Starting phenix.real_space_refine on Sat Mar 7 13:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i84_4429/03_2026/6i84_4429.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i84_4429/03_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_4429/03_2026/6i84_4429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i84_4429/03_2026/6i84_4429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i84_4429/03_2026/6i84_4429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i84_4429/03_2026/6i84_4429.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: 8.93, per 1000 atoms: 0.20 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: 3.68 Conformation dependent library (CDL) restraints added in 1.1 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: 6.39 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: 14.35 Time building geometry restraints manager: 4.87 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=" 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=" C ASN I 82 " pdb=" N VAL I 83 " ideal model delta sigma weight residual 1.329 1.281 0.048 1.32e-02 5.74e+03 1.33e+01 bond pdb=" C CYS B 523 " pdb=" N PRO B 524 " ideal model delta sigma weight residual 1.335 1.302 0.033 9.40e-03 1.13e+04 1.25e+01 bond pdb=" C LEU I 13 " pdb=" N TYR I 14 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.47e-02 4.63e+03 1.24e+01 bond pdb=" C LEU H 46 " pdb=" N PHE H 47 " ideal model delta sigma weight residual 1.331 1.295 0.036 1.39e-02 5.18e+03 6.59e+00 ... (remaining 45451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 62021 3.64 - 7.28: 724 7.28 - 10.92: 73 10.92 - 14.55: 6 14.55 - 18.19: 2 Bond angle restraints: 62826 Sorted by residual: 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=" N GLY W 101 " pdb=" CA GLY W 101 " pdb=" C GLY W 101 " ideal model delta sigma weight residual 112.64 120.28 -7.64 1.21e+00 6.83e-01 3.99e+01 angle pdb=" N GLY A 807 " pdb=" CA GLY A 807 " pdb=" C GLY A 807 " ideal model delta sigma weight residual 110.60 119.58 -8.98 1.46e+00 4.69e-01 3.78e+01 angle pdb=" C SER H 108 " pdb=" N LYS H 109 " pdb=" CA LYS H 109 " ideal model delta sigma weight residual 121.54 132.93 -11.39 1.91e+00 2.74e-01 3.56e+01 angle pdb=" C ARG A1241 " pdb=" N VAL A1242 " pdb=" CA VAL A1242 " ideal model delta sigma weight residual 121.97 131.78 -9.81 1.80e+00 3.09e-01 2.97e+01 ... (remaining 62821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 24594 35.64 - 71.28: 2209 71.28 - 106.93: 87 106.93 - 142.57: 4 142.57 - 178.21: 3 Dihedral angle restraints: 26897 sinusoidal: 13359 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 26894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5858 0.079 - 0.158: 1154 0.158 - 0.237: 76 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 52.800 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 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: 58.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 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= 0.433 Angle : 1.154 40.094 62835 Z= 0.627 Chirality : 0.060 0.394 7100 Planarity : 0.008 0.127 6914 Dihedral : 22.282 178.210 18131 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 covalent geometry : bond 0.00804 (45456) covalent geometry : angle 1.11223 (62826) hydrogen bonds : bond 0.15372 ( 1891) hydrogen bonds : angle 7.07219 ( 5035) metal coordination : bond 0.31230 ( 22) metal coordination : angle 25.68911 ( 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 : 1.450 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: 0.2865 time to fit residues: 119.1766 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 : 1.499 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 92 GLN ** W 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS A 171 GLN A 297 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 510 GLN A 517 ASN A 525 GLN 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 838 GLN ** 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 968 GLN A1033 GLN A1140 HIS A1203 ASN A1270 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 236 HIS B 300 HIS ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 515 HIS B 516 ASN B 538 ASN B 657 HIS B 762 ASN B 776 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1093 GLN B1193 GLN C 31 ASN C 73 GLN C 79 GLN C 112 ASN C 184 ASN 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 K 29 ASN L 53 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.040769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.027088 restraints weight = 842486.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.025003 restraints weight = 648466.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.025137 restraints weight = 526969.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.025257 restraints weight = 455647.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.025417 restraints weight = 410396.934| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45478 Z= 0.180 Angle : 0.721 18.448 62835 Z= 0.393 Chirality : 0.044 0.224 7100 Planarity : 0.006 0.112 6914 Dihedral : 25.317 177.533 8828 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.02 % Allowed : 4.45 % Favored : 95.53 % 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: -3.10 (0.11), residues: 4595 helix: -1.10 (0.11), residues: 1819 sheet: -2.34 (0.23), residues: 416 loop : -2.86 (0.11), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 52 TYR 0.025 0.002 TYR A1349 PHE 0.021 0.002 PHE A 444 TRP 0.014 0.002 TRP B 681 HIS 0.013 0.001 HIS A1173 Details of bonding type rmsd covalent geometry : bond 0.00382 (45456) covalent geometry : angle 0.71172 (62826) hydrogen bonds : bond 0.06211 ( 1891) hydrogen bonds : angle 5.48929 ( 5035) metal coordination : bond 0.01868 ( 22) metal coordination : angle 9.80414 ( 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 189 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.456 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: R 97 LEU cc_start: 0.3481 (mt) cc_final: 0.2067 (mt) REVERT: U 34 ILE cc_start: 0.8445 (mm) cc_final: 0.8013 (mt) REVERT: A 146 MET cc_start: 0.9630 (pmm) cc_final: 0.9412 (mmm) REVERT: A 1209 MET cc_start: 0.6946 (tmm) cc_final: 0.6303 (ttm) REVERT: A 1375 MET cc_start: 0.8362 (tpt) cc_final: 0.8086 (ttt) REVERT: B 313 MET cc_start: 0.9405 (tpt) cc_final: 0.9097 (tpp) REVERT: B 773 MET cc_start: 0.4198 (ptp) cc_final: 0.3950 (ptt) REVERT: B 1152 MET cc_start: 0.8085 (mmt) cc_final: 0.7712 (tpt) REVERT: D 145 MET cc_start: 0.7931 (mmp) cc_final: 0.7612 (tpp) REVERT: F 122 MET cc_start: 0.9510 (tmm) cc_final: 0.9227 (mtp) REVERT: G 46 LEU cc_start: 0.4942 (mt) cc_final: 0.4453 (mt) REVERT: G 86 VAL cc_start: -0.3726 (p) cc_final: -0.3997 (p) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.2649 time to fit residues: 84.1555 Evaluate side-chains 154 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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: 6.9990 chunk 315 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 375 optimal weight: 10.0000 chunk 157 optimal weight: 0.5980 chunk 186 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 136 optimal weight: 0.3980 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 39 HIS ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 HIS ** 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 399 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS ** A1427 ASN ** 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 587 HIS B 734 HIS ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN E 146 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 137 GLN K 52 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.040628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.027108 restraints weight = 832359.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.024278 restraints weight = 631057.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.024494 restraints weight = 530623.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.024572 restraints weight = 437089.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.024601 restraints weight = 408398.065| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2611 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= 0.160 Angle : 0.660 10.602 62835 Z= 0.361 Chirality : 0.042 0.231 7100 Planarity : 0.005 0.105 6914 Dihedral : 25.050 178.456 8828 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -2.45 (0.12), residues: 4595 helix: -0.37 (0.12), residues: 1843 sheet: -2.32 (0.24), residues: 423 loop : -2.60 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG U 67 TYR 0.029 0.001 TYR H 95 PHE 0.018 0.001 PHE D 8 TRP 0.010 0.001 TRP A1304 HIS 0.006 0.001 HIS U 75 Details of bonding type rmsd covalent geometry : bond 0.00337 (45456) covalent geometry : angle 0.65721 (62826) hydrogen bonds : bond 0.05526 ( 1891) hydrogen bonds : angle 5.02683 ( 5035) metal coordination : bond 0.01079 ( 22) metal coordination : angle 5.05835 ( 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 177 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 34 ILE cc_start: 0.7605 (mm) cc_final: 0.7365 (mt) REVERT: A 1209 MET cc_start: 0.6667 (tmm) cc_final: 0.6057 (ttm) REVERT: A 1375 MET cc_start: 0.8259 (tpt) cc_final: 0.8010 (ttt) REVERT: B 313 MET cc_start: 0.9392 (tpt) cc_final: 0.9049 (tpp) REVERT: B 747 MET cc_start: 0.8489 (mtm) cc_final: 0.7929 (tmm) REVERT: D 145 MET cc_start: 0.8068 (mmp) cc_final: 0.7759 (tpp) REVERT: F 122 MET cc_start: 0.9493 (tmm) cc_final: 0.9215 (mtp) REVERT: G 1 MET cc_start: 0.8708 (mmt) cc_final: 0.8479 (mpp) REVERT: G 46 LEU cc_start: 0.5052 (mt) cc_final: 0.4261 (mt) REVERT: G 86 VAL cc_start: -0.4481 (p) cc_final: -0.4727 (p) REVERT: H 123 MET cc_start: 0.9395 (tmm) cc_final: 0.9190 (tmm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2553 time to fit residues: 77.7009 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 : 1.531 ------------------------------------------------------------------------------- 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: 8.9990 chunk 180 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 155 optimal weight: 0.2980 chunk 434 optimal weight: 7.9990 chunk 362 optimal weight: 30.0000 chunk 241 optimal weight: 10.0000 chunk 171 optimal weight: 40.0000 chunk 211 optimal weight: 20.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 HIS ** 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 969 GLN A1059 HIS ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 309 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 59 GLN ** K 65 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 = 0.3412 r_free = 0.3412 target = 0.039779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.025822 restraints weight = 852396.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.025680 restraints weight = 689792.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.024396 restraints weight = 622851.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.024711 restraints weight = 511911.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.024916 restraints weight = 423545.909| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45478 Z= 0.183 Angle : 0.659 9.245 62835 Z= 0.361 Chirality : 0.042 0.263 7100 Planarity : 0.005 0.112 6914 Dihedral : 25.041 177.905 8828 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: -2.11 (0.12), residues: 4595 helix: -0.06 (0.12), residues: 1849 sheet: -2.25 (0.23), residues: 444 loop : -2.42 (0.12), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 67 TYR 0.024 0.002 TYR G 51 PHE 0.041 0.001 PHE B1204 TRP 0.014 0.002 TRP B 561 HIS 0.008 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00384 (45456) covalent geometry : angle 0.65750 (62826) hydrogen bonds : bond 0.06055 ( 1891) hydrogen bonds : angle 4.95839 ( 5035) metal coordination : bond 0.01038 ( 22) metal coordination : angle 4.02456 ( 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 174 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.630 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: U 34 ILE cc_start: 0.8330 (mm) cc_final: 0.8126 (mt) REVERT: A 1209 MET cc_start: 0.6745 (tmm) cc_final: 0.6123 (ttm) REVERT: B 313 MET cc_start: 0.9418 (tpt) cc_final: 0.9109 (tpp) REVERT: B 747 MET cc_start: 0.8296 (mtm) cc_final: 0.7897 (tmm) REVERT: B 1152 MET cc_start: 0.8915 (mmt) cc_final: 0.8620 (tpp) REVERT: D 145 MET cc_start: 0.8195 (mmp) cc_final: 0.7686 (tpp) REVERT: F 122 MET cc_start: 0.9504 (tmm) cc_final: 0.9238 (mtp) REVERT: G 1 MET cc_start: 0.8744 (mmt) cc_final: 0.8475 (mpp) REVERT: G 46 LEU cc_start: 0.4512 (mt) cc_final: 0.4229 (mt) REVERT: G 86 VAL cc_start: -0.4375 (p) cc_final: -0.4624 (p) REVERT: H 123 MET cc_start: 0.9398 (tmm) cc_final: 0.9149 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2529 time to fit residues: 75.9517 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 : 1.587 ------------------------------------------------------------------------------- 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: 8.9990 chunk 279 optimal weight: 40.0000 chunk 196 optimal weight: 3.9990 chunk 440 optimal weight: 0.0030 chunk 434 optimal weight: 7.9990 chunk 379 optimal weight: 40.0000 chunk 325 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 456 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** W 106 HIS ** 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 736 ASN A 862 ASN A1218 GLN A1258 HIS ** 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 518 HIS B 776 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN C 242 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.039743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.025986 restraints weight = 844875.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.024517 restraints weight = 682642.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.024813 restraints weight = 552058.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.025025 restraints weight = 453070.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.025037 restraints weight = 401644.333| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 45478 Z= 0.166 Angle : 0.636 11.767 62835 Z= 0.347 Chirality : 0.042 0.229 7100 Planarity : 0.005 0.109 6914 Dihedral : 25.030 179.321 8828 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 1861 sheet: -2.12 (0.23), residues: 454 loop : -2.28 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1116 TYR 0.020 0.001 TYR G 51 PHE 0.023 0.001 PHE B1204 TRP 0.018 0.001 TRP B 308 HIS 0.009 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00350 (45456) covalent geometry : angle 0.63476 (62826) hydrogen bonds : bond 0.05462 ( 1891) hydrogen bonds : angle 4.83981 ( 5035) metal coordination : bond 0.00744 ( 22) metal coordination : angle 3.02472 ( 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 170 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.537 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: U 34 ILE cc_start: 0.8499 (mm) cc_final: 0.8070 (mt) REVERT: U 72 TYR cc_start: 0.6645 (m-10) cc_final: 0.6405 (m-80) REVERT: A 1209 MET cc_start: 0.6743 (tmm) cc_final: 0.6115 (ttm) REVERT: B 313 MET cc_start: 0.9393 (tpt) cc_final: 0.9063 (tpp) REVERT: B 747 MET cc_start: 0.8338 (mtm) cc_final: 0.7806 (tmm) REVERT: D 145 MET cc_start: 0.8266 (mmp) cc_final: 0.7778 (tpp) REVERT: F 122 MET cc_start: 0.9472 (tmm) cc_final: 0.9207 (mtp) REVERT: G 46 LEU cc_start: 0.5120 (mt) cc_final: 0.4499 (mt) REVERT: H 123 MET cc_start: 0.9445 (tmm) cc_final: 0.9222 (tmm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2448 time to fit residues: 72.0399 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 : 1.494 ------------------------------------------------------------------------------- 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: 5.9990 chunk 486 optimal weight: 40.0000 chunk 363 optimal weight: 40.0000 chunk 203 optimal weight: 20.0000 chunk 151 optimal weight: 0.3980 chunk 302 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 371 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 309 optimal weight: 5.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 64 ASN ** 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 736 ASN ** 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 ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN ** K 65 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 = 0.3423 r_free = 0.3423 target = 0.039900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.025931 restraints weight = 831327.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.024041 restraints weight = 664483.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.024289 restraints weight = 537201.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.024397 restraints weight = 450412.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.024609 restraints weight = 397825.634| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45478 Z= 0.147 Angle : 0.616 10.663 62835 Z= 0.336 Chirality : 0.042 0.334 7100 Planarity : 0.004 0.108 6914 Dihedral : 24.942 179.381 8828 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -1.63 (0.12), residues: 4595 helix: 0.39 (0.12), residues: 1842 sheet: -2.12 (0.24), residues: 429 loop : -2.16 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 83 TYR 0.026 0.001 TYR G 51 PHE 0.022 0.001 PHE A 444 TRP 0.019 0.001 TRP B 519 HIS 0.010 0.001 HIS W 106 Details of bonding type rmsd covalent geometry : bond 0.00312 (45456) covalent geometry : angle 0.61542 (62826) hydrogen bonds : bond 0.05010 ( 1891) hydrogen bonds : angle 4.72713 ( 5035) metal coordination : bond 0.00655 ( 22) metal coordination : angle 2.55673 ( 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 171 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.592 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: U 72 TYR cc_start: 0.6640 (m-10) cc_final: 0.6389 (m-80) REVERT: A 746 MET cc_start: 0.8105 (ttm) cc_final: 0.7803 (mtt) REVERT: A 873 MET cc_start: 0.5773 (mmp) cc_final: 0.5248 (mmm) REVERT: A 1209 MET cc_start: 0.6120 (tmm) cc_final: 0.5672 (ttp) REVERT: A 1368 MET cc_start: 0.9454 (ptm) cc_final: 0.9211 (ptt) REVERT: B 313 MET cc_start: 0.9428 (tpt) cc_final: 0.9122 (tpp) REVERT: B 747 MET cc_start: 0.8181 (mtm) cc_final: 0.7722 (tmm) REVERT: D 145 MET cc_start: 0.8238 (mmp) cc_final: 0.7721 (tpp) REVERT: F 122 MET cc_start: 0.9461 (tmm) cc_final: 0.9199 (mtp) REVERT: G 46 LEU cc_start: 0.4921 (mt) cc_final: 0.4486 (mt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2499 time to fit residues: 73.7699 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 : 1.584 ------------------------------------------------------------------------------- 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: 40.0000 chunk 454 optimal weight: 9.9990 chunk 312 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 428 optimal weight: 50.0000 chunk 233 optimal weight: 8.9990 chunk 323 optimal weight: 40.0000 chunk 307 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 64 ASN ** A 71 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 736 ASN A 854 ASN A1033 GLN ** 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 47 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 ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN H 33 GLN H 134 ASN H 137 GLN K 40 HIS ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.039265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.022747 restraints weight = 850244.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.022301 restraints weight = 699390.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.022479 restraints weight = 581569.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.022631 restraints weight = 509897.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.022694 restraints weight = 465507.977| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 45478 Z= 0.192 Angle : 0.652 11.766 62835 Z= 0.356 Chirality : 0.042 0.258 7100 Planarity : 0.005 0.104 6914 Dihedral : 25.034 178.235 8828 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % 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: -1.70 (0.12), residues: 4595 helix: 0.35 (0.12), residues: 1836 sheet: -2.18 (0.23), residues: 465 loop : -2.19 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 80 TYR 0.016 0.001 TYR A 478 PHE 0.017 0.001 PHE B1146 TRP 0.014 0.002 TRP B 561 HIS 0.012 0.001 HIS W 106 Details of bonding type rmsd covalent geometry : bond 0.00403 (45456) covalent geometry : angle 0.65152 (62826) hydrogen bonds : bond 0.06083 ( 1891) hydrogen bonds : angle 4.86203 ( 5035) metal coordination : bond 0.00816 ( 22) metal coordination : angle 2.53638 ( 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 169 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 1.671 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: U 72 TYR cc_start: 0.6266 (m-10) cc_final: 0.5940 (m-80) REVERT: A 746 MET cc_start: 0.8074 (ttm) cc_final: 0.7780 (mtt) REVERT: A 873 MET cc_start: 0.5238 (mmp) cc_final: 0.4995 (mmp) REVERT: A 1209 MET cc_start: 0.6138 (tmm) cc_final: 0.5556 (ttm) REVERT: A 1368 MET cc_start: 0.9493 (ptm) cc_final: 0.9246 (ptt) REVERT: B 313 MET cc_start: 0.9491 (tpt) cc_final: 0.9205 (tpp) REVERT: B 747 MET cc_start: 0.8082 (mtm) cc_final: 0.7665 (tmm) REVERT: B 809 MET cc_start: 0.8819 (ptp) cc_final: 0.8511 (ptp) REVERT: D 145 MET cc_start: 0.8266 (mmp) cc_final: 0.7880 (tpp) REVERT: F 122 MET cc_start: 0.9494 (tmm) cc_final: 0.9244 (mtp) REVERT: G 46 LEU cc_start: 0.4862 (mt) cc_final: 0.4244 (mt) outliers start: 2 outliers final: 1 residues processed: 169 average time/residue: 0.2413 time to fit residues: 70.8840 Evaluate side-chains 151 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 193 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 329 optimal weight: 30.0000 chunk 371 optimal weight: 7.9990 chunk 470 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN ** 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 A 306 ASN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 838 GLN A1070 GLN ** 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 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 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN H 137 GLN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.039395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.025555 restraints weight = 844494.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.023820 restraints weight = 680435.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.023986 restraints weight = 553587.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.024099 restraints weight = 467369.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.024277 restraints weight = 421964.371| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45478 Z= 0.165 Angle : 0.631 14.075 62835 Z= 0.343 Chirality : 0.042 0.247 7100 Planarity : 0.004 0.105 6914 Dihedral : 25.036 178.926 8828 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -1.57 (0.12), residues: 4595 helix: 0.46 (0.12), residues: 1829 sheet: -2.13 (0.23), residues: 450 loop : -2.11 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 344 TYR 0.028 0.001 TYR G 51 PHE 0.018 0.001 PHE B1146 TRP 0.011 0.001 TRP B 561 HIS 0.011 0.001 HIS W 106 Details of bonding type rmsd covalent geometry : bond 0.00350 (45456) covalent geometry : angle 0.62985 (62826) hydrogen bonds : bond 0.05333 ( 1891) hydrogen bonds : angle 4.79401 ( 5035) metal coordination : bond 0.00703 ( 22) metal coordination : angle 2.49025 ( 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 163 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 746 MET cc_start: 0.8163 (ttm) cc_final: 0.7868 (mtt) REVERT: A 873 MET cc_start: 0.5116 (mmp) cc_final: 0.4866 (mmp) REVERT: A 1209 MET cc_start: 0.6208 (tmm) cc_final: 0.5599 (ttm) REVERT: A 1368 MET cc_start: 0.9516 (ptm) cc_final: 0.9261 (ptt) REVERT: B 313 MET cc_start: 0.9489 (tpt) cc_final: 0.9220 (tpp) REVERT: B 747 MET cc_start: 0.7861 (mtm) cc_final: 0.7568 (tmm) REVERT: D 145 MET cc_start: 0.8269 (mmp) cc_final: 0.7875 (tpp) REVERT: F 122 MET cc_start: 0.9473 (tmm) cc_final: 0.9222 (mtp) REVERT: G 46 LEU cc_start: 0.4862 (mt) cc_final: 0.4431 (mt) REVERT: G 51 TYR cc_start: 0.3249 (t80) cc_final: 0.2997 (t80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2432 time to fit residues: 68.8972 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 : 1.648 ------------------------------------------------------------------------------- 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: 4.9990 chunk 325 optimal weight: 0.4980 chunk 112 optimal weight: 40.0000 chunk 93 optimal weight: 40.0000 chunk 217 optimal weight: 30.0000 chunk 417 optimal weight: 8.9990 chunk 322 optimal weight: 0.2980 chunk 18 optimal weight: 30.0000 chunk 232 optimal weight: 9.9990 chunk 392 optimal weight: 50.0000 chunk 483 optimal weight: 8.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN ** 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 ** 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 C 31 ASN C 79 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 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 = 0.3411 r_free = 0.3411 target = 0.039541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.025466 restraints weight = 836931.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.023796 restraints weight = 684319.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.024020 restraints weight = 548335.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.024104 restraints weight = 459045.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.024299 restraints weight = 417243.678| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45478 Z= 0.154 Angle : 0.626 11.669 62835 Z= 0.339 Chirality : 0.042 0.231 7100 Planarity : 0.004 0.105 6914 Dihedral : 24.979 178.492 8828 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4595 helix: 0.56 (0.12), residues: 1830 sheet: -2.06 (0.24), residues: 433 loop : -2.05 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 348 TYR 0.022 0.001 TYR G 51 PHE 0.021 0.001 PHE B1146 TRP 0.010 0.001 TRP A 954 HIS 0.007 0.001 HIS B 984 Details of bonding type rmsd covalent geometry : bond 0.00328 (45456) covalent geometry : angle 0.62545 (62826) hydrogen bonds : bond 0.05074 ( 1891) hydrogen bonds : angle 4.74308 ( 5035) metal coordination : bond 0.00737 ( 22) metal coordination : angle 2.49425 ( 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 160 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.285 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 746 MET cc_start: 0.8329 (ttm) cc_final: 0.8057 (mtt) REVERT: A 873 MET cc_start: 0.5243 (mmp) cc_final: 0.4996 (mmp) REVERT: A 1209 MET cc_start: 0.6381 (tmm) cc_final: 0.5748 (ttm) REVERT: A 1368 MET cc_start: 0.9527 (ptm) cc_final: 0.9257 (ptt) REVERT: B 313 MET cc_start: 0.9507 (tpt) cc_final: 0.9247 (tpp) REVERT: B 747 MET cc_start: 0.8088 (mtm) cc_final: 0.7775 (tmm) REVERT: D 145 MET cc_start: 0.8220 (mmp) cc_final: 0.7813 (tpp) REVERT: F 122 MET cc_start: 0.9484 (tmm) cc_final: 0.9237 (mtp) REVERT: G 46 LEU cc_start: 0.4713 (mt) cc_final: 0.4128 (mt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2432 time to fit residues: 68.0067 Evaluate side-chains 149 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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: 20.0000 chunk 436 optimal weight: 0.3980 chunk 85 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 450 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 chunk 258 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 82 HIS ** 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 503 GLN A 736 ASN ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 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 = 0.3424 r_free = 0.3424 target = 0.039800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.025628 restraints weight = 831191.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.023710 restraints weight = 676347.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.023991 restraints weight = 549197.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.024240 restraints weight = 457705.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.024302 restraints weight = 395877.533| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45478 Z= 0.135 Angle : 0.608 10.832 62835 Z= 0.329 Chirality : 0.041 0.235 7100 Planarity : 0.004 0.105 6914 Dihedral : 24.828 178.800 8828 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.12), residues: 4595 helix: 0.69 (0.12), residues: 1840 sheet: -1.95 (0.23), residues: 453 loop : -1.95 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 344 TYR 0.014 0.001 TYR E 187 PHE 0.018 0.001 PHE B1146 TRP 0.010 0.001 TRP A1304 HIS 0.008 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00288 (45456) covalent geometry : angle 0.60630 (62826) hydrogen bonds : bond 0.04536 ( 1891) hydrogen bonds : angle 4.61988 ( 5035) metal coordination : bond 0.00635 ( 22) metal coordination : angle 3.71601 ( 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 160 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.166 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 873 MET cc_start: 0.5380 (mmp) cc_final: 0.5134 (mmp) REVERT: A 1209 MET cc_start: 0.6282 (tmm) cc_final: 0.5641 (ttm) REVERT: A 1317 MET cc_start: 0.8950 (ptp) cc_final: 0.8729 (ptp) REVERT: A 1368 MET cc_start: 0.9531 (ptm) cc_final: 0.9257 (ptt) REVERT: B 313 MET cc_start: 0.9511 (tpt) cc_final: 0.9260 (tpp) REVERT: B 747 MET cc_start: 0.8077 (mtm) cc_final: 0.7736 (tmm) REVERT: B 809 MET cc_start: 0.8809 (pmm) cc_final: 0.8426 (pmm) REVERT: D 145 MET cc_start: 0.8270 (mmp) cc_final: 0.7862 (tpp) REVERT: G 46 LEU cc_start: 0.4640 (mt) cc_final: 0.4236 (mt) REVERT: G 51 TYR cc_start: 0.3006 (t80) cc_final: 0.2723 (t80) REVERT: H 97 MET cc_start: 0.9610 (mmp) cc_final: 0.9378 (mmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2347 time to fit residues: 65.0787 Evaluate side-chains 148 residues out of total 4071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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: 20.0000 chunk 365 optimal weight: 9.9990 chunk 429 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 392 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 HIS ** 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 736 ASN ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN A1354 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN B1097 HIS ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 79 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 82 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 = 0.3397 r_free = 0.3397 target = 0.039176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.025489 restraints weight = 852275.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.023620 restraints weight = 682236.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.023763 restraints weight = 549240.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.023901 restraints weight = 467511.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.024075 restraints weight = 418877.960| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 45478 Z= 0.179 Angle : 0.644 11.292 62835 Z= 0.348 Chirality : 0.042 0.254 7100 Planarity : 0.005 0.101 6914 Dihedral : 24.935 177.970 8828 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.12), residues: 4595 helix: 0.61 (0.12), residues: 1830 sheet: -2.05 (0.23), residues: 467 loop : -1.98 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 344 TYR 0.022 0.001 TYR F 137 PHE 0.020 0.001 PHE B1146 TRP 0.012 0.002 TRP A1304 HIS 0.008 0.001 HIS B 984 Details of bonding type rmsd covalent geometry : bond 0.00378 (45456) covalent geometry : angle 0.64234 (62826) hydrogen bonds : bond 0.05731 ( 1891) hydrogen bonds : angle 4.76567 ( 5035) metal coordination : bond 0.00796 ( 22) metal coordination : angle 3.65260 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13292.32 seconds wall clock time: 228 minutes 21.74 seconds (13701.74 seconds total)