Starting phenix.real_space_refine on Tue Sep 15 19:21:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6i84_4429/09_2026/6i84_4429.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 335 5.49 5 Mg 1 5.21 5 S 192 5.16 5 C 26668 2.51 5 N 7829 2.21 5 O 8955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.28s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43988 Number of models: 1 Model: "" Number of chains: 29 Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Q" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "V" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "T" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 3453 Classifications: {'DNA': 169} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 168} Chain: "N" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3248 Classifications: {'DNA': 158} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 157} Chain: "O" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "R" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "S" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "U" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "W" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "A" Number of atoms: 11143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1416, 11143 Classifications: {'peptide': 1416} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1349} Chain breaks: 4 Chain: "B" Number of atoms: 8779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8779 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 50, 'TRANS': 1053} Chain breaks: 9 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1434 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1076 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 919 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "P" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13480 SG CYS A 107 85.161 98.942 126.274 1.00 81.96 S ATOM 13504 SG CYS A 110 82.285 100.879 127.374 1.00 74.34 S ATOM 13947 SG CYS A 167 84.138 99.228 130.098 1.00108.81 S ATOM 13175 SG CYS A 67 41.378 105.212 103.608 1.00 79.23 S ATOM 13197 SG CYS A 70 41.306 110.350 104.843 1.00 70.58 S ATOM 13250 SG CYS A 77 42.547 108.277 102.231 1.00 61.04 S ATOM 32107 SG CYS B1166 54.038 114.770 112.966 1.00 62.06 S ATOM 32251 SG CYS B1185 52.439 112.108 114.622 1.00 65.17 S ATOM 33255 SG CYS C 88 17.677 117.631 43.543 1.00123.61 S ATOM 33288 SG CYS C 92 17.662 117.731 39.181 1.00 89.98 S ATOM 33311 SG CYS C 95 21.004 117.846 40.704 1.00 87.03 S ATOM 41037 SG CYS I 6 125.236 70.355 79.839 1.00124.89 S ATOM 41062 SG CYS I 9 123.890 67.850 82.022 1.00110.54 S ATOM 41228 SG CYS I 28 124.593 71.074 83.338 1.00108.67 S ATOM 41252 SG CYS I 31 127.239 67.736 83.251 1.00105.08 S ATOM 41579 SG CYS I 74 122.497 91.622 40.496 1.00111.81 S ATOM 41601 SG CYS I 77 121.546 88.473 39.351 1.00112.61 S ATOM 42009 SG CYS J 7 51.619 111.581 31.583 1.00 45.47 S ATOM 42032 SG CYS J 10 49.053 115.012 29.701 1.00 42.20 S ATOM 42318 SG CYS J 46 52.548 114.871 29.413 1.00 33.98 S ATOM 43461 SG CYS L 31 37.331 77.312 52.081 1.00110.76 S Time building chain proxies: 9.18, per 1000 atoms: 0.21 Number of scatterers: 43988 At special positions: 0 Unit cell: (207.9, 193.2, 176.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 192 16.00 P 335 15.00 Mg 1 11.99 O 8955 8.00 N 7829 7.00 C 26668 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: 3.93 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I1201 " pdb="ZN ZN I1201 " - pdb=" SG CYS I 6 " pdb="ZN ZN I1201 " - pdb=" SG CYS I 31 " pdb="ZN ZN I1201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I1201 " - pdb=" SG CYS I 9 " pdb=" ZN I1202 " pdb="ZN ZN I1202 " - pdb=" SG CYS I 74 " pdb="ZN ZN I1202 " - pdb=" SG CYS I 77 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 9 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8766 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 48 sheets defined 42.2% alpha, 10.2% beta 160 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'M' and resid 44 through 55 removed outlier: 3.710A pdb=" N GLN M 55 " --> pdb=" O ILE M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 79 removed outlier: 3.802A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 4.560A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.994A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 38 removed outlier: 3.548A pdb=" N ASN Q 38 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 73 removed outlier: 4.093A pdb=" N ALA Q 52 " --> pdb=" O PRO Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 90 removed outlier: 3.517A pdb=" N ARG Q 88 " --> pdb=" O GLN Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 97 Processing helix chain 'V' and resid 27 through 36 Processing helix chain 'V' and resid 45 through 73 removed outlier: 3.761A pdb=" N VAL V 49 " --> pdb=" O ALA V 45 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU V 65 " --> pdb=" O GLU V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 89 removed outlier: 3.825A pdb=" N LEU V 83 " --> pdb=" O ILE V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 96 removed outlier: 3.574A pdb=" N LEU V 96 " --> pdb=" O GLU V 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 42 removed outlier: 3.585A pdb=" N ILE O 34 " --> pdb=" O THR O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 62 removed outlier: 4.101A pdb=" N TYR O 51 " --> pdb=" O SER O 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU O 52 " --> pdb=" O GLY O 48 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY O 56 " --> pdb=" O GLU O 52 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL O 57 " --> pdb=" O GLU O 53 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS O 59 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 removed outlier: 3.956A pdb=" N ILE O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG O 67 " --> pdb=" O GLU O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 90 removed outlier: 3.522A pdb=" N VAL O 86 " --> pdb=" O THR O 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 46 removed outlier: 4.329A pdb=" N VAL R 38 " --> pdb=" O TYR R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 78 Processing helix chain 'R' and resid 87 through 98 Processing helix chain 'R' and resid 104 through 119 Processing helix chain 'S' and resid 45 through 56 removed outlier: 4.492A pdb=" N ARG S 49 " --> pdb=" O THR S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.778A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 115 removed outlier: 3.894A pdb=" N TYR S 99 " --> pdb=" O ALA S 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 131 removed outlier: 3.789A pdb=" N ILE S 124 " --> pdb=" O MET S 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 40 Processing helix chain 'U' and resid 48 through 62 removed outlier: 4.525A pdb=" N GLU U 52 " --> pdb=" O GLY U 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 removed outlier: 3.922A pdb=" N THR U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS U 77 " --> pdb=" O THR U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 92 Processing helix chain 'W' and resid 34 through 46 removed outlier: 3.938A pdb=" N VAL W 38 " --> pdb=" O TYR W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 81 removed outlier: 3.785A pdb=" N HIS W 79 " --> pdb=" O SER W 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 87 through 96 removed outlier: 4.153A pdb=" N ILE W 91 " --> pdb=" O THR W 87 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG W 96 " --> pdb=" O GLN W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 121 removed outlier: 4.222A pdb=" N ALA W 114 " --> pdb=" O GLU W 110 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA W 121 " --> pdb=" O LYS W 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.890A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 305 removed outlier: 3.562A pdb=" N SER A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.823A pdb=" N GLY A 319 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.638A pdb=" N GLN A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.671A pdb=" N VAL A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.697A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.804A pdb=" N ASN A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.979A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 922 through 947 removed outlier: 5.063A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.539A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.522A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1144 through 1147 removed outlier: 3.707A pdb=" N THR A1147 " --> pdb=" O LYS A1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1144 through 1147' Processing helix chain 'A' and resid 1163 through 1167 removed outlier: 3.551A pdb=" N ASP A1166 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A1167 " --> pdb=" O PRO A1164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1163 through 1167' Processing helix chain 'A' and resid 1168 through 1174 Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1256 through 1270 removed outlier: 4.891A pdb=" N LYS A1262 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.530A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1327 removed outlier: 3.851A pdb=" N ILE A1327 " --> pdb=" O PRO A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.296A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.790A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 42 removed outlier: 4.136A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 58 removed outlier: 4.339A pdb=" N PHE B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.749A pdb=" N ALA B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.593A pdb=" N LYS B 404 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 509 through 513 removed outlier: 4.179A pdb=" N ARG B 512 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.971A pdb=" N ALA B 532 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 593 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 4.267A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 4.185A pdb=" N GLU B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 748 Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.671A pdb=" N SER B 754 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 775 removed outlier: 4.192A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.807A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 838 removed outlier: 3.995A pdb=" N ASP B 837 " --> pdb=" O ASN B 834 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER B 838 " --> pdb=" O GLN B 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 834 through 838' Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 4.550A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.975A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 removed outlier: 3.659A pdb=" N LYS B1102 " --> pdb=" O VAL B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1125 removed outlier: 3.746A pdb=" N ARG B1124 " --> pdb=" O GLY B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1154 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.845A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 209 removed outlier: 4.024A pdb=" N CYS C 207 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 209 " --> pdb=" O ASN C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 209' Processing helix chain 'C' and resid 239 through 268 removed outlier: 4.060A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 73 Processing helix chain 'D' and resid 119 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'E' and resid 5 through 27 removed outlier: 3.699A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.039A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.919A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.843A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.331A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.728A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 58 through 64 removed outlier: 4.224A pdb=" N GLY I 62 " --> pdb=" O GLN I 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 removed outlier: 4.618A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 53 removed outlier: 5.210A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.718A pdb=" N LEU K 9 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.032A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.362A pdb=" N ARG M 83 " --> pdb=" O VAL O 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'Q' and resid 101 through 102 removed outlier: 7.178A pdb=" N THR Q 101 " --> pdb=" O TYR U 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'V' and resid 42 through 43 removed outlier: 7.035A pdb=" N ARG V 42 " --> pdb=" O ILE W 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'V' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.623A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER A 184 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 175 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 182 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 345 removed outlier: 4.007A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.980A pdb=" N MET A 487 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.016A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 458 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 442 " --> pdb=" O HIS A 458 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.435A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.551A pdb=" N ILE A 565 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 662 through 663 removed outlier: 4.479A pdb=" N PHE A 662 " --> pdb=" O CYS B 829 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 662 through 663 removed outlier: 4.479A pdb=" N PHE A 662 " --> pdb=" O CYS B 829 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 827 " --> pdb=" O PHE B1086 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 766 through 767 removed outlier: 3.836A pdb=" N GLY A 766 " --> pdb=" O VAL A 800 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 849 through 851 removed outlier: 6.379A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 879 through 881 Processing sheet with id=AB8, first strand: chain 'A' and resid 1283 through 1285 removed outlier: 3.765A pdb=" N VAL A1118 " --> pdb=" O LEU A1306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 6.271A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1150 through 1152 removed outlier: 3.888A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id=AC3, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC4, first strand: chain 'B' and resid 91 through 97 removed outlier: 4.742A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 131 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.871A pdb=" N VAL B 102 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.548A pdb=" N GLN B 224 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AC9, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AD1, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD2, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD3, first strand: chain 'B' and resid 585 through 589 removed outlier: 5.265A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 623 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP B 618 " --> pdb=" O GLU B 623 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 627 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 614 " --> pdb=" O PHE B 627 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 856 through 858 removed outlier: 6.588A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 861 through 862 removed outlier: 3.904A pdb=" N VAL B 964 " --> pdb=" O ASP B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.534A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1159 through 1160 removed outlier: 3.702A pdb=" N ILE B1194 " --> pdb=" O VAL B1160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 10 removed outlier: 3.929A pdb=" N VAL C 18 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 232 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE C 20 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C 230 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 229 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU C 179 " --> pdb=" O TYR C 229 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 97 through 104 removed outlier: 3.821A pdb=" N LEU C 101 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 52 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 51 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE3, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.739A pdb=" N GLN D 37 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.129A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.277A pdb=" N ASN E 63 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA E 62 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 78 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.277A pdb=" N ASN E 63 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA E 62 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 78 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 154 removed outlier: 4.055A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 208 " --> pdb=" O ARG E 200 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 170 through 171 removed outlier: 4.068A pdb=" N ARG G 142 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 95 through 97 removed outlier: 3.619A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AF2, first strand: chain 'I' and resid 82 through 85 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 1492 hydrogen bonds defined for protein. 4233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 405 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 160 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 13.93 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9414 1.33 - 1.45: 11398 1.45 - 1.57: 23665 1.57 - 1.70: 669 1.70 - 1.82: 310 Bond restraints: 45456 Sorted by residual: bond pdb=" C3' DA T 210 " pdb=" O3' DA T 210 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.26e+01 bond pdb=" C3' DC T 132 " pdb=" O3' DC T 132 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.21e+01 bond pdb=" C THR A 351 " pdb=" N VAL A 352 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.36e-02 5.41e+03 2.16e+01 bond pdb=" C1' DT N 155 " pdb=" N1 DT N 155 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" C5' DA T 115 " pdb=" C4' DA T 115 " ideal model delta sigma weight residual 1.512 1.542 -0.030 7.00e-03 2.04e+04 1.78e+01 ... (remaining 45451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 61955 3.64 - 7.28: 790 7.28 - 10.92: 73 10.92 - 14.55: 6 14.55 - 18.19: 2 Bond angle restraints: 62826 Sorted by residual: angle pdb=" O4' DG N 106 " pdb=" C1' DG N 106 " pdb=" N9 DG N 106 " ideal model delta sigma weight residual 108.00 113.78 -5.78 7.00e-01 2.04e+00 6.81e+01 angle pdb=" O4' DT T 140 " pdb=" C1' DT T 140 " pdb=" N1 DT T 140 " ideal model delta sigma weight residual 108.00 112.79 -4.79 7.00e-01 2.04e+00 4.68e+01 angle pdb=" N GLY B 588 " pdb=" CA GLY B 588 " pdb=" C GLY B 588 " ideal model delta sigma weight residual 110.38 119.10 -8.72 1.28e+00 6.10e-01 4.64e+01 angle pdb=" O4' DA T 114 " pdb=" C4' DA T 114 " pdb=" C3' DA T 114 " ideal model delta sigma weight residual 106.00 102.06 3.94 6.00e-01 2.78e+00 4.31e+01 angle pdb=" O4' DT N 47 " pdb=" C4' DT N 47 " pdb=" C3' DT N 47 " ideal model delta sigma weight residual 106.00 102.07 3.93 6.00e-01 2.78e+00 4.30e+01 ... (remaining 62821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 24569 35.64 - 71.28: 2201 71.28 - 106.93: 84 106.93 - 142.57: 4 142.57 - 178.21: 3 Dihedral angle restraints: 26861 sinusoidal: 13323 harmonic: 13538 Sorted by residual: dihedral pdb=" CA LYS A 567 " pdb=" C LYS A 567 " pdb=" N PRO A 568 " pdb=" CA PRO A 568 " ideal model delta harmonic sigma weight residual 180.00 130.62 49.38 0 5.00e+00 4.00e-02 9.75e+01 dihedral pdb=" CA SER L 39 " pdb=" C SER L 39 " pdb=" N LEU L 40 " pdb=" CA LEU L 40 " ideal model delta harmonic sigma weight residual 180.00 133.92 46.08 0 5.00e+00 4.00e-02 8.49e+01 dihedral pdb=" CA ASP A 55 " pdb=" C ASP A 55 " pdb=" N PRO A 56 " pdb=" CA PRO A 56 " ideal model delta harmonic sigma weight residual 180.00 138.24 41.76 0 5.00e+00 4.00e-02 6.97e+01 ... (remaining 26858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5833 0.079 - 0.158: 1166 0.158 - 0.237: 89 0.237 - 0.316: 10 0.316 - 0.394: 2 Chirality restraints: 7100 Sorted by residual: chirality pdb=" CB ILE G 45 " pdb=" CA ILE G 45 " pdb=" CG1 ILE G 45 " pdb=" CG2 ILE G 45 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CB ILE D 59 " pdb=" CA ILE D 59 " pdb=" CG1 ILE D 59 " pdb=" CG2 ILE D 59 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE G 56 " pdb=" CA ILE G 56 " pdb=" CG1 ILE G 56 " pdb=" CG2 ILE G 56 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 7097 not shown) Planarity restraints: 6914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 567 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO A 568 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 156 " 0.005 2.00e-02 2.50e+03 2.41e-02 1.74e+01 pdb=" N9 DG N 156 " -0.005 2.00e-02 2.50e+03 pdb=" C8 DG N 156 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG N 156 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG N 156 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG N 156 " 0.058 2.00e-02 2.50e+03 pdb=" O6 DG N 156 " -0.036 2.00e-02 2.50e+03 pdb=" N1 DG N 156 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG N 156 " 0.032 2.00e-02 2.50e+03 pdb=" N2 DG N 156 " -0.031 2.00e-02 2.50e+03 pdb=" N3 DG N 156 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG N 156 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.062 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 245 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.053 5.00e-02 4.00e+02 ... (remaining 6911 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 928 2.63 - 3.20: 37358 3.20 - 3.77: 76953 3.77 - 4.33: 97677 4.33 - 4.90: 147075 Nonbonded interactions: 359991 Sorted by model distance: nonbonded pdb=" O3' A P 10 " pdb="MG MG A1803 " model vdw 2.063 2.170 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1803 " model vdw 2.079 2.170 nonbonded pdb=" O CYS J 7 " pdb="ZN ZN J 101 " model vdw 2.093 2.230 nonbonded pdb=" OD2 ASP A 485 " pdb="MG MG A1803 " model vdw 2.103 2.170 nonbonded pdb=" OE1 GLU L 33 " pdb="ZN ZN L 101 " model vdw 2.155 2.230 ... (remaining 359986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'M' and resid 39 through 134) selection = (chain 'S' and resid 39 through 134) } ncs_group { reference = (chain 'O' and resid 25 through 102) selection = chain 'U' } ncs_group { reference = chain 'Q' selection = (chain 'V' and resid 16 through 118) } ncs_group { reference = (chain 'R' and resid 29 through 121) selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 53.440 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.110 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 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 : 0.011 0.666 45478 Z= 0.561 Angle : 1.191 40.094 62835 Z= 0.755 Chirality : 0.061 0.394 7100 Planarity : 0.008 0.127 6914 Dihedral : 22.246 178.210 18095 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.77 % Favored : 88.16 % Rotamer: Outliers : 0.79 % Allowed : 11.67 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.27 % 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: -4.33 (0.10), residues: 4595 helix: -2.56 (0.09), residues: 1779 sheet: -2.67 (0.22), residues: 401 loop : -3.22 (0.11), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 57 TYR 0.039 0.003 TYR A 551 PHE 0.027 0.003 PHE D 8 TRP 0.016 0.003 TRP A 556 HIS 0.018 0.003 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.51 (45456) covalent geometry : angle 1.15116 / 0.75 (62826) hydrogen bonds : bond 0.15372 / 10.37 ( 1891) hydrogen bonds : angle 7.07219 / 7.29 ( 5035) metal coordination : bond 0.31230 / 21.69 ( 22) metal coordination : angle 25.68911 / 14.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 41 GLU cc_start: 0.9172 (pt0) cc_final: 0.8874 (tp30) REVERT: U 72 TYR cc_start: 0.8288 (m-10) cc_final: 0.7979 (m-80) REVERT: G 1 MET cc_start: 0.8254 (mtt) cc_final: 0.7797 (mmt) REVERT: G 22 MET cc_start: 0.8081 (ttm) cc_final: 0.7836 (ppp) outliers start: 32 outliers final: 10 residues processed: 255 average time/residue: 0.2947 time to fit residues: 122.6740 Evaluate side-chains 172 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 9.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 68 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 ASN Q 104 GLN ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 84 GLN V 104 GLN ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 HIS S 76 GLN W 106 HIS A 92 HIS ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN A 299 HIS ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 517 ASN A 525 GLN A 548 ASN A 654 ASN A 659 HIS A 736 ASN A 742 ASN A 757 ASN A 768 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1033 GLN A1140 HIS A1173 HIS A1270 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 300 HIS ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS B 516 ASN B 538 ASN B 657 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1193 GLN C 31 ASN C 73 GLN C 79 GLN C 242 GLN D 146 GLN D 173 HIS E 113 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN I 21 ASN I 45 HIS I 59 GLN K 29 ASN L 53 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.040914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.026269 restraints weight = 840061.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.026270 restraints weight = 676818.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.026270 restraints weight = 676700.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.026270 restraints weight = 676700.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.026270 restraints weight = 676700.863| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 45478 Z= 0.182 Angle : 0.806 21.855 62835 Z= 0.432 Chirality : 0.051 0.295 7100 Planarity : 0.006 0.112 6914 Dihedral : 25.343 178.151 8792 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.07 % 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: -3.31 (0.11), residues: 4595 helix: -1.31 (0.11), residues: 1828 sheet: -2.45 (0.23), residues: 416 loop : -2.94 (0.11), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 71 TYR 0.028 0.002 TYR A1349 PHE 0.021 0.002 PHE A 777 TRP 0.024 0.002 TRP B 681 HIS 0.018 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (45456) covalent geometry : angle 0.79076 / 0.43 (62826) hydrogen bonds : bond 0.06791 / 4.57 ( 1891) hydrogen bonds : angle 5.69607 / 5.75 ( 5035) metal coordination : bond 0.01811 / 1.39 ( 22) metal coordination : angle 12.90078 / 7.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 LEU cc_start: 0.2113 (mt) cc_final: 0.1038 (mt) REVERT: A 146 MET cc_start: 0.9623 (pmm) cc_final: 0.9413 (mmm) REVERT: A 849 MET cc_start: 0.5441 (ttp) cc_final: 0.4873 (tmm) REVERT: A 1063 MET cc_start: 0.7546 (mmp) cc_final: 0.7009 (mmt) REVERT: A 1209 MET cc_start: 0.7196 (tmm) cc_final: 0.6600 (ttm) REVERT: A 1375 MET cc_start: 0.8333 (tpt) cc_final: 0.8056 (ttt) REVERT: B 313 MET cc_start: 0.9364 (tpt) cc_final: 0.9063 (tpp) REVERT: C 75 MET cc_start: 0.8691 (mmp) cc_final: 0.8481 (mmm) REVERT: D 145 MET cc_start: 0.7894 (mmp) cc_final: 0.7570 (tpp) REVERT: F 85 MET cc_start: 0.9417 (ttt) cc_final: 0.9072 (tpp) REVERT: G 46 LEU cc_start: 0.5226 (mt) cc_final: 0.4807 (mt) REVERT: G 86 VAL cc_start: -0.3853 (p) cc_final: -0.4110 (p) REVERT: H 123 MET cc_start: 0.9304 (tmm) cc_final: 0.9079 (tmm) outliers start: 2 outliers final: 1 residues processed: 193 average time/residue: 0.2790 time to fit residues: 90.4866 Evaluate side-chains 156 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 227 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 375 optimal weight: 30.0000 chunk 157 optimal weight: 0.2980 chunk 186 optimal weight: 9.9990 chunk 29 optimal weight: 50.0000 chunk 136 optimal weight: 20.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN A 171 GLN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 996 ASN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1211 ASN C 31 ASN C 79 GLN C 112 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 137 GLN K 52 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.040668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.027041 restraints weight = 838971.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.026633 restraints weight = 654543.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.025579 restraints weight = 510803.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.025695 restraints weight = 436770.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.025793 restraints weight = 373685.141| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 45478 Z= 0.170 Angle : 0.729 11.817 62835 Z= 0.396 Chirality : 0.048 0.277 7100 Planarity : 0.005 0.105 6914 Dihedral : 25.145 179.445 8792 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.11), residues: 4595 helix: -0.69 (0.11), residues: 1821 sheet: -2.42 (0.23), residues: 431 loop : -2.70 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1274 TYR 0.022 0.001 TYR A1349 PHE 0.030 0.002 PHE A 444 TRP 0.011 0.001 TRP A 572 HIS 0.007 0.001 HIS U 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (45456) covalent geometry : angle 0.72197 / 0.40 (62826) hydrogen bonds : bond 0.06562 / 4.42 ( 1891) hydrogen bonds : angle 5.38323 / 5.42 ( 5035) metal coordination : bond 0.00962 / 0.72 ( 22) metal coordination : angle 8.23354 / 4.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.9628 (pmm) cc_final: 0.9400 (mmp) REVERT: A 849 MET cc_start: 0.5899 (ttp) cc_final: 0.5256 (tmm) REVERT: A 1063 MET cc_start: 0.7489 (mmp) cc_final: 0.6801 (mmt) REVERT: A 1209 MET cc_start: 0.7060 (tmm) cc_final: 0.6473 (ttm) REVERT: A 1375 MET cc_start: 0.8334 (tpt) cc_final: 0.8097 (ttt) REVERT: B 313 MET cc_start: 0.9473 (tpt) cc_final: 0.9131 (tpp) REVERT: B 542 MET cc_start: 0.8074 (mmt) cc_final: 0.7738 (mmt) REVERT: B 747 MET cc_start: 0.8563 (mtm) cc_final: 0.7931 (tmm) REVERT: B 1152 MET cc_start: 0.8478 (mmt) cc_final: 0.8192 (tpt) REVERT: D 145 MET cc_start: 0.7910 (mmp) cc_final: 0.7654 (tpp) REVERT: G 46 LEU cc_start: 0.5010 (mt) cc_final: 0.4395 (mt) REVERT: H 123 MET cc_start: 0.9306 (tmm) cc_final: 0.9079 (tmm) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.2667 time to fit residues: 82.0674 Evaluate side-chains 155 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 131 optimal weight: 9.9990 chunk 180 optimal weight: 40.0000 chunk 193 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 434 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 171 optimal weight: 40.0000 chunk 211 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 548 ASN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN E 5 ASN E 146 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.040571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.027245 restraints weight = 848028.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.024914 restraints weight = 643355.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.024988 restraints weight = 551400.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.025175 restraints weight = 466870.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.025237 restraints weight = 410894.980| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45478 Z= 0.152 Angle : 0.692 10.118 62835 Z= 0.377 Chirality : 0.047 0.269 7100 Planarity : 0.005 0.112 6914 Dihedral : 25.008 178.943 8792 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4595 helix: -0.36 (0.12), residues: 1834 sheet: -2.31 (0.23), residues: 428 loop : -2.58 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 446 TYR 0.024 0.001 TYR G 51 PHE 0.022 0.001 PHE A 444 TRP 0.009 0.001 TRP A1228 HIS 0.007 0.001 HIS U 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (45456) covalent geometry : angle 0.68933 / 0.38 (62826) hydrogen bonds : bond 0.06004 / 4.05 ( 1891) hydrogen bonds : angle 5.16607 / 5.21 ( 5035) metal coordination : bond 0.01333 / 0.81 ( 22) metal coordination : angle 5.56258 / 3.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.9124 (mmm) cc_final: 0.8836 (tpp) REVERT: A 1209 MET cc_start: 0.6954 (tmm) cc_final: 0.6382 (ttm) REVERT: A 1375 MET cc_start: 0.8332 (tpt) cc_final: 0.8091 (ttt) REVERT: B 313 MET cc_start: 0.9457 (tpt) cc_final: 0.9100 (tpp) REVERT: B 747 MET cc_start: 0.8582 (mtm) cc_final: 0.8076 (tmm) REVERT: D 145 MET cc_start: 0.7981 (mmp) cc_final: 0.7721 (tpp) REVERT: F 85 MET cc_start: 0.9050 (ttp) cc_final: 0.8809 (tmm) REVERT: G 46 LEU cc_start: 0.4749 (mt) cc_final: 0.4460 (mt) REVERT: H 123 MET cc_start: 0.9308 (tmm) cc_final: 0.9071 (tmm) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2597 time to fit residues: 80.5364 Evaluate side-chains 152 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 334 optimal weight: 2.9990 chunk 279 optimal weight: 40.0000 chunk 196 optimal weight: 8.9990 chunk 440 optimal weight: 0.7980 chunk 434 optimal weight: 7.9990 chunk 379 optimal weight: 50.0000 chunk 325 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 456 optimal weight: 30.0000 chunk 436 optimal weight: 50.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 736 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 587 HIS B 734 HIS ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 65 HIS C 79 GLN E 5 ASN ** E 147 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 = 0.3426 r_free = 0.3426 target = 0.040536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.026771 restraints weight = 834174.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.025254 restraints weight = 654081.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.025432 restraints weight = 557485.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.025642 restraints weight = 466318.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.025852 restraints weight = 404680.620| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45478 Z= 0.147 Angle : 0.678 13.424 62835 Z= 0.366 Chirality : 0.046 0.266 7100 Planarity : 0.004 0.108 6914 Dihedral : 24.916 179.208 8792 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.12), residues: 4595 helix: -0.10 (0.12), residues: 1833 sheet: -2.29 (0.23), residues: 453 loop : -2.43 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 146 TYR 0.021 0.001 TYR A1349 PHE 0.019 0.001 PHE B 37 TRP 0.010 0.001 TRP H 79 HIS 0.008 0.001 HIS U 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (45456) covalent geometry : angle 0.67513 / 0.37 (62826) hydrogen bonds : bond 0.05806 / 3.91 ( 1891) hydrogen bonds : angle 5.02625 / 5.07 ( 5035) metal coordination : bond 0.01074 / 0.75 ( 22) metal coordination : angle 5.29365 / 2.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LEU cc_start: 0.9568 (tp) cc_final: 0.9324 (mp) REVERT: A 873 MET cc_start: 0.5235 (mmm) cc_final: 0.4989 (mmm) REVERT: A 1375 MET cc_start: 0.8301 (tpt) cc_final: 0.8052 (ttm) REVERT: A 1430 LEU cc_start: 0.9069 (mp) cc_final: 0.8835 (mp) REVERT: B 313 MET cc_start: 0.9425 (tpt) cc_final: 0.9071 (tpp) REVERT: B 747 MET cc_start: 0.8481 (mtm) cc_final: 0.7967 (tmm) REVERT: D 145 MET cc_start: 0.8141 (mmp) cc_final: 0.7849 (tpp) REVERT: G 46 LEU cc_start: 0.4869 (mt) cc_final: 0.4207 (mt) REVERT: H 123 MET cc_start: 0.9394 (tmm) cc_final: 0.9165 (tmm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2583 time to fit residues: 77.6961 Evaluate side-chains 154 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 200 optimal weight: 6.9990 chunk 486 optimal weight: 8.9990 chunk 363 optimal weight: 30.0000 chunk 203 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 302 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 349 optimal weight: 1.9990 chunk 371 optimal weight: 9.9990 chunk 55 optimal weight: 50.0000 chunk 309 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 969 GLN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN C 242 GLN E 5 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.040205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.024891 restraints weight = 829334.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.023600 restraints weight = 685024.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.023809 restraints weight = 556277.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.023971 restraints weight = 486617.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.024112 restraints weight = 437474.379| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45478 Z= 0.151 Angle : 0.665 11.241 62835 Z= 0.360 Chirality : 0.046 0.278 7100 Planarity : 0.004 0.105 6914 Dihedral : 24.866 179.325 8792 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 4595 helix: 0.05 (0.12), residues: 1832 sheet: -2.17 (0.24), residues: 444 loop : -2.34 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 344 TYR 0.028 0.001 TYR F 88 PHE 0.027 0.001 PHE A 444 TRP 0.022 0.001 TRP B 308 HIS 0.007 0.001 HIS U 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (45456) covalent geometry : angle 0.66335 / 0.36 (62826) hydrogen bonds : bond 0.05751 / 3.87 ( 1891) hydrogen bonds : angle 4.95801 / 4.97 ( 5035) metal coordination : bond 0.00876 / 0.64 ( 22) metal coordination : angle 4.49125 / 2.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.5997 (ttt) cc_final: 0.4830 (tmm) REVERT: A 487 MET cc_start: 0.8684 (tpp) cc_final: 0.8165 (tmm) REVERT: A 489 LEU cc_start: 0.9545 (tp) cc_final: 0.9293 (mp) REVERT: A 873 MET cc_start: 0.5093 (mmm) cc_final: 0.4853 (mmm) REVERT: A 1209 MET cc_start: 0.6595 (tmm) cc_final: 0.6064 (ttm) REVERT: B 313 MET cc_start: 0.9446 (tpt) cc_final: 0.9112 (tpp) REVERT: B 747 MET cc_start: 0.8406 (mtm) cc_final: 0.7991 (tmm) REVERT: D 145 MET cc_start: 0.8169 (mmp) cc_final: 0.7872 (tpp) REVERT: G 46 LEU cc_start: 0.4484 (mt) cc_final: 0.4009 (mt) REVERT: H 123 MET cc_start: 0.9467 (tmm) cc_final: 0.9257 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2535 time to fit residues: 76.7915 Evaluate side-chains 154 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 236 optimal weight: 50.0000 chunk 454 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 428 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN C 31 ASN C 79 GLN E 5 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.040236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.023608 restraints weight = 841929.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.022937 restraints weight = 681674.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.023144 restraints weight = 560944.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.023250 restraints weight = 494580.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.023367 restraints weight = 454212.290| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45478 Z= 0.145 Angle : 0.662 11.120 62835 Z= 0.357 Chirality : 0.046 0.266 7100 Planarity : 0.004 0.103 6914 Dihedral : 24.821 179.084 8792 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.12), residues: 4595 helix: 0.17 (0.12), residues: 1852 sheet: -2.04 (0.24), residues: 439 loop : -2.29 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 200 TYR 0.016 0.001 TYR F 88 PHE 0.019 0.001 PHE A 444 TRP 0.019 0.002 TRP A 185 HIS 0.007 0.001 HIS U 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (45456) covalent geometry : angle 0.66031 / 0.36 (62826) hydrogen bonds : bond 0.05557 / 3.74 ( 1891) hydrogen bonds : angle 4.89714 / 4.92 ( 5035) metal coordination : bond 0.00740 / 0.58 ( 22) metal coordination : angle 3.96859 / 2.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LEU cc_start: 0.9548 (tp) cc_final: 0.9326 (mp) REVERT: A 873 MET cc_start: 0.5091 (mmm) cc_final: 0.4753 (mmp) REVERT: A 1209 MET cc_start: 0.6492 (tmm) cc_final: 0.6178 (ttp) REVERT: A 1317 MET cc_start: 0.9008 (ptp) cc_final: 0.8783 (ptp) REVERT: B 313 MET cc_start: 0.9449 (tpt) cc_final: 0.9122 (tpp) REVERT: B 747 MET cc_start: 0.8304 (mtm) cc_final: 0.7984 (tmm) REVERT: D 145 MET cc_start: 0.8250 (mmp) cc_final: 0.7994 (tpp) REVERT: G 46 LEU cc_start: 0.4108 (mt) cc_final: 0.3494 (mt) REVERT: G 106 MET cc_start: -0.2708 (mmm) cc_final: -0.3037 (mpp) REVERT: H 123 MET cc_start: 0.9452 (tmm) cc_final: 0.9251 (tmm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2459 time to fit residues: 72.8876 Evaluate side-chains 153 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 283 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 chunk 215 optimal weight: 6.9990 chunk 87 optimal weight: 40.0000 chunk 193 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 284 optimal weight: 7.9990 chunk 329 optimal weight: 40.0000 chunk 371 optimal weight: 6.9990 chunk 470 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN E 5 ASN E 136 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.039766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.026159 restraints weight = 845300.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.023616 restraints weight = 692303.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.023809 restraints weight = 567321.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.023954 restraints weight = 458040.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.024132 restraints weight = 417161.687| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 45478 Z= 0.178 Angle : 0.689 12.760 62835 Z= 0.369 Chirality : 0.046 0.265 7100 Planarity : 0.005 0.100 6914 Dihedral : 24.854 179.820 8792 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.12), residues: 4595 helix: 0.19 (0.12), residues: 1858 sheet: -2.10 (0.24), residues: 439 loop : -2.25 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.022 0.001 TYR G 51 PHE 0.020 0.001 PHE A 444 TRP 0.014 0.002 TRP B 561 HIS 0.008 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (45456) covalent geometry : angle 0.68703 / 0.37 (62826) hydrogen bonds : bond 0.06319 / 4.23 ( 1891) hydrogen bonds : angle 4.94564 / 4.95 ( 5035) metal coordination : bond 0.00854 / 0.68 ( 22) metal coordination : angle 4.60401 / 2.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.7867 (tpp) cc_final: 0.7629 (tpp) REVERT: A 873 MET cc_start: 0.4992 (mmm) cc_final: 0.4728 (mmm) REVERT: A 1209 MET cc_start: 0.6614 (tmm) cc_final: 0.6291 (ttp) REVERT: B 747 MET cc_start: 0.8288 (mtm) cc_final: 0.7841 (tmm) REVERT: D 145 MET cc_start: 0.8249 (mmp) cc_final: 0.7988 (tpp) REVERT: G 46 LEU cc_start: 0.3790 (mt) cc_final: 0.3407 (mt) REVERT: G 106 MET cc_start: -0.2665 (mmm) cc_final: -0.3022 (mpp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2622 time to fit residues: 74.9500 Evaluate side-chains 150 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 81 optimal weight: 8.9990 chunk 325 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 40.0000 chunk 217 optimal weight: 20.0000 chunk 417 optimal weight: 0.0270 chunk 322 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 232 optimal weight: 8.9990 chunk 392 optimal weight: 8.9990 chunk 483 optimal weight: 30.0000 overall best weight: 7.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1258 HIS A1354 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN E 5 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.039678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.025560 restraints weight = 839198.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.023913 restraints weight = 682012.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.024132 restraints weight = 544768.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.024315 restraints weight = 462042.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.024315 restraints weight = 412237.030| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45478 Z= 0.175 Angle : 0.698 21.940 62835 Z= 0.371 Chirality : 0.046 0.394 7100 Planarity : 0.005 0.099 6914 Dihedral : 24.893 178.886 8792 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.02 % Allowed : 0.84 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.12), residues: 4595 helix: 0.24 (0.12), residues: 1846 sheet: -2.14 (0.23), residues: 455 loop : -2.22 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 446 TYR 0.035 0.002 TYR A1287 PHE 0.018 0.001 PHE B1146 TRP 0.015 0.002 TRP B 561 HIS 0.008 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (45456) covalent geometry : angle 0.69657 / 0.37 (62826) hydrogen bonds : bond 0.06114 / 4.09 ( 1891) hydrogen bonds : angle 4.93209 / 4.93 ( 5035) metal coordination : bond 0.01261 / 0.82 ( 22) metal coordination : angle 3.60191 / 1.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.7988 (tpp) cc_final: 0.7755 (tpp) REVERT: A 873 MET cc_start: 0.4975 (mmm) cc_final: 0.4692 (mmm) REVERT: A 1209 MET cc_start: 0.6428 (tmm) cc_final: 0.6030 (ttp) REVERT: B 747 MET cc_start: 0.8061 (mtm) cc_final: 0.7734 (tmm) REVERT: D 145 MET cc_start: 0.8245 (mmp) cc_final: 0.7969 (tpp) REVERT: G 46 LEU cc_start: 0.3860 (mt) cc_final: 0.3269 (mt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2467 time to fit residues: 71.2084 Evaluate side-chains 151 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 142 optimal weight: 7.9990 chunk 436 optimal weight: 50.0000 chunk 85 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 450 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 41 optimal weight: 50.0000 chunk 154 optimal weight: 6.9990 chunk 257 optimal weight: 30.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 854 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 147 HIS ** 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 = 0.3420 r_free = 0.3420 target = 0.039921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.025659 restraints weight = 839648.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.024099 restraints weight = 678573.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.024369 restraints weight = 541403.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.024592 restraints weight = 458636.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.024688 restraints weight = 395906.066| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45478 Z= 0.145 Angle : 0.673 14.543 62835 Z= 0.358 Chirality : 0.046 0.321 7100 Planarity : 0.004 0.102 6914 Dihedral : 24.860 178.088 8792 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.12), residues: 4595 helix: 0.31 (0.12), residues: 1846 sheet: -2.17 (0.23), residues: 470 loop : -2.18 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1399 TYR 0.024 0.001 TYR A 478 PHE 0.032 0.001 PHE A 444 TRP 0.012 0.001 TRP B 561 HIS 0.021 0.001 HIS B1076 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (45456) covalent geometry : angle 0.67183 / 0.36 (62826) hydrogen bonds : bond 0.05458 / 3.67 ( 1891) hydrogen bonds : angle 4.87312 / 4.87 ( 5035) metal coordination : bond 0.00876 / 0.64 ( 22) metal coordination : angle 3.14985 / 1.79 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9183 (mmm) cc_final: 0.8953 (mmt) REVERT: A 818 MET cc_start: 0.9209 (mmp) cc_final: 0.8870 (mmp) REVERT: B 747 MET cc_start: 0.8207 (mtm) cc_final: 0.7831 (tmm) REVERT: B 999 MET cc_start: 0.7403 (mtm) cc_final: 0.7116 (mtt) REVERT: D 145 MET cc_start: 0.8228 (mmp) cc_final: 0.7731 (tpp) REVERT: G 46 LEU cc_start: 0.3677 (mt) cc_final: 0.3330 (mt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2480 time to fit residues: 70.6353 Evaluate side-chains 150 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 55 optimal weight: 40.0000 chunk 365 optimal weight: 0.7980 chunk 429 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 392 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 275 optimal weight: 30.0000 chunk 234 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 736 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN E 5 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** 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 = 0.3422 r_free = 0.3422 target = 0.039902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.025865 restraints weight = 832758.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.023605 restraints weight = 673474.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.023692 restraints weight = 567899.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.023862 restraints weight = 490735.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.024010 restraints weight = 437966.683| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45478 Z= 0.147 Angle : 0.668 12.364 62835 Z= 0.356 Chirality : 0.045 0.262 7100 Planarity : 0.004 0.100 6914 Dihedral : 24.831 178.568 8792 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.12), residues: 4595 helix: 0.38 (0.12), residues: 1847 sheet: -2.18 (0.23), residues: 456 loop : -2.16 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 434 TYR 0.025 0.001 TYR F 137 PHE 0.039 0.001 PHE A 444 TRP 0.036 0.002 TRP B 519 HIS 0.009 0.001 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (45456) covalent geometry : angle 0.66722 / 0.36 (62826) hydrogen bonds : bond 0.05491 / 3.68 ( 1891) hydrogen bonds : angle 4.84585 / 4.84 ( 5035) metal coordination : bond 0.00846 / 0.62 ( 22) metal coordination : angle 3.02897 / 1.76 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13249.63 seconds wall clock time: 227 minutes 11.45 seconds (13631.45 seconds total)