 Dihedral : 4.326 25.529 3422 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.95 % Allowed : 20.07 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 3056 helix: 1.60 (0.16), residues: 1078 sheet: -0.11 (0.23), residues: 504 loop : -0.50 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 202 TYR 0.011 0.001 TYR J 43 PHE 0.013 0.001 PHE K 13 TRP 0.013 0.001 TRP B 27 HIS 0.005 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00299 (25553) covalent geometry : angle 0.65551 (34530) hydrogen bonds : bond 0.03274 ( 1061) hydrogen bonds : angle 4.47064 ( 2970) metal coordination : bond 0.00707 ( 20) metal coordination : angle 3.21731 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7407 (pmt-80) REVERT: A 457 ILE cc_start: 0.9204 (pt) cc_final: 0.8904 (pp) REVERT: A 561 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.8584 (mtm) REVERT: A 1286 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8136 (mtp-110) REVERT: A 1309 MET cc_start: 0.8923 (ttp) cc_final: 0.8691 (ttt) REVERT: A 1337 GLU cc_start: 0.8515 (mp0) cc_final: 0.8100 (mp0) REVERT: B 198 GLU cc_start: 0.8098 (tt0) cc_final: 0.7711 (tt0) REVERT: B 407 MET cc_start: 0.5447 (mtm) cc_final: 0.5021 (mpp) REVERT: B 546 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: B 673 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.8992 (m) REVERT: B 798 ARG cc_start: 0.8823 (tpp80) cc_final: 0.8168 (tpp80) REVERT: B 976 MET cc_start: 0.8239 (ptp) cc_final: 0.7723 (mtm) REVERT: C 27 ASP cc_start: 0.8219 (p0) cc_final: 0.7783 (p0) REVERT: C 172 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8642 (mm-30) REVERT: E 94 MET cc_start: 0.8654 (mtp) cc_final: 0.8206 (mtp) REVERT: E 121 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7556 (ppp) REVERT: F 59 LYS cc_start: 0.7942 (pmtt) cc_final: 0.7652 (pptt) REVERT: F 94 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8648 (mpp) REVERT: F 107 ARG cc_start: 0.6784 (pmt170) cc_final: 0.5816 (pmt-80) REVERT: H 55 LYS cc_start: 0.9370 (tppt) cc_final: 0.9167 (tppt) REVERT: H 111 ARG cc_start: 0.8784 (tpm170) cc_final: 0.8558 (mmm-85) REVERT: I 54 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7671 (p90) REVERT: I 56 ASN cc_start: 0.9206 (t0) cc_final: 0.8891 (t0) REVERT: I 83 ASP cc_start: 0.8722 (p0) cc_final: 0.8373 (p0) REVERT: I 88 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8672 (tmmt) REVERT: I 93 GLU cc_start: 0.8930 (tt0) cc_final: 0.8627 (tt0) REVERT: I 108 MET cc_start: 0.8873 (tpt) cc_final: 0.8540 (tpt) REVERT: K 8 GLU cc_start: 0.7844 (pm20) cc_final: 0.7517 (pm20) REVERT: K 48 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8954 (t) REVERT: K 85 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: L 25 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7967 (mm-30) REVERT: L 50 LYS cc_start: 0.9241 (mmmm) cc_final: 0.9023 (mmpt) REVERT: M 59 LEU cc_start: 0.9755 (tt) cc_final: 0.9362 (pp) REVERT: M 61 ILE cc_start: 0.9429 (mp) cc_final: 0.8928 (tp) REVERT: M 64 GLN cc_start: 0.9343 (mt0) cc_final: 0.8978 (mt0) REVERT: M 73 GLU cc_start: 0.8975 (tp30) cc_final: 0.8512 (tm-30) REVERT: M 88 SER cc_start: 0.9258 (m) cc_final: 0.8462 (p) REVERT: M 89 ASP cc_start: 0.9141 (m-30) cc_final: 0.8739 (m-30) REVERT: M 92 ASP cc_start: 0.9387 (m-30) cc_final: 0.9055 (m-30) REVERT: M 112 VAL cc_start: 0.8632 (t) cc_final: 0.8379 (p) REVERT: M 141 TYR cc_start: 0.9079 (t80) cc_final: 0.8442 (t80) REVERT: M 146 PHE cc_start: 0.8939 (t80) cc_final: 0.8639 (t80) outliers start: 54 outliers final: 29 residues processed: 304 average time/residue: 0.6635 time to fit residues: 232.4865 Evaluate side-chains 300 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 118 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 10 optimal weight: 0.0870 chunk 111 optimal weight: 0.0670 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 238 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 226 optimal weight: 0.4980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN E 132 GLN I 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.083590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063086 restraints weight = 65760.020| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.10 r_work: 0.2930 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25573 Z= 0.126 Angle : 0.667 13.719 34554 Z= 0.332 Chirality : 0.045 0.268 3883 Planarity : 0.004 0.045 4462 Dihedral : 4.267 25.731 3422 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.74 % Allowed : 20.75 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 3056 helix: 1.61 (0.16), residues: 1080 sheet: -0.09 (0.23), residues: 510 loop : -0.51 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 56 TYR 0.027 0.001 TYR F 115 PHE 0.012 0.001 PHE K 7 TRP 0.012 0.001 TRP B 27 HIS 0.006 0.001 HIS M 60 Details of bonding type rmsd covalent geometry : bond 0.00294 (25553) covalent geometry : angle 0.66201 (34530) hydrogen bonds : bond 0.03308 ( 1061) hydrogen bonds : angle 4.42960 ( 2970) metal coordination : bond 0.00707 ( 20) metal coordination : angle 3.05456 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6112 Ramachandran restraints generated. 3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.798 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: A 457 ILE cc_start: 0.9164 (pt) cc_final: 0.8876 (pp) REVERT: A 561 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: A 1286 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (mtp85) REVERT: A 1309 MET cc_start: 0.8937 (ttp) cc_final: 0.8710 (ttt) REVERT: A 1337 GLU cc_start: 0.8503 (mp0) cc_final: 0.8079 (mp0) REVERT: B 198 GLU cc_start: 0.8041 (tt0) cc_final: 0.7550 (tt0) REVERT: B 407 MET cc_start: 0.5480 (mtm) cc_final: 0.5054 (mpp) REVERT: B 546 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: B 673 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9016 (m) REVERT: B 798 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8204 (tpp80) REVERT: B 976 MET cc_start: 0.8217 (ptp) cc_final: 0.7811 (mtp) REVERT: C 27 ASP cc_start: 0.8172 (p0) cc_final: 0.7738 (p0) REVERT: C 172 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8613 (mm-30) REVERT: E 94 MET cc_start: 0.8656 (mtp) cc_final: 0.8210 (mtp) REVERT: E 121 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7467 (ppp) REVERT: F 59 LYS cc_start: 0.8186 (pmtt) cc_final: 0.7897 (pmtt) REVERT: F 94 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8658 (mpp) REVERT: F 100 ARG cc_start: 0.8987 (mmm-85) cc_final: 0.8317 (tpt90) REVERT: F 107 ARG cc_start: 0.6754 (pmt170) cc_final: 0.5728 (pmt-80) REVERT: H 11 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: H 55 LYS cc_start: 0.9348 (tppt) cc_final: 0.9137 (tppt) REVERT: H 111 ARG cc_start: 0.8778 (tpm170) cc_final: 0.8563 (mmm-85) REVERT: H 118 TYR cc_start: 0.9278 (m-80) cc_final: 0.8908 (m-80) REVERT: H 123 MET cc_start: 0.9408 (ttp) cc_final: 0.9111 (ttp) REVERT: I 54 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7867 (p90) REVERT: I 56 ASN cc_start: 0.9193 (t0) cc_final: 0.8974 (t0) REVERT: I 83 ASP cc_start: 0.8728 (p0) cc_final: 0.8371 (p0) REVERT: I 88 LYS cc_start: 0.9102 (ttpp) cc_final: 0.8672 (tmmt) REVERT: I 93 GLU cc_start: 0.8936 (tt0) cc_final: 0.8627 (tt0) REVERT: I 108 MET cc_start: 0.8930 (tpt) cc_final: 0.8655 (tpt) REVERT: K 8 GLU cc_start: 0.7787 (pm20) cc_final: 0.7456 (pm20) REVERT: K 48 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8947 (t) REVERT: K 85 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: L 50 LYS cc_start: 0.9231 (mmmm) cc_final: 0.9022 (mmpt) REVERT: M 61 ILE cc_start: 0.9398 (mp) cc_final: 0.9167 (tp) REVERT: M 73 GLU cc_start: 0.9018 (tp30) cc_final: 0.8568 (tm-30) REVERT: M 88 SER cc_start: 0.9226 (m) cc_final: 0.8420 (p) REVERT: M 89 ASP cc_start: 0.9138 (m-30) cc_final: 0.8731 (m-30) REVERT: M 92 ASP cc_start: 0.9367 (m-30) cc_final: 0.9029 (m-30) REVERT: M 112 VAL cc_start: 0.8653 (t) cc_final: 0.8394 (p) REVERT: M 141 TYR cc_start: 0.9066 (t80) cc_final: 0.8458 (t80) REVERT: M 146 PHE cc_start: 0.8922 (t80) cc_final: 0.8649 (t80) outliers start: 48 outliers final: 31 residues processed: 298 average time/residue: 0.6495 time to fit residues: 222.9037 Evaluate side-chains 303 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1405 MET Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 HIS I 32 ASN I 45 GLN ** K 2 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 = 0.3537 r_free = 0.3537 target = 0.083099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062363 restraints weight = 65726.488| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.11 r_work: 0.2915 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25573 Z= 0.148 Angle : 0.674 14.247 34554 Z= 0.335 Chirality : 0.046 0.331 3883 Planarity : 0.004 0.045 4462 Dihedral : 4.276 25.525 3422 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.84 % Allowed : 20.72 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 3056 helix: 1.59 (0.16), residues: 1079 sheet: 0.02 (0.23), residues: 495 loop : -0.49 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 928 TYR 0.055 0.001 TYR F 60 PHE 0.015 0.001 PHE K 13 TRP 0.012 0.001 TRP B 27 HIS 0.004 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00351 (25553) covalent geometry : angle 0.66928 (34530) hydrogen bonds : bond 0.03332 ( 1061) hydrogen bonds : angle 4.44032 ( 2970) metal coordination : bond 0.00810 ( 20) metal coordination : angle 3.06346 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7742.07 seconds wall clock time: 132 minutes 51.58 seconds (7971.58 seconds total)