Starting phenix.real_space_refine on Mon Sep 30 07:00:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syo_25535/09_2024/7syo_25535.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syo_25535/09_2024/7syo_25535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syo_25535/09_2024/7syo_25535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syo_25535/09_2024/7syo_25535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syo_25535/09_2024/7syo_25535.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syo_25535/09_2024/7syo_25535.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1862 5.49 5 S 180 5.16 5 C 42435 2.51 5 N 14511 2.21 5 O 19856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78846 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 143, 'rna2p_pyr': 112, 'rna3p_pur': 754, 'rna3p_pyr': 688} Link IDs: {'rna2p': 254, 'rna3p': 1442} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 956 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "z" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3550 Classifications: {'RNA': 166} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 15, 'rna3p_pur': 73, 'rna3p_pyr': 65} Link IDs: {'rna2p': 28, 'rna3p': 137} Chain breaks: 1 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: "g" 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 66495 SG CYS b 23 95.557 132.809 136.148 1.00 79.33 S ATOM 66516 SG CYS b 26 98.893 133.397 139.103 1.00 80.74 S ATOM 66899 SG CYS b 74 97.027 130.838 137.187 1.00 75.08 S ATOM 66918 SG CYS b 77 97.872 131.849 139.200 1.00 74.77 S ATOM 69560 SG CYS g 121 143.198 108.470 250.106 1.00733.67 S ATOM 69596 SG CYS g 126 141.459 105.417 248.394 1.00747.77 S ATOM 69714 SG CYS g 141 142.665 109.029 246.994 1.00646.28 S ATOM 69733 SG CYS g 144 139.768 107.512 247.515 1.00666.72 S Time building chain proxies: 31.62, per 1000 atoms: 0.40 Number of scatterers: 78846 At special positions: 0 Unit cell: (232.75, 197.6, 269.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 180 16.00 P 1862 15.00 O 19856 8.00 N 14511 7.00 C 42435 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: 13.99 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " Number of angles added : 12 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9066 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 58 sheets defined 34.0% alpha, 15.2% beta 468 base pairs and 925 stacking pairs defined. Time for finding SS restraints: 24.56 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.954A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.670A pdb=" N GLY B 45 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.963A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.982A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.716A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.724A pdb=" N MET C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.560A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.990A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 233 through 246 removed outlier: 3.551A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.677A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 5.194A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 removed outlier: 3.607A pdb=" N TRP F 18 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 removed outlier: 4.061A pdb=" N GLU F 40 " --> pdb=" O LYS F 37 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS F 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 37 through 41' Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 59 through 66 Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 247 through 263 removed outlier: 4.287A pdb=" N GLY F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 36 removed outlier: 4.100A pdb=" N LEU G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN G 36 " --> pdb=" O ILE G 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 36' Processing helix chain 'G' and resid 61 through 66 Processing helix chain 'G' and resid 67 through 75 Processing helix chain 'G' and resid 86 through 105 removed outlier: 3.676A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 Processing helix chain 'G' and resid 142 through 162 removed outlier: 3.654A pdb=" N VAL G 147 " --> pdb=" O PRO G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 173 through 178 removed outlier: 3.589A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 173 through 178' Processing helix chain 'G' and resid 179 through 182 removed outlier: 3.536A pdb=" N LYS G 182 " --> pdb=" O ASN G 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 179 through 182' Processing helix chain 'G' and resid 188 through 203 Processing helix chain 'H' and resid 22 through 28 removed outlier: 3.509A pdb=" N ARG H 25 " --> pdb=" O ARG H 22 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR H 26 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.686A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 Processing helix chain 'I' and resid 68 through 74 removed outlier: 3.745A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 3.747A pdb=" N LEU I 79 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.161A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.704A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 118 Processing helix chain 'J' and resid 133 through 139 removed outlier: 4.483A pdb=" N LEU J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 4.491A pdb=" N LYS J 148 " --> pdb=" O LYS J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 61 removed outlier: 4.095A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 Processing helix chain 'K' and resid 93 through 98 removed outlier: 3.813A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 4.066A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 removed outlier: 3.562A pdb=" N VAL K 128 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN K 132 " --> pdb=" O VAL K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 154 removed outlier: 3.573A pdb=" N GLN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 186 removed outlier: 4.225A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS K 176 " --> pdb=" O ARG K 172 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY K 186 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 16 removed outlier: 3.664A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 55 Processing helix chain 'L' and resid 72 through 84 removed outlier: 3.753A pdb=" N HIS L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.837A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 removed outlier: 4.488A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.717A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 130 removed outlier: 3.872A pdb=" N CYS N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.524A pdb=" N GLY O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.625A pdb=" N ILE O 50 " --> pdb=" O THR O 46 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 3.676A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 132 removed outlier: 4.287A pdb=" N ARG O 127 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 62 removed outlier: 4.058A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 62' Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.019A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 5.289A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 47 removed outlier: 3.573A pdb=" N ARG Q 47 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'Q' and resid 108 through 112 removed outlier: 4.343A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 119 removed outlier: 3.942A pdb=" N GLU Q 118 " --> pdb=" O TYR Q 115 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE Q 119 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 115 through 119' Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.612A pdb=" N ARG R 62 " --> pdb=" O GLY R 59 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA R 64 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 100 removed outlier: 4.226A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 116 removed outlier: 4.059A pdb=" N GLN R 114 " --> pdb=" O ASP R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'T' and resid 43 through 48 removed outlier: 3.586A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 11 through 26 removed outlier: 4.069A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 28 through 46 Processing helix chain 'V' and resid 94 through 104 removed outlier: 3.945A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.784A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY W 63 " --> pdb=" O ILE W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 76 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 84 through 94 removed outlier: 4.298A pdb=" N LYS X 88 " --> pdb=" O LYS X 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU X 94 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 31 removed outlier: 3.822A pdb=" N ALA Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS Y 31 " --> pdb=" O TYR Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 39 removed outlier: 3.895A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 94 removed outlier: 4.289A pdb=" N ASN Y 92 " --> pdb=" O GLY Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 4.124A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.615A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.665A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 Processing helix chain 'Z' and resid 121 through 126 Processing helix chain 'a' and resid 51 through 62 Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 79 Processing helix chain 'c' and resid 11 through 18 Processing helix chain 'e' and resid 3 through 7 removed outlier: 3.512A pdb=" N TYR e 7 " --> pdb=" O GLN e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 46 through 51 Processing helix chain 'f' and resid 83 through 88 removed outlier: 3.699A pdb=" N GLY f 87 " --> pdb=" O GLY f 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 115 removed outlier: 3.882A pdb=" N GLN f 110 " --> pdb=" O LYS f 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'n' and resid 2 through 25 removed outlier: 3.556A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 54 through 58 Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.562A pdb=" N ARG E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.585A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY E 111 " --> pdb=" O TYR E 107 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.550A pdb=" N ALA E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.926A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 39 removed outlier: 3.508A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 75 through 83 Processing helix chain 'S' and resid 99 through 108 removed outlier: 3.615A pdb=" N LYS S 103 " --> pdb=" O ASP S 99 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.765A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 28 through 34 removed outlier: 3.753A pdb=" N VAL C 33 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.536A pdb=" N ASP C 104 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.641A pdb=" N VAL C 140 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 211 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 103 through 108 removed outlier: 4.015A pdb=" N LYS D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY D 131 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 105 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 129 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE D 127 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 103 through 108 removed outlier: 4.015A pdb=" N LYS D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY D 131 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 105 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 129 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE D 127 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 144 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 126 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS D 142 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 140 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.766A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU D 195 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY D 186 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 193 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 191 " --> pdb=" O CYS D 188 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 223 " --> pdb=" O ILE D 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AA9, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.554A pdb=" N LYS F 122 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE F 162 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 126 through 131 removed outlier: 4.115A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 139 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 147 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 217 through 221 removed outlier: 7.751A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB4, first strand: chain 'G' and resid 123 through 127 removed outlier: 3.562A pdb=" N GLN G 137 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.830A pdb=" N VAL H 108 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.528A pdb=" N VAL H 73 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 160 through 161 removed outlier: 4.077A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 48 through 52 removed outlier: 3.753A pdb=" N VAL I 93 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 184 through 188 removed outlier: 4.652A pdb=" N ASP I 184 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.620A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.691A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL J 81 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU J 103 " --> pdb=" O VAL J 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AC4, first strand: chain 'L' and resid 21 through 23 removed outlier: 4.332A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP L 69 " --> pdb=" O MET L 21 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 72 through 79 removed outlier: 6.911A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET M 109 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 91 through 93 removed outlier: 3.854A pdb=" N TYR M 92 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG M 105 " --> pdb=" O TYR M 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.590A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 52 through 53 removed outlier: 6.371A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 54 through 57 removed outlier: 3.718A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 16 through 17 Processing sheet with id=AD2, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.587A pdb=" N THR R 20 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE R 68 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS R 33 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL R 70 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 13 through 14 Processing sheet with id=AD4, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.795A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AD6, first strand: chain 'V' and resid 85 through 92 Processing sheet with id=AD7, first strand: chain 'V' and resid 63 through 66 removed outlier: 3.837A pdb=" N ILE V 63 " --> pdb=" O PHE V 80 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE V 80 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 35 through 39 removed outlier: 3.822A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.961A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY X 127 " --> pdb=" O VAL X 103 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL X 103 " --> pdb=" O GLY X 127 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY X 109 " --> pdb=" O THR X 106 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 128 through 129 removed outlier: 6.584A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY Y 49 " --> pdb=" O VAL Y 100 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL Y 122 " --> pdb=" O PHE Y 84 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 6 through 15 removed outlier: 5.009A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET Z 23 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL Z 27 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 97 through 101 removed outlier: 3.570A pdb=" N THR a 110 " --> pdb=" O LYS a 98 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AE5, first strand: chain 'b' and resid 36 through 43 removed outlier: 4.129A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.733A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 64 through 65 Processing sheet with id=AE8, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.866A pdb=" N CYS d 27 " --> pdb=" O THR d 21 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE d 42 " --> pdb=" O VAL d 32 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.866A pdb=" N CYS d 27 " --> pdb=" O THR d 21 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR d 15 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.681A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 139 through 140 removed outlier: 4.542A pdb=" N HIS g 139 " --> pdb=" O TYR g 148 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR g 148 " --> pdb=" O HIS g 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'h' and resid 5 through 6 removed outlier: 3.509A pdb=" N THR h 6 " --> pdb=" O GLN h 311 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'h' and resid 5 through 6 removed outlier: 3.509A pdb=" N THR h 6 " --> pdb=" O GLN h 311 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 18 through 22 removed outlier: 3.503A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE h 41 " --> pdb=" O SER h 33 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 66 through 71 removed outlier: 4.154A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.705A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN h 133 " --> pdb=" O CYS h 138 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS h 138 " --> pdb=" O ASN h 133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 153 through 156 removed outlier: 3.946A pdb=" N ILE h 165 " --> pdb=" O TRP h 177 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL h 174 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN h 187 " --> pdb=" O VAL h 174 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL h 176 " --> pdb=" O LYS h 185 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 195 through 200 Processing sheet with id=AG1, first strand: chain 'h' and resid 239 through 240 removed outlier: 3.596A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE h 258 " --> pdb=" O ASP h 268 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.948A pdb=" N LEU E 51 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE E 49 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL E 39 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.948A pdb=" N LEU E 51 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE E 49 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL E 39 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU E 89 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 147 through 155 removed outlier: 3.536A pdb=" N LYS E 148 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY E 140 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N CYS E 134 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET E 189 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS E 141 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL E 181 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 182 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL E 175 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 184 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL E 186 " --> pdb=" O ALA E 171 " (cutoff:3.500A) 1318 hydrogen bonds defined for protein. 3759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1187 hydrogen bonds 2016 hydrogen bond angles 0 basepair planarities 468 basepair parallelities 925 stacking parallelities Total time for adding SS restraints: 64.32 Time building geometry restraints manager: 17.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 17458 1.34 - 1.46: 29667 1.46 - 1.58: 33092 1.58 - 1.70: 3709 1.70 - 1.83: 274 Bond restraints: 84200 Sorted by residual: bond pdb=" C THR S 130 " pdb=" N PRO S 131 " ideal model delta sigma weight residual 1.333 1.357 -0.023 1.01e-02 9.80e+03 5.32e+00 bond pdb=" CA PRO L 86 " pdb=" C PRO L 86 " ideal model delta sigma weight residual 1.517 1.503 0.014 6.70e-03 2.23e+04 4.40e+00 bond pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " ideal model delta sigma weight residual 1.427 1.458 -0.031 1.50e-02 4.44e+03 4.18e+00 bond pdb=" CB ASP S 101 " pdb=" CG ASP S 101 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.05e+00 bond pdb=" CA SER G 75 " pdb=" C SER G 75 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.80e-02 3.09e+03 3.43e+00 ... (remaining 84195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 120760 2.98 - 5.95: 1536 5.95 - 8.93: 254 8.93 - 11.91: 40 11.91 - 14.88: 7 Bond angle restraints: 122597 Sorted by residual: angle pdb=" C VAL d 6 " pdb=" N GLN d 7 " pdb=" CA GLN d 7 " ideal model delta sigma weight residual 121.20 130.56 -9.36 1.40e+00 5.10e-01 4.47e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 128.27 -8.07 1.50e+00 4.44e-01 2.90e+01 angle pdb=" C LEU T 16 " pdb=" N ASN T 17 " pdb=" CA ASN T 17 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.78e+01 angle pdb=" CA GLU G 195 " pdb=" CB GLU G 195 " pdb=" CG GLU G 195 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CB MET U 88 " pdb=" CG MET U 88 " pdb=" SD MET U 88 " ideal model delta sigma weight residual 112.70 127.58 -14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 122592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 48583 36.00 - 71.99: 4555 71.99 - 107.99: 599 107.99 - 143.98: 9 143.98 - 179.98: 30 Dihedral angle restraints: 53776 sinusoidal: 39720 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual -160.00 -2.55 -157.45 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual -160.00 -3.02 -156.98 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual 200.00 46.29 153.71 1 1.50e+01 4.44e-03 8.09e+01 ... (remaining 53773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 14480 0.096 - 0.192: 679 0.192 - 0.288: 43 0.288 - 0.385: 11 0.385 - 0.481: 1 Chirality restraints: 15214 Sorted by residual: chirality pdb=" CB ILE F 45 " pdb=" CA ILE F 45 " pdb=" CG1 ILE F 45 " pdb=" CG2 ILE F 45 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CB ILE C 189 " pdb=" CA ILE C 189 " pdb=" CG1 ILE C 189 " pdb=" CG2 ILE C 189 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB VAL R 100 " pdb=" CA VAL R 100 " pdb=" CG1 VAL R 100 " pdb=" CG2 VAL R 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 15211 not shown) Planarity restraints: 8638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL O 22 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO O 23 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO O 23 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO O 23 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 597 " 0.036 2.00e-02 2.50e+03 2.50e-02 1.87e+01 pdb=" N9 G 2 597 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G 2 597 " -0.048 2.00e-02 2.50e+03 pdb=" N7 G 2 597 " 0.030 2.00e-02 2.50e+03 pdb=" C5 G 2 597 " 0.017 2.00e-02 2.50e+03 pdb=" C6 G 2 597 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G 2 597 " 0.000 2.00e-02 2.50e+03 pdb=" N1 G 2 597 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 597 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 2 597 " -0.016 2.00e-02 2.50e+03 pdb=" N3 G 2 597 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G 2 597 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 69 " 0.024 2.00e-02 2.50e+03 2.51e-02 1.58e+01 pdb=" CG TRP L 69 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP L 69 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP L 69 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP L 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 69 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP L 69 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 69 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 69 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP L 69 " 0.010 2.00e-02 2.50e+03 ... (remaining 8635 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 11527 2.76 - 3.30: 66467 3.30 - 3.83: 148799 3.83 - 4.37: 168131 4.37 - 4.90: 248396 Nonbonded interactions: 643320 Sorted by model distance: nonbonded pdb=" OG1 THR P 45 " pdb=" O GLU P 51 " model vdw 2.226 3.040 nonbonded pdb=" O2 U z 144 " pdb=" O6 G z 249 " model vdw 2.254 2.432 nonbonded pdb=" O ASP h 107 " pdb=" OG SER h 124 " model vdw 2.266 3.040 nonbonded pdb=" N CYS b 26 " pdb="ZN ZN b 201 " model vdw 2.271 2.310 nonbonded pdb=" O2' A 21332 " pdb=" O GLN E 145 " model vdw 2.276 3.040 ... (remaining 643315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.810 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: 0.080 Extract box with map and model: 2.430 Check model and map are aligned: 0.450 Set scattering table: 0.550 Process input model: 189.830 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.260 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: 0.030 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 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 : 0.003 0.060 84200 Z= 0.219 Angle : 0.854 14.883 122597 Z= 0.420 Chirality : 0.043 0.481 15214 Planarity : 0.007 0.111 8638 Dihedral : 22.275 179.981 44710 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.05 % Allowed : 0.50 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.10), residues: 4821 helix: -1.80 (0.11), residues: 1463 sheet: -1.21 (0.20), residues: 679 loop : -2.26 (0.10), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP L 69 HIS 0.021 0.001 HIS U 91 PHE 0.059 0.002 PHE X 129 TYR 0.056 0.002 TYR G 188 ARG 0.015 0.001 ARG Y 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 996 time to evaluate : 4.300 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: B 37 TYR cc_start: 0.7816 (m-80) cc_final: 0.7464 (m-10) REVERT: B 42 LYS cc_start: 0.6688 (ptmt) cc_final: 0.6479 (pttp) REVERT: B 82 THR cc_start: 0.8906 (p) cc_final: 0.8687 (p) REVERT: B 136 GLU cc_start: 0.7400 (tt0) cc_final: 0.5892 (pm20) REVERT: B 148 CYS cc_start: 0.6325 (t) cc_final: 0.5949 (t) REVERT: B 170 SER cc_start: 0.6752 (m) cc_final: 0.6535 (p) REVERT: B 185 MET cc_start: 0.8363 (tpp) cc_final: 0.7713 (mmm) REVERT: B 196 GLU cc_start: 0.7868 (pp20) cc_final: 0.7314 (pm20) REVERT: B 198 MET cc_start: 0.7236 (mtt) cc_final: 0.6662 (tpt) REVERT: C 42 ARG cc_start: 0.6802 (mmm160) cc_final: 0.5807 (ttm-80) REVERT: C 76 ASN cc_start: 0.8238 (p0) cc_final: 0.7319 (p0) REVERT: C 78 GLU cc_start: 0.4894 (tt0) cc_final: 0.4177 (tt0) REVERT: C 85 LYS cc_start: 0.8632 (mttm) cc_final: 0.8390 (mmtm) REVERT: C 110 MET cc_start: 0.6083 (mpp) cc_final: 0.5363 (ptp) REVERT: C 113 MET cc_start: 0.4251 (mmm) cc_final: 0.3793 (mtt) REVERT: C 120 MET cc_start: 0.7582 (tmm) cc_final: 0.6665 (tmm) REVERT: C 150 ILE cc_start: 0.7610 (mp) cc_final: 0.7090 (mm) REVERT: C 173 THR cc_start: 0.5955 (t) cc_final: 0.5426 (m) REVERT: D 105 GLU cc_start: 0.6935 (pm20) cc_final: 0.6675 (mm-30) REVERT: D 130 ILE cc_start: 0.6504 (tp) cc_final: 0.6239 (tp) REVERT: D 134 ASN cc_start: 0.5840 (t0) cc_final: 0.5237 (t0) REVERT: D 166 ARG cc_start: 0.5810 (ptt180) cc_final: 0.5218 (ttp-170) REVERT: D 176 LYS cc_start: 0.8792 (mttm) cc_final: 0.8506 (mtmm) REVERT: D 241 PHE cc_start: 0.8292 (t80) cc_final: 0.7871 (t80) REVERT: D 248 TYR cc_start: 0.5333 (t80) cc_final: 0.4667 (t80) REVERT: F 47 PHE cc_start: 0.7656 (t80) cc_final: 0.7265 (t80) REVERT: F 66 MET cc_start: 0.5487 (ttp) cc_final: 0.5270 (mmm) REVERT: F 113 ARG cc_start: 0.6583 (mtt90) cc_final: 0.5930 (mtp-110) REVERT: F 164 LEU cc_start: 0.8546 (mt) cc_final: 0.8292 (mt) REVERT: F 171 ASP cc_start: 0.7499 (t0) cc_final: 0.5807 (m-30) REVERT: F 183 VAL cc_start: 0.8206 (p) cc_final: 0.7120 (p) REVERT: F 207 VAL cc_start: 0.8337 (p) cc_final: 0.7605 (t) REVERT: F 212 ASP cc_start: 0.7898 (t70) cc_final: 0.7478 (t70) REVERT: F 250 GLU cc_start: 0.6103 (pm20) cc_final: 0.5758 (tt0) REVERT: G 45 TYR cc_start: 0.6336 (m-80) cc_final: 0.6107 (m-10) REVERT: G 103 LEU cc_start: 0.8093 (mt) cc_final: 0.7576 (tt) REVERT: G 126 THR cc_start: 0.8676 (t) cc_final: 0.8322 (p) REVERT: G 130 ARG cc_start: 0.4939 (mmp80) cc_final: 0.3230 (tpt90) REVERT: G 204 ARG cc_start: 0.5622 (ttp-170) cc_final: 0.4826 (ttp-170) REVERT: H 1 MET cc_start: 0.7231 (ttm) cc_final: 0.6867 (ttm) REVERT: H 68 LEU cc_start: 0.7935 (mp) cc_final: 0.7414 (tt) REVERT: H 72 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7267 (tpp80) REVERT: H 205 GLU cc_start: 0.6527 (tp30) cc_final: 0.5957 (pt0) REVERT: H 222 GLU cc_start: 0.6242 (pp20) cc_final: 0.5957 (tm-30) REVERT: I 19 PHE cc_start: 0.5904 (m-80) cc_final: 0.5703 (m-80) REVERT: I 41 ARG cc_start: 0.6470 (mtm110) cc_final: 0.5891 (tpt170) REVERT: I 80 VAL cc_start: 0.7624 (t) cc_final: 0.7394 (t) REVERT: I 84 GLU cc_start: 0.6763 (tp30) cc_final: 0.6398 (pt0) REVERT: I 93 VAL cc_start: 0.6767 (m) cc_final: 0.6388 (m) REVERT: I 97 GLN cc_start: 0.6398 (tp40) cc_final: 0.5332 (tm-30) REVERT: I 167 GLU cc_start: 0.6701 (tt0) cc_final: 0.6172 (pt0) REVERT: J 17 LYS cc_start: 0.7429 (ptpp) cc_final: 0.6823 (mtpt) REVERT: J 37 LYS cc_start: 0.8228 (tppt) cc_final: 0.7847 (tppt) REVERT: J 94 LYS cc_start: 0.6968 (mtpt) cc_final: 0.6582 (mttt) REVERT: J 105 ASP cc_start: 0.7121 (t70) cc_final: 0.6708 (t70) REVERT: J 145 ILE cc_start: 0.8323 (mp) cc_final: 0.8059 (tp) REVERT: J 175 ILE cc_start: 0.7302 (mp) cc_final: 0.7045 (mm) REVERT: J 186 ASP cc_start: 0.5783 (t0) cc_final: 0.4176 (m-30) REVERT: K 27 GLN cc_start: 0.8306 (tp40) cc_final: 0.8028 (tp-100) REVERT: K 34 GLU cc_start: 0.6477 (tp30) cc_final: 0.6116 (tp30) REVERT: K 97 ILE cc_start: 0.7579 (pt) cc_final: 0.7310 (pt) REVERT: L 46 MET cc_start: 0.6436 (mmt) cc_final: 0.6199 (mmp) REVERT: M 10 TYR cc_start: 0.8097 (t80) cc_final: 0.7858 (t80) REVERT: M 49 GLU cc_start: 0.6929 (pp20) cc_final: 0.6728 (pm20) REVERT: M 59 LYS cc_start: 0.4973 (mtmt) cc_final: 0.4711 (mtmt) REVERT: M 71 ARG cc_start: 0.6154 (mtt90) cc_final: 0.5652 (mtt90) REVERT: M 92 TYR cc_start: 0.7656 (p90) cc_final: 0.7264 (p90) REVERT: M 140 PHE cc_start: 0.8117 (m-80) cc_final: 0.7293 (m-80) REVERT: M 146 THR cc_start: 0.4236 (m) cc_final: 0.3776 (m) REVERT: O 36 GLN cc_start: 0.8319 (tt0) cc_final: 0.8104 (tt0) REVERT: O 54 LEU cc_start: 0.8461 (mt) cc_final: 0.8242 (mt) REVERT: O 55 ARG cc_start: 0.7075 (ttt180) cc_final: 0.6739 (mmm-85) REVERT: O 117 LEU cc_start: 0.8526 (mp) cc_final: 0.8167 (mt) REVERT: P 51 GLU cc_start: 0.8326 (pp20) cc_final: 0.7753 (pp20) REVERT: P 63 LYS cc_start: 0.4641 (tptt) cc_final: 0.3943 (tmtt) REVERT: Q 21 ASP cc_start: 0.4505 (t0) cc_final: 0.3482 (t0) REVERT: Q 28 MET cc_start: 0.4651 (mpp) cc_final: 0.3762 (mtm) REVERT: Q 64 LYS cc_start: 0.5512 (mmtt) cc_final: 0.5183 (mmmt) REVERT: Q 83 MET cc_start: 0.7407 (tpt) cc_final: 0.7119 (tpp) REVERT: R 106 LYS cc_start: 0.6996 (tttt) cc_final: 0.6390 (mmmt) REVERT: R 132 PHE cc_start: 0.8082 (p90) cc_final: 0.7693 (p90) REVERT: T 38 ARG cc_start: 0.6508 (mtt180) cc_final: 0.5967 (mtt180) REVERT: U 45 LEU cc_start: 0.6841 (mm) cc_final: 0.6626 (tp) REVERT: V 61 LEU cc_start: 0.6811 (mm) cc_final: 0.6555 (mm) REVERT: V 86 LYS cc_start: 0.4755 (tmtt) cc_final: 0.4521 (tptm) REVERT: W 12 TYR cc_start: 0.6165 (p90) cc_final: 0.5963 (p90) REVERT: W 18 SER cc_start: 0.7993 (m) cc_final: 0.7465 (p) REVERT: W 45 ARG cc_start: 0.3402 (mtm180) cc_final: 0.3178 (mtm180) REVERT: X 24 GLN cc_start: 0.7677 (mt0) cc_final: 0.7265 (mt0) REVERT: X 94 LEU cc_start: 0.8195 (mt) cc_final: 0.7980 (mt) REVERT: X 110 ILE cc_start: 0.7294 (mp) cc_final: 0.6715 (mt) REVERT: X 111 MET cc_start: 0.7357 (pmm) cc_final: 0.6820 (pmm) REVERT: X 118 ARG cc_start: 0.6809 (mpp80) cc_final: 0.5919 (mtp180) REVERT: Y 8 ARG cc_start: 0.6449 (mtp-110) cc_final: 0.6034 (mtt180) REVERT: Y 37 LYS cc_start: 0.6024 (ttmm) cc_final: 0.5795 (ttmm) REVERT: Y 72 VAL cc_start: 0.6825 (t) cc_final: 0.6433 (m) REVERT: Y 94 ILE cc_start: 0.8343 (tp) cc_final: 0.7995 (mm) REVERT: Y 114 ASP cc_start: 0.7476 (p0) cc_final: 0.6939 (p0) REVERT: Y 129 SER cc_start: 0.7443 (t) cc_final: 0.7235 (p) REVERT: Y 135 LYS cc_start: 0.8281 (mttt) cc_final: 0.7728 (mmtt) REVERT: Z 18 LEU cc_start: 0.7526 (mt) cc_final: 0.6523 (mt) REVERT: Z 25 ILE cc_start: 0.8195 (mm) cc_final: 0.7916 (tp) REVERT: Z 40 ILE cc_start: 0.8262 (mm) cc_final: 0.7949 (tp) REVERT: Z 64 PHE cc_start: 0.7375 (t80) cc_final: 0.7115 (t80) REVERT: Z 79 LEU cc_start: 0.8105 (mt) cc_final: 0.7598 (pp) REVERT: a 61 GLU cc_start: 0.5996 (tm-30) cc_final: 0.5397 (tt0) REVERT: a 85 ARG cc_start: 0.5229 (ptp90) cc_final: 0.4926 (ptp90) REVERT: b 42 ARG cc_start: 0.7695 (mtp85) cc_final: 0.7153 (ttm110) REVERT: b 43 ASN cc_start: 0.7911 (t0) cc_final: 0.7703 (t0) REVERT: b 63 VAL cc_start: 0.5508 (m) cc_final: 0.5213 (p) REVERT: c 26 GLN cc_start: 0.8461 (pm20) cc_final: 0.8086 (pm20) REVERT: c 55 LEU cc_start: 0.7814 (mt) cc_final: 0.7537 (mp) REVERT: d 34 PHE cc_start: 0.5202 (m-80) cc_final: 0.4667 (m-80) REVERT: d 35 MET cc_start: 0.4608 (mtt) cc_final: 0.4242 (mtm) REVERT: e 27 ARG cc_start: 0.7350 (ptp-110) cc_final: 0.6611 (ptm160) REVERT: e 54 LYS cc_start: 0.5720 (mmtt) cc_final: 0.4580 (mmtt) REVERT: f 107 ARG cc_start: 0.5944 (mtt90) cc_final: 0.5138 (ptp-170) REVERT: h 32 LEU cc_start: 0.6344 (mp) cc_final: 0.5968 (mt) REVERT: h 62 HIS cc_start: 0.5855 (m-70) cc_final: 0.5572 (m-70) REVERT: h 64 HIS cc_start: 0.6383 (t-90) cc_final: 0.5911 (t-90) REVERT: h 89 LEU cc_start: 0.5616 (mt) cc_final: 0.5330 (mt) REVERT: h 145 GLU cc_start: 0.4874 (tp30) cc_final: 0.4616 (tp30) REVERT: h 154 VAL cc_start: 0.6219 (m) cc_final: 0.5874 (p) REVERT: h 177 TRP cc_start: 0.4885 (m100) cc_final: 0.4020 (m100) REVERT: h 184 LEU cc_start: 0.8338 (pt) cc_final: 0.7712 (tt) REVERT: h 217 MET cc_start: 0.5415 (tmm) cc_final: 0.5082 (tmm) REVERT: h 228 TYR cc_start: 0.6204 (p90) cc_final: 0.5944 (m-80) REVERT: h 241 PHE cc_start: 0.3365 (m-10) cc_final: 0.2568 (m-10) REVERT: E 1 MET cc_start: 0.1661 (ttt) cc_final: 0.1461 (ttt) REVERT: E 32 ASP cc_start: 0.5035 (p0) cc_final: 0.4572 (p0) REVERT: E 74 GLN cc_start: 0.5982 (mm-40) cc_final: 0.5464 (tp40) REVERT: S 28 PHE cc_start: 0.6997 (t80) cc_final: 0.6795 (t80) REVERT: S 44 LYS cc_start: 0.7613 (mtpt) cc_final: 0.7367 (ttmt) REVERT: S 53 TYR cc_start: 0.7731 (t80) cc_final: 0.7480 (t80) REVERT: S 107 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6807 (mttp) outliers start: 2 outliers final: 0 residues processed: 998 average time/residue: 0.8046 time to fit residues: 1341.7272 Evaluate side-chains 673 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 673 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 0.0570 chunk 499 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 516 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 314 optimal weight: 0.5980 chunk 384 optimal weight: 7.9990 chunk 598 optimal weight: 9.9990 overall best weight: 2.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN F 112 HIS F 201 HIS G 65 GLN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 ASN K 143 ASN L 7 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN O 123 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 114 GLN T 42 HIS T 87 GLN T 101 ASN U 85 ASN U 91 HIS X 44 HIS ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 GLN d 29 GLN d 45 ASN ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 ASN S 48 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 84200 Z= 0.159 Angle : 0.590 13.818 122597 Z= 0.298 Chirality : 0.035 0.249 15214 Planarity : 0.005 0.070 8638 Dihedral : 23.581 179.967 34598 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.11), residues: 4821 helix: -0.32 (0.13), residues: 1489 sheet: -1.17 (0.19), residues: 752 loop : -2.02 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 259 HIS 0.007 0.001 HIS h 226 PHE 0.019 0.001 PHE I 173 TYR 0.021 0.001 TYR E 120 ARG 0.007 0.001 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 820 time to evaluate : 4.408 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: B 33 GLN cc_start: 0.7715 (mm110) cc_final: 0.7503 (mm110) REVERT: B 66 VAL cc_start: 0.8051 (p) cc_final: 0.7840 (p) REVERT: B 103 PHE cc_start: 0.8264 (t80) cc_final: 0.8031 (t80) REVERT: B 170 SER cc_start: 0.6744 (m) cc_final: 0.6542 (p) REVERT: C 42 ARG cc_start: 0.6840 (mmm160) cc_final: 0.5803 (ttm-80) REVERT: C 99 ASN cc_start: 0.7638 (t0) cc_final: 0.6838 (t0) REVERT: C 110 MET cc_start: 0.5784 (mpp) cc_final: 0.5159 (ptm) REVERT: C 120 MET cc_start: 0.7564 (tmm) cc_final: 0.6899 (tmm) REVERT: C 150 ILE cc_start: 0.7385 (mp) cc_final: 0.7147 (mm) REVERT: C 201 CYS cc_start: 0.4745 (m) cc_final: 0.4383 (m) REVERT: D 105 GLU cc_start: 0.7143 (pm20) cc_final: 0.6663 (mm-30) REVERT: D 117 ARG cc_start: 0.5266 (tpt90) cc_final: 0.4718 (mtp180) REVERT: D 130 ILE cc_start: 0.6672 (tp) cc_final: 0.6436 (tp) REVERT: D 166 ARG cc_start: 0.5791 (ptt180) cc_final: 0.5556 (ptt90) REVERT: D 248 TYR cc_start: 0.5535 (t80) cc_final: 0.5198 (t80) REVERT: F 19 MET cc_start: 0.7090 (tpp) cc_final: 0.6141 (mtp) REVERT: F 47 PHE cc_start: 0.7902 (t80) cc_final: 0.7656 (t80) REVERT: F 62 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7225 (ttpt) REVERT: F 66 MET cc_start: 0.5549 (ttp) cc_final: 0.5295 (mmm) REVERT: F 113 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6126 (mtp-110) REVERT: F 164 LEU cc_start: 0.8474 (mt) cc_final: 0.8213 (mt) REVERT: F 212 ASP cc_start: 0.7901 (t70) cc_final: 0.7440 (t70) REVERT: F 250 GLU cc_start: 0.5911 (pm20) cc_final: 0.5707 (tt0) REVERT: G 78 MET cc_start: 0.5846 (mmp) cc_final: 0.5539 (mmp) REVERT: G 91 ARG cc_start: 0.7164 (ppt170) cc_final: 0.6764 (ptm-80) REVERT: G 103 LEU cc_start: 0.7867 (mt) cc_final: 0.7372 (tt) REVERT: G 104 THR cc_start: 0.8954 (t) cc_final: 0.8716 (t) REVERT: G 126 THR cc_start: 0.8486 (t) cc_final: 0.8026 (m) REVERT: G 204 ARG cc_start: 0.5568 (ttp-170) cc_final: 0.4629 (ttp-170) REVERT: H 1 MET cc_start: 0.7059 (ttm) cc_final: 0.6800 (ttm) REVERT: H 32 MET cc_start: 0.7572 (tpp) cc_final: 0.7281 (tpp) REVERT: H 68 LEU cc_start: 0.8007 (mp) cc_final: 0.7425 (tt) REVERT: H 105 ASN cc_start: 0.8399 (t0) cc_final: 0.7883 (t0) REVERT: H 205 GLU cc_start: 0.6408 (tp30) cc_final: 0.5959 (pt0) REVERT: I 17 ASP cc_start: 0.6243 (t70) cc_final: 0.5854 (m-30) REVERT: I 19 PHE cc_start: 0.5925 (m-80) cc_final: 0.5723 (m-80) REVERT: I 31 GLU cc_start: 0.7096 (tm-30) cc_final: 0.5934 (tp30) REVERT: I 41 ARG cc_start: 0.6528 (mtm110) cc_final: 0.5975 (tpt170) REVERT: I 84 GLU cc_start: 0.6613 (tp30) cc_final: 0.5993 (tp30) REVERT: I 97 GLN cc_start: 0.6243 (tp40) cc_final: 0.5270 (tm-30) REVERT: I 168 HIS cc_start: 0.6888 (p-80) cc_final: 0.6594 (p90) REVERT: J 17 LYS cc_start: 0.7376 (ptpp) cc_final: 0.6369 (ttmt) REVERT: J 84 ASN cc_start: 0.7619 (t0) cc_final: 0.7369 (t0) REVERT: J 94 LYS cc_start: 0.6740 (mtpt) cc_final: 0.6461 (mttt) REVERT: J 186 ASP cc_start: 0.5819 (t0) cc_final: 0.5362 (t70) REVERT: K 34 GLU cc_start: 0.6501 (tp30) cc_final: 0.6155 (tp30) REVERT: K 71 LEU cc_start: 0.8486 (pp) cc_final: 0.8246 (tp) REVERT: L 46 MET cc_start: 0.6519 (mmt) cc_final: 0.6230 (mmp) REVERT: L 70 TYR cc_start: 0.5312 (t80) cc_final: 0.4734 (t80) REVERT: L 78 TYR cc_start: 0.5123 (t80) cc_final: 0.4576 (t80) REVERT: M 49 GLU cc_start: 0.6941 (pp20) cc_final: 0.6656 (pm20) REVERT: M 92 TYR cc_start: 0.7666 (p90) cc_final: 0.7233 (p90) REVERT: M 130 GLU cc_start: 0.7614 (mp0) cc_final: 0.7304 (mp0) REVERT: M 138 VAL cc_start: 0.7974 (t) cc_final: 0.7504 (p) REVERT: O 36 GLN cc_start: 0.8480 (tt0) cc_final: 0.7737 (tt0) REVERT: O 105 ASN cc_start: 0.6166 (m-40) cc_final: 0.5956 (m-40) REVERT: O 117 LEU cc_start: 0.8743 (mp) cc_final: 0.8430 (mp) REVERT: O 120 SER cc_start: 0.8512 (p) cc_final: 0.8173 (p) REVERT: O 132 LYS cc_start: 0.8249 (tppt) cc_final: 0.8036 (mmmt) REVERT: P 51 GLU cc_start: 0.8210 (pp20) cc_final: 0.7427 (pp20) REVERT: P 63 LYS cc_start: 0.4687 (tptt) cc_final: 0.3935 (tmtt) REVERT: P 90 ILE cc_start: 0.7917 (mm) cc_final: 0.7487 (mm) REVERT: Q 83 MET cc_start: 0.7283 (tpt) cc_final: 0.6419 (mmm) REVERT: R 99 TYR cc_start: 0.6644 (m-80) cc_final: 0.6364 (m-10) REVERT: R 106 LYS cc_start: 0.7028 (tttt) cc_final: 0.6490 (mmmt) REVERT: T 141 ARG cc_start: 0.4701 (mmt180) cc_final: 0.2085 (tpt-90) REVERT: U 45 LEU cc_start: 0.7187 (mm) cc_final: 0.6589 (tp) REVERT: V 87 ARG cc_start: 0.4272 (ptm-80) cc_final: 0.3460 (mtm110) REVERT: W 18 SER cc_start: 0.7968 (m) cc_final: 0.7407 (p) REVERT: X 24 GLN cc_start: 0.7640 (mt0) cc_final: 0.7155 (mt0) REVERT: X 42 MET cc_start: 0.8737 (tmm) cc_final: 0.8451 (tmm) REVERT: X 101 PHE cc_start: 0.6417 (m-10) cc_final: 0.5438 (m-10) REVERT: X 110 ILE cc_start: 0.7332 (mp) cc_final: 0.6822 (mt) REVERT: X 111 MET cc_start: 0.6906 (pmm) cc_final: 0.6543 (pmm) REVERT: X 118 ARG cc_start: 0.6705 (mpp80) cc_final: 0.5967 (mtp180) REVERT: Y 129 SER cc_start: 0.7559 (t) cc_final: 0.7278 (p) REVERT: Z 40 ILE cc_start: 0.8360 (mm) cc_final: 0.8019 (tp) REVERT: Z 44 LEU cc_start: 0.7297 (tp) cc_final: 0.7013 (tp) REVERT: Z 79 LEU cc_start: 0.8157 (mt) cc_final: 0.7732 (pp) REVERT: b 42 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7223 (ttm110) REVERT: b 43 ASN cc_start: 0.8275 (t0) cc_final: 0.7879 (t0) REVERT: b 55 GLU cc_start: 0.6250 (tm-30) cc_final: 0.5867 (tp30) REVERT: b 63 VAL cc_start: 0.6132 (m) cc_final: 0.5753 (p) REVERT: d 30 VAL cc_start: 0.7710 (t) cc_final: 0.7462 (p) REVERT: d 68 LEU cc_start: 0.5320 (mp) cc_final: 0.4982 (pt) REVERT: e 37 ASN cc_start: 0.7779 (m-40) cc_final: 0.7233 (t0) REVERT: f 107 ARG cc_start: 0.5591 (mtt90) cc_final: 0.4896 (ptp-170) REVERT: h 184 LEU cc_start: 0.8446 (pt) cc_final: 0.8200 (mp) REVERT: h 241 PHE cc_start: 0.3811 (m-10) cc_final: 0.2849 (m-10) REVERT: E 1 MET cc_start: 0.1921 (ttt) cc_final: 0.1694 (tpp) REVERT: E 32 ASP cc_start: 0.5115 (p0) cc_final: 0.4603 (p0) REVERT: E 68 GLU cc_start: 0.4528 (pp20) cc_final: 0.3952 (mt-10) REVERT: E 74 GLN cc_start: 0.5927 (mm-40) cc_final: 0.5486 (tp40) REVERT: E 173 ARG cc_start: 0.7187 (tpp80) cc_final: 0.6880 (tpp80) REVERT: S 107 LYS cc_start: 0.7277 (mmtt) cc_final: 0.6711 (mtmm) outliers start: 4 outliers final: 0 residues processed: 821 average time/residue: 0.7698 time to fit residues: 1082.6736 Evaluate side-chains 617 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 617 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 498 optimal weight: 2.9990 chunk 407 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 599 optimal weight: 3.9990 chunk 647 optimal weight: 20.0000 chunk 533 optimal weight: 9.9990 chunk 594 optimal weight: 30.0000 chunk 204 optimal weight: 5.9990 chunk 480 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 42 HIS ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 135 HIS U 126 GLN X 44 HIS ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN d 29 GLN e 3 HIS ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 187 ASN h 191 HIS E 179 GLN S 48 ASN S 127 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 84200 Z= 0.179 Angle : 0.591 12.962 122597 Z= 0.297 Chirality : 0.036 0.244 15214 Planarity : 0.005 0.081 8638 Dihedral : 23.562 179.953 34598 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4821 helix: 0.20 (0.13), residues: 1499 sheet: -1.26 (0.19), residues: 737 loop : -1.86 (0.11), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP h 259 HIS 0.009 0.001 HIS D 136 PHE 0.028 0.002 PHE I 173 TYR 0.019 0.002 TYR E 120 ARG 0.016 0.001 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 768 time to evaluate : 4.327 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: B 136 GLU cc_start: 0.7797 (tt0) cc_final: 0.6290 (tp30) REVERT: B 142 LEU cc_start: 0.7731 (tp) cc_final: 0.7486 (tp) REVERT: B 185 MET cc_start: 0.8323 (tpp) cc_final: 0.7966 (tpp) REVERT: B 198 MET cc_start: 0.7107 (mtt) cc_final: 0.6246 (tpt) REVERT: C 42 ARG cc_start: 0.6673 (mmm160) cc_final: 0.5981 (ttm-80) REVERT: C 103 MET cc_start: 0.8054 (tmm) cc_final: 0.7827 (tmm) REVERT: C 110 MET cc_start: 0.5817 (mpp) cc_final: 0.5406 (mtp) REVERT: C 120 MET cc_start: 0.7529 (tmm) cc_final: 0.7013 (tmm) REVERT: C 150 ILE cc_start: 0.7514 (mp) cc_final: 0.7312 (mm) REVERT: C 201 CYS cc_start: 0.4383 (m) cc_final: 0.4167 (m) REVERT: C 224 GLU cc_start: 0.5786 (tp30) cc_final: 0.3642 (pm20) REVERT: D 105 GLU cc_start: 0.7314 (pm20) cc_final: 0.6345 (mm-30) REVERT: D 121 ARG cc_start: 0.6288 (tmm160) cc_final: 0.6050 (tmm160) REVERT: D 169 TYR cc_start: 0.8411 (m-80) cc_final: 0.8142 (m-80) REVERT: D 248 TYR cc_start: 0.5498 (t80) cc_final: 0.5052 (t80) REVERT: F 19 MET cc_start: 0.7203 (tpp) cc_final: 0.6784 (mtp) REVERT: F 62 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7258 (ttmt) REVERT: F 164 LEU cc_start: 0.8596 (mt) cc_final: 0.8347 (mt) REVERT: F 212 ASP cc_start: 0.7722 (t70) cc_final: 0.7378 (t70) REVERT: H 1 MET cc_start: 0.7174 (ttm) cc_final: 0.6926 (ttm) REVERT: H 32 MET cc_start: 0.7663 (tpp) cc_final: 0.7348 (tpp) REVERT: H 68 LEU cc_start: 0.8094 (mp) cc_final: 0.7242 (tt) REVERT: H 103 ASP cc_start: 0.6490 (m-30) cc_final: 0.5994 (m-30) REVERT: H 105 ASN cc_start: 0.8072 (t0) cc_final: 0.7748 (t0) REVERT: I 41 ARG cc_start: 0.6522 (mtm110) cc_final: 0.5922 (tpp-160) REVERT: I 84 GLU cc_start: 0.6728 (tp30) cc_final: 0.6051 (tp30) REVERT: I 167 GLU cc_start: 0.7138 (pt0) cc_final: 0.6794 (tt0) REVERT: I 168 HIS cc_start: 0.6988 (p-80) cc_final: 0.6543 (p90) REVERT: J 17 LYS cc_start: 0.7466 (ptpp) cc_final: 0.6532 (ttmt) REVERT: J 84 ASN cc_start: 0.7650 (t0) cc_final: 0.7442 (t0) REVERT: J 94 LYS cc_start: 0.6750 (mtpt) cc_final: 0.6467 (mttt) REVERT: J 186 ASP cc_start: 0.5945 (t0) cc_final: 0.5733 (t70) REVERT: K 39 ASN cc_start: 0.8259 (p0) cc_final: 0.7843 (m-40) REVERT: K 71 LEU cc_start: 0.8430 (pp) cc_final: 0.8186 (tp) REVERT: L 70 TYR cc_start: 0.5438 (t80) cc_final: 0.4841 (t80) REVERT: M 49 GLU cc_start: 0.6914 (pp20) cc_final: 0.6642 (pm20) REVERT: M 92 TYR cc_start: 0.7687 (p90) cc_final: 0.7303 (p90) REVERT: O 4 MET cc_start: 0.8283 (tpp) cc_final: 0.7996 (tpp) REVERT: O 36 GLN cc_start: 0.8346 (tt0) cc_final: 0.7912 (tt0) REVERT: O 105 ASN cc_start: 0.6209 (m-40) cc_final: 0.5991 (m-40) REVERT: O 132 LYS cc_start: 0.8338 (tppt) cc_final: 0.7934 (mmmt) REVERT: P 52 THR cc_start: 0.6836 (t) cc_final: 0.6410 (m) REVERT: P 63 LYS cc_start: 0.5089 (mmtt) cc_final: 0.4205 (tmtt) REVERT: P 90 ILE cc_start: 0.7909 (mm) cc_final: 0.7498 (mm) REVERT: Q 83 MET cc_start: 0.7284 (tpt) cc_final: 0.7050 (mmm) REVERT: Q 89 MET cc_start: 0.7856 (tpp) cc_final: 0.7316 (mmt) REVERT: R 8 GLN cc_start: 0.4832 (mp10) cc_final: 0.4361 (mm-40) REVERT: R 99 TYR cc_start: 0.6656 (m-80) cc_final: 0.6316 (m-10) REVERT: R 106 LYS cc_start: 0.7072 (tttt) cc_final: 0.6590 (mmmt) REVERT: T 76 GLN cc_start: 0.5431 (pm20) cc_final: 0.5090 (pm20) REVERT: U 45 LEU cc_start: 0.7287 (mm) cc_final: 0.6718 (tp) REVERT: W 28 ASP cc_start: 0.7669 (t0) cc_final: 0.7427 (t0) REVERT: X 24 GLN cc_start: 0.7553 (mt0) cc_final: 0.7260 (mt0) REVERT: X 42 MET cc_start: 0.8721 (tmm) cc_final: 0.8336 (tmm) REVERT: X 71 LYS cc_start: 0.6212 (ptmm) cc_final: 0.5460 (ptmm) REVERT: X 84 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7339 (mmtp) REVERT: X 110 ILE cc_start: 0.7309 (mp) cc_final: 0.6826 (mt) REVERT: X 111 MET cc_start: 0.6515 (pmm) cc_final: 0.6297 (pmm) REVERT: X 118 ARG cc_start: 0.6718 (mpp80) cc_final: 0.5858 (mtp180) REVERT: Y 21 LYS cc_start: 0.8495 (ptpp) cc_final: 0.8294 (pttm) REVERT: Y 99 GLU cc_start: 0.8101 (tp30) cc_final: 0.7679 (mm-30) REVERT: Y 129 SER cc_start: 0.7337 (t) cc_final: 0.6905 (p) REVERT: Z 16 ARG cc_start: 0.6839 (mtm180) cc_final: 0.6450 (tpt170) REVERT: Z 40 ILE cc_start: 0.8413 (mm) cc_final: 0.8072 (tp) REVERT: Z 79 LEU cc_start: 0.8231 (mt) cc_final: 0.7763 (pp) REVERT: b 42 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7168 (ttt-90) REVERT: b 43 ASN cc_start: 0.8384 (t0) cc_final: 0.8042 (t0) REVERT: b 55 GLU cc_start: 0.6302 (tm-30) cc_final: 0.5726 (tp30) REVERT: d 68 LEU cc_start: 0.5420 (mp) cc_final: 0.5094 (pt) REVERT: e 41 GLN cc_start: 0.7147 (mp10) cc_final: 0.6928 (mp-120) REVERT: f 107 ARG cc_start: 0.5602 (mtt90) cc_final: 0.4976 (ptp-170) REVERT: h 241 PHE cc_start: 0.4039 (m-10) cc_final: 0.3155 (m-10) REVERT: h 304 ASP cc_start: 0.6202 (t0) cc_final: 0.5412 (p0) REVERT: E 32 ASP cc_start: 0.5431 (p0) cc_final: 0.4869 (p0) REVERT: E 68 GLU cc_start: 0.4496 (pp20) cc_final: 0.3997 (mt-10) REVERT: S 107 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6823 (mtmm) outliers start: 7 outliers final: 1 residues processed: 770 average time/residue: 0.7842 time to fit residues: 1042.0264 Evaluate side-chains 599 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 598 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 7.9990 chunk 450 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 402 optimal weight: 1.9990 chunk 601 optimal weight: 30.0000 chunk 636 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 570 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN F 112 HIS F 138 HIS F 157 ASN H 186 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS O 123 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN W 29 HIS X 16 ASN ** Y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 187 ASN S 48 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 84200 Z= 0.261 Angle : 0.691 27.860 122597 Z= 0.347 Chirality : 0.039 0.235 15214 Planarity : 0.006 0.082 8638 Dihedral : 23.675 179.823 34598 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4821 helix: 0.18 (0.13), residues: 1475 sheet: -1.37 (0.18), residues: 776 loop : -1.94 (0.11), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 67 HIS 0.011 0.002 HIS C 208 PHE 0.031 0.002 PHE M 62 TYR 0.032 0.002 TYR h 246 ARG 0.013 0.001 ARG f 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 744 time to evaluate : 4.350 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: B 34 MET cc_start: 0.7165 (mmm) cc_final: 0.6616 (mtt) REVERT: B 82 THR cc_start: 0.8996 (p) cc_final: 0.8778 (p) REVERT: B 136 GLU cc_start: 0.7856 (tt0) cc_final: 0.6554 (tp30) REVERT: B 185 MET cc_start: 0.8297 (tpp) cc_final: 0.7811 (tpp) REVERT: C 42 ARG cc_start: 0.5691 (mmm160) cc_final: 0.4567 (ttm-80) REVERT: C 103 MET cc_start: 0.7991 (tmm) cc_final: 0.7639 (tmm) REVERT: C 110 MET cc_start: 0.5725 (mpp) cc_final: 0.5475 (mtp) REVERT: C 201 CYS cc_start: 0.4535 (m) cc_final: 0.4333 (m) REVERT: C 224 GLU cc_start: 0.5670 (tp30) cc_final: 0.3649 (pm20) REVERT: D 82 TYR cc_start: 0.7104 (m-10) cc_final: 0.6713 (m-80) REVERT: D 248 TYR cc_start: 0.5303 (t80) cc_final: 0.5000 (t80) REVERT: F 19 MET cc_start: 0.7386 (tpp) cc_final: 0.7057 (mtp) REVERT: F 164 LEU cc_start: 0.8589 (mt) cc_final: 0.8339 (mt) REVERT: F 183 VAL cc_start: 0.8493 (p) cc_final: 0.8276 (p) REVERT: F 212 ASP cc_start: 0.7798 (t70) cc_final: 0.7212 (p0) REVERT: G 104 THR cc_start: 0.8791 (t) cc_final: 0.8578 (t) REVERT: H 1 MET cc_start: 0.7194 (ttm) cc_final: 0.6974 (ttm) REVERT: H 28 TYR cc_start: 0.7150 (m-80) cc_final: 0.6471 (m-80) REVERT: H 32 MET cc_start: 0.7591 (tpp) cc_final: 0.7213 (tpp) REVERT: H 45 TRP cc_start: 0.6734 (m100) cc_final: 0.6016 (m100) REVERT: H 59 GLN cc_start: 0.7562 (tp40) cc_final: 0.7168 (mp10) REVERT: H 68 LEU cc_start: 0.8090 (mp) cc_final: 0.7435 (tt) REVERT: H 103 ASP cc_start: 0.6459 (m-30) cc_final: 0.5796 (m-30) REVERT: H 105 ASN cc_start: 0.8447 (t0) cc_final: 0.7898 (t0) REVERT: I 41 ARG cc_start: 0.6351 (mtm110) cc_final: 0.5971 (tpt170) REVERT: I 84 GLU cc_start: 0.6634 (tp30) cc_final: 0.5917 (tp30) REVERT: I 168 HIS cc_start: 0.7312 (p-80) cc_final: 0.7112 (p-80) REVERT: J 94 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6645 (mtpt) REVERT: J 109 TYR cc_start: 0.6703 (m-80) cc_final: 0.6299 (m-80) REVERT: K 71 LEU cc_start: 0.8512 (pp) cc_final: 0.8226 (tp) REVERT: L 6 LYS cc_start: 0.6378 (tttp) cc_final: 0.6027 (mmtt) REVERT: L 64 TRP cc_start: 0.5043 (m-10) cc_final: 0.4795 (m-10) REVERT: L 70 TYR cc_start: 0.5403 (t80) cc_final: 0.4898 (t80) REVERT: M 49 GLU cc_start: 0.7160 (pp20) cc_final: 0.6795 (pm20) REVERT: M 82 MET cc_start: 0.6393 (ptp) cc_final: 0.6130 (ptp) REVERT: M 92 TYR cc_start: 0.7810 (p90) cc_final: 0.7577 (p90) REVERT: O 4 MET cc_start: 0.8406 (tpp) cc_final: 0.7907 (tpp) REVERT: O 14 SER cc_start: 0.7432 (p) cc_final: 0.7056 (p) REVERT: O 36 GLN cc_start: 0.8239 (tt0) cc_final: 0.7961 (tt0) REVERT: O 105 ASN cc_start: 0.6297 (m-40) cc_final: 0.6042 (m-40) REVERT: O 120 SER cc_start: 0.8517 (p) cc_final: 0.8244 (p) REVERT: O 132 LYS cc_start: 0.8382 (tppt) cc_final: 0.7982 (tppt) REVERT: P 63 LYS cc_start: 0.4932 (mmtt) cc_final: 0.4292 (tmtt) REVERT: P 90 ILE cc_start: 0.7935 (mm) cc_final: 0.7659 (mm) REVERT: P 143 LYS cc_start: 0.5916 (tmtt) cc_final: 0.5441 (mmmm) REVERT: P 151 LEU cc_start: 0.4854 (pp) cc_final: 0.4140 (tp) REVERT: Q 111 MET cc_start: 0.5307 (tpp) cc_final: 0.4483 (mtm) REVERT: R 8 GLN cc_start: 0.4896 (mp10) cc_final: 0.4551 (mm-40) REVERT: R 97 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7415 (tm-30) REVERT: R 106 LYS cc_start: 0.7060 (tttt) cc_final: 0.6576 (mmmt) REVERT: T 58 GLU cc_start: 0.4106 (pm20) cc_final: 0.3778 (pt0) REVERT: U 45 LEU cc_start: 0.7184 (mm) cc_final: 0.6746 (tp) REVERT: W 11 LEU cc_start: 0.5954 (pt) cc_final: 0.5730 (pt) REVERT: W 12 TYR cc_start: 0.6386 (p90) cc_final: 0.6117 (p90) REVERT: W 28 ASP cc_start: 0.7824 (t0) cc_final: 0.7409 (t0) REVERT: X 42 MET cc_start: 0.8666 (tmm) cc_final: 0.8317 (tmm) REVERT: X 70 ASN cc_start: 0.6775 (m110) cc_final: 0.6116 (m110) REVERT: X 71 LYS cc_start: 0.6470 (ptmm) cc_final: 0.5738 (ptmm) REVERT: X 82 GLN cc_start: 0.7863 (mm-40) cc_final: 0.6856 (mm110) REVERT: X 94 LEU cc_start: 0.8826 (mt) cc_final: 0.8560 (mt) REVERT: X 110 ILE cc_start: 0.7522 (mp) cc_final: 0.7057 (mt) REVERT: Y 16 HIS cc_start: 0.8248 (t-90) cc_final: 0.8004 (t-90) REVERT: Z 16 ARG cc_start: 0.6891 (mtm180) cc_final: 0.6572 (mmm160) REVERT: Z 40 ILE cc_start: 0.8494 (mm) cc_final: 0.8185 (tp) REVERT: Z 114 MET cc_start: 0.6935 (mmt) cc_final: 0.6457 (ttt) REVERT: a 108 ILE cc_start: 0.7549 (mp) cc_final: 0.7334 (mt) REVERT: b 42 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7181 (ttt-90) REVERT: b 43 ASN cc_start: 0.8445 (t0) cc_final: 0.8131 (t0) REVERT: b 55 GLU cc_start: 0.6590 (tm-30) cc_final: 0.5910 (tp30) REVERT: c 18 LYS cc_start: 0.6955 (mtmm) cc_final: 0.6755 (mtmm) REVERT: d 68 LEU cc_start: 0.5326 (mp) cc_final: 0.4978 (pt) REVERT: f 107 ARG cc_start: 0.5520 (mtt90) cc_final: 0.4729 (ptp-170) REVERT: h 241 PHE cc_start: 0.4259 (m-10) cc_final: 0.3679 (m-10) REVERT: E 189 MET cc_start: 0.5698 (ppp) cc_final: 0.5394 (ppp) REVERT: S 107 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6955 (mtmm) outliers start: 4 outliers final: 1 residues processed: 745 average time/residue: 0.7638 time to fit residues: 981.8806 Evaluate side-chains 585 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 584 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 0.5980 chunk 361 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 474 optimal weight: 3.9990 chunk 262 optimal weight: 30.0000 chunk 543 optimal weight: 2.9990 chunk 440 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 571 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 overall best weight: 5.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS F 157 ASN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS W 29 HIS X 16 ASN X 44 HIS ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN h 64 HIS ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 84200 Z= 0.233 Angle : 0.654 26.565 122597 Z= 0.328 Chirality : 0.038 0.237 15214 Planarity : 0.005 0.058 8638 Dihedral : 23.661 179.819 34598 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4821 helix: 0.20 (0.13), residues: 1488 sheet: -1.36 (0.18), residues: 755 loop : -1.94 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP h 259 HIS 0.009 0.001 HIS C 208 PHE 0.019 0.002 PHE M 62 TYR 0.037 0.002 TYR G 188 ARG 0.013 0.001 ARG Y 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 731 time to evaluate : 4.361 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: B 82 THR cc_start: 0.8977 (p) cc_final: 0.8728 (p) REVERT: B 136 GLU cc_start: 0.7817 (tt0) cc_final: 0.6483 (tp30) REVERT: B 185 MET cc_start: 0.8354 (tpp) cc_final: 0.7868 (tpp) REVERT: B 205 ARG cc_start: 0.7509 (mpt-90) cc_final: 0.6679 (mmm-85) REVERT: C 42 ARG cc_start: 0.5538 (mmm160) cc_final: 0.4438 (ttm-80) REVERT: C 103 MET cc_start: 0.8013 (tmm) cc_final: 0.7810 (tmm) REVERT: C 110 MET cc_start: 0.5782 (mpp) cc_final: 0.5532 (mtp) REVERT: C 133 TYR cc_start: 0.4595 (m-80) cc_final: 0.4305 (m-80) REVERT: C 224 GLU cc_start: 0.5971 (tp30) cc_final: 0.3892 (pm20) REVERT: D 105 GLU cc_start: 0.7398 (pm20) cc_final: 0.6523 (pm20) REVERT: D 248 TYR cc_start: 0.5393 (t80) cc_final: 0.4919 (t80) REVERT: F 62 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7457 (tppt) REVERT: F 164 LEU cc_start: 0.8589 (mt) cc_final: 0.8339 (mt) REVERT: F 183 VAL cc_start: 0.8436 (p) cc_final: 0.8235 (p) REVERT: F 212 ASP cc_start: 0.7876 (t70) cc_final: 0.7236 (p0) REVERT: G 104 THR cc_start: 0.8709 (t) cc_final: 0.8495 (t) REVERT: G 204 ARG cc_start: 0.5187 (ttp-170) cc_final: 0.4615 (ttp-110) REVERT: H 32 MET cc_start: 0.7613 (tpp) cc_final: 0.7249 (tpp) REVERT: H 45 TRP cc_start: 0.6446 (m100) cc_final: 0.6085 (m100) REVERT: H 52 ILE cc_start: 0.7052 (tp) cc_final: 0.6714 (tp) REVERT: H 59 GLN cc_start: 0.7597 (tp40) cc_final: 0.7201 (mp10) REVERT: H 68 LEU cc_start: 0.8108 (mp) cc_final: 0.7447 (tt) REVERT: H 103 ASP cc_start: 0.6363 (m-30) cc_final: 0.5849 (m-30) REVERT: H 105 ASN cc_start: 0.8460 (t0) cc_final: 0.7837 (t0) REVERT: I 41 ARG cc_start: 0.6480 (mtm110) cc_final: 0.6177 (tpt170) REVERT: I 84 GLU cc_start: 0.6638 (tp30) cc_final: 0.5940 (tp30) REVERT: I 159 ASP cc_start: 0.5376 (t0) cc_final: 0.5169 (t0) REVERT: J 109 TYR cc_start: 0.6584 (m-80) cc_final: 0.6112 (m-80) REVERT: K 71 LEU cc_start: 0.8500 (pp) cc_final: 0.8217 (tp) REVERT: L 6 LYS cc_start: 0.6458 (tttp) cc_final: 0.6151 (mmtt) REVERT: L 34 GLU cc_start: 0.6369 (pm20) cc_final: 0.6131 (pm20) REVERT: L 78 TYR cc_start: 0.5193 (t80) cc_final: 0.4873 (t80) REVERT: M 49 GLU cc_start: 0.7256 (pp20) cc_final: 0.6869 (pm20) REVERT: M 124 ASP cc_start: 0.6300 (m-30) cc_final: 0.5880 (m-30) REVERT: O 4 MET cc_start: 0.8406 (tpp) cc_final: 0.7828 (tpp) REVERT: O 105 ASN cc_start: 0.6232 (m-40) cc_final: 0.5955 (m-40) REVERT: O 132 LYS cc_start: 0.8274 (tppt) cc_final: 0.7893 (tppt) REVERT: P 63 LYS cc_start: 0.4972 (mmtt) cc_final: 0.4273 (tmtt) REVERT: P 90 ILE cc_start: 0.7849 (mm) cc_final: 0.7515 (mm) REVERT: P 143 LYS cc_start: 0.6020 (tmtt) cc_final: 0.5557 (mmmm) REVERT: P 151 LEU cc_start: 0.4817 (pp) cc_final: 0.4043 (tp) REVERT: Q 61 ARG cc_start: 0.5773 (tpm170) cc_final: 0.5533 (tpp-160) REVERT: Q 83 MET cc_start: 0.7180 (tpt) cc_final: 0.6719 (tpp) REVERT: Q 88 GLU cc_start: 0.7950 (pt0) cc_final: 0.7114 (pm20) REVERT: R 8 GLN cc_start: 0.4978 (mp10) cc_final: 0.4603 (mm-40) REVERT: R 97 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7434 (tm-30) REVERT: R 106 LYS cc_start: 0.6924 (tttt) cc_final: 0.6490 (mmmt) REVERT: U 45 LEU cc_start: 0.7254 (mm) cc_final: 0.6719 (tp) REVERT: W 11 LEU cc_start: 0.5940 (pt) cc_final: 0.5517 (pt) REVERT: W 28 ASP cc_start: 0.7835 (t0) cc_final: 0.7367 (t0) REVERT: X 42 MET cc_start: 0.8654 (tmm) cc_final: 0.8307 (tmm) REVERT: X 71 LYS cc_start: 0.6496 (ptmm) cc_final: 0.5745 (ptmm) REVERT: X 82 GLN cc_start: 0.7720 (mm-40) cc_final: 0.6714 (mm110) REVERT: X 94 LEU cc_start: 0.8800 (mt) cc_final: 0.8531 (mt) REVERT: X 105 THR cc_start: 0.7587 (p) cc_final: 0.7224 (p) REVERT: X 110 ILE cc_start: 0.7506 (mp) cc_final: 0.7006 (mt) REVERT: Y 114 ASP cc_start: 0.7908 (p0) cc_final: 0.7620 (p0) REVERT: Z 13 MET cc_start: 0.6086 (tmm) cc_final: 0.5691 (tmm) REVERT: Z 16 ARG cc_start: 0.6989 (mtm180) cc_final: 0.6582 (mmm160) REVERT: Z 18 LEU cc_start: 0.7380 (mt) cc_final: 0.7042 (mt) REVERT: Z 40 ILE cc_start: 0.8475 (mm) cc_final: 0.8169 (tp) REVERT: Z 114 MET cc_start: 0.6752 (mmt) cc_final: 0.6406 (ttt) REVERT: a 108 ILE cc_start: 0.7563 (mp) cc_final: 0.7343 (mt) REVERT: b 42 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7204 (ttt-90) REVERT: b 43 ASN cc_start: 0.8366 (t0) cc_final: 0.8083 (t0) REVERT: b 55 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6130 (tp30) REVERT: c 26 GLN cc_start: 0.8803 (pm20) cc_final: 0.8568 (pm20) REVERT: d 35 MET cc_start: 0.4763 (mpp) cc_final: 0.4457 (mtm) REVERT: e 27 ARG cc_start: 0.7578 (ptp-110) cc_final: 0.6647 (ptp-110) REVERT: f 107 ARG cc_start: 0.5407 (mtt90) cc_final: 0.4637 (ptp-170) REVERT: h 64 HIS cc_start: 0.6924 (t-90) cc_final: 0.6389 (t-90) REVERT: h 135 LEU cc_start: 0.7234 (mt) cc_final: 0.7000 (pp) REVERT: E 189 MET cc_start: 0.5823 (ppp) cc_final: 0.5397 (ppp) REVERT: S 107 LYS cc_start: 0.7327 (mmtt) cc_final: 0.6876 (mtmm) outliers start: 2 outliers final: 1 residues processed: 732 average time/residue: 0.7512 time to fit residues: 941.7284 Evaluate side-chains 595 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 594 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 7.9990 chunk 573 optimal weight: 0.9990 chunk 125 optimal weight: 30.0000 chunk 373 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 0.3980 chunk 529 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 42 HIS ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS W 29 HIS X 16 ASN X 44 HIS ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 129 ASN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN S 48 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 84200 Z= 0.205 Angle : 0.633 24.438 122597 Z= 0.319 Chirality : 0.038 0.238 15214 Planarity : 0.005 0.069 8638 Dihedral : 23.630 179.993 34598 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4821 helix: 0.21 (0.13), residues: 1502 sheet: -1.39 (0.18), residues: 762 loop : -1.90 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 64 HIS 0.009 0.001 HIS U 91 PHE 0.022 0.002 PHE D 241 TYR 0.019 0.002 TYR G 45 ARG 0.008 0.001 ARG T 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 724 time to evaluate : 4.323 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: B 57 LYS cc_start: 0.8783 (tptt) cc_final: 0.8582 (mmmm) REVERT: B 82 THR cc_start: 0.8963 (p) cc_final: 0.8677 (p) REVERT: B 136 GLU cc_start: 0.7760 (tt0) cc_final: 0.6529 (tp30) REVERT: B 185 MET cc_start: 0.8259 (tpp) cc_final: 0.7695 (tpp) REVERT: B 205 ARG cc_start: 0.7440 (mpt-90) cc_final: 0.6558 (mmm-85) REVERT: C 42 ARG cc_start: 0.5619 (mmm160) cc_final: 0.4537 (ttm-80) REVERT: C 103 MET cc_start: 0.7945 (tmm) cc_final: 0.7707 (tmm) REVERT: C 110 MET cc_start: 0.5907 (mpp) cc_final: 0.5577 (mtp) REVERT: C 224 GLU cc_start: 0.5828 (tp30) cc_final: 0.3756 (pm20) REVERT: D 84 PHE cc_start: 0.7639 (m-80) cc_final: 0.7256 (m-80) REVERT: D 105 GLU cc_start: 0.7435 (pm20) cc_final: 0.6947 (pm20) REVERT: D 248 TYR cc_start: 0.5573 (t80) cc_final: 0.5079 (t80) REVERT: D 263 LYS cc_start: 0.6799 (mtpt) cc_final: 0.6544 (tttm) REVERT: F 62 LYS cc_start: 0.7804 (mmmm) cc_final: 0.7443 (tppt) REVERT: F 164 LEU cc_start: 0.8611 (mt) cc_final: 0.8065 (mm) REVERT: F 183 VAL cc_start: 0.8481 (p) cc_final: 0.8259 (p) REVERT: F 198 ARG cc_start: 0.7817 (ttt90) cc_final: 0.7343 (ttt180) REVERT: F 212 ASP cc_start: 0.7891 (t70) cc_final: 0.7537 (t0) REVERT: G 104 THR cc_start: 0.8710 (t) cc_final: 0.8488 (t) REVERT: H 1 MET cc_start: 0.7331 (ttm) cc_final: 0.6752 (ttp) REVERT: H 28 TYR cc_start: 0.7087 (m-80) cc_final: 0.6866 (m-80) REVERT: H 32 MET cc_start: 0.7487 (tpp) cc_final: 0.7194 (tpp) REVERT: H 45 TRP cc_start: 0.6611 (m100) cc_final: 0.6170 (m100) REVERT: H 59 GLN cc_start: 0.7624 (tp40) cc_final: 0.7210 (mp10) REVERT: H 68 LEU cc_start: 0.8128 (mp) cc_final: 0.7454 (tt) REVERT: H 103 ASP cc_start: 0.6456 (m-30) cc_final: 0.5932 (m-30) REVERT: H 105 ASN cc_start: 0.8460 (t0) cc_final: 0.8213 (t0) REVERT: H 218 LYS cc_start: 0.6296 (tmmt) cc_final: 0.5457 (mmmt) REVERT: I 41 ARG cc_start: 0.6230 (mtm110) cc_final: 0.6008 (tpt170) REVERT: I 84 GLU cc_start: 0.6676 (tp30) cc_final: 0.6009 (tp30) REVERT: I 159 ASP cc_start: 0.5495 (t0) cc_final: 0.5179 (t0) REVERT: J 109 TYR cc_start: 0.6601 (m-80) cc_final: 0.6138 (m-80) REVERT: K 71 LEU cc_start: 0.8524 (pp) cc_final: 0.8263 (tp) REVERT: L 5 LYS cc_start: 0.6889 (tttp) cc_final: 0.6474 (tptt) REVERT: L 6 LYS cc_start: 0.6440 (tttp) cc_final: 0.6180 (mmtt) REVERT: L 34 GLU cc_start: 0.6380 (pm20) cc_final: 0.6130 (pm20) REVERT: L 49 MET cc_start: 0.5819 (mmp) cc_final: 0.5600 (mmp) REVERT: M 11 GLN cc_start: 0.7838 (mm110) cc_final: 0.7286 (mm-40) REVERT: M 49 GLU cc_start: 0.7292 (pp20) cc_final: 0.6932 (pm20) REVERT: M 124 ASP cc_start: 0.6305 (m-30) cc_final: 0.5829 (m-30) REVERT: O 4 MET cc_start: 0.8426 (tpp) cc_final: 0.7796 (tpp) REVERT: O 36 GLN cc_start: 0.8144 (tt0) cc_final: 0.7937 (tt0) REVERT: O 105 ASN cc_start: 0.6177 (m-40) cc_final: 0.5903 (m-40) REVERT: O 132 LYS cc_start: 0.8274 (tppt) cc_final: 0.8004 (tppt) REVERT: P 63 LYS cc_start: 0.4926 (mmtt) cc_final: 0.4298 (tmtt) REVERT: P 90 ILE cc_start: 0.7856 (mm) cc_final: 0.7481 (mm) REVERT: P 143 LYS cc_start: 0.5979 (tmtt) cc_final: 0.5541 (mmmm) REVERT: P 151 LEU cc_start: 0.4672 (pp) cc_final: 0.3885 (tp) REVERT: Q 83 MET cc_start: 0.7012 (tpt) cc_final: 0.6779 (tpp) REVERT: Q 88 GLU cc_start: 0.7734 (pt0) cc_final: 0.7077 (pm20) REVERT: R 8 GLN cc_start: 0.4898 (mp10) cc_final: 0.4572 (mm-40) REVERT: R 97 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7474 (tm-30) REVERT: R 106 LYS cc_start: 0.6966 (tttt) cc_final: 0.6537 (mmmt) REVERT: T 38 ARG cc_start: 0.6626 (mtt180) cc_final: 0.6386 (mtt180) REVERT: T 73 ASN cc_start: 0.7405 (m-40) cc_final: 0.6851 (m-40) REVERT: U 45 LEU cc_start: 0.7237 (mm) cc_final: 0.6718 (tp) REVERT: V 56 MET cc_start: 0.5579 (mmm) cc_final: 0.5335 (tpt) REVERT: W 11 LEU cc_start: 0.5847 (pt) cc_final: 0.5582 (pt) REVERT: X 15 ASN cc_start: 0.8068 (t0) cc_final: 0.7848 (t0) REVERT: X 70 ASN cc_start: 0.6742 (m110) cc_final: 0.6134 (m110) REVERT: X 71 LYS cc_start: 0.6614 (ptmm) cc_final: 0.6088 (tmtt) REVERT: X 94 LEU cc_start: 0.8749 (mt) cc_final: 0.8487 (mt) REVERT: X 105 THR cc_start: 0.7318 (p) cc_final: 0.7050 (p) REVERT: X 110 ILE cc_start: 0.7306 (mp) cc_final: 0.6853 (mt) REVERT: Y 114 ASP cc_start: 0.7935 (p0) cc_final: 0.7559 (p0) REVERT: Z 13 MET cc_start: 0.6154 (tmm) cc_final: 0.5789 (tmm) REVERT: Z 16 ARG cc_start: 0.7053 (mtm180) cc_final: 0.6680 (mmm160) REVERT: Z 18 LEU cc_start: 0.7488 (mt) cc_final: 0.7242 (mt) REVERT: Z 40 ILE cc_start: 0.8471 (mm) cc_final: 0.8155 (tp) REVERT: Z 114 MET cc_start: 0.6615 (mmt) cc_final: 0.6297 (ttt) REVERT: a 108 ILE cc_start: 0.7623 (mp) cc_final: 0.7314 (mt) REVERT: b 42 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7245 (ttt-90) REVERT: b 43 ASN cc_start: 0.8318 (t0) cc_final: 0.8073 (t0) REVERT: b 55 GLU cc_start: 0.6510 (tm-30) cc_final: 0.5913 (tp30) REVERT: c 18 LYS cc_start: 0.6904 (mtmm) cc_final: 0.6623 (mtmm) REVERT: d 35 MET cc_start: 0.4932 (mpp) cc_final: 0.4498 (mtm) REVERT: d 68 LEU cc_start: 0.4802 (mt) cc_final: 0.4533 (pt) REVERT: e 27 ARG cc_start: 0.7672 (ptp-110) cc_final: 0.7147 (ptm160) REVERT: f 107 ARG cc_start: 0.5398 (mtt90) cc_final: 0.4586 (ptp-170) REVERT: h 135 LEU cc_start: 0.7231 (mt) cc_final: 0.7024 (pp) REVERT: h 304 ASP cc_start: 0.6023 (t0) cc_final: 0.5389 (p0) REVERT: E 189 MET cc_start: 0.6017 (ppp) cc_final: 0.5567 (ppp) REVERT: S 107 LYS cc_start: 0.7298 (mmtt) cc_final: 0.6796 (mtmm) outliers start: 4 outliers final: 1 residues processed: 725 average time/residue: 0.7491 time to fit residues: 934.8375 Evaluate side-chains 582 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 360 optimal weight: 7.9990 chunk 536 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 635 optimal weight: 3.9990 chunk 397 optimal weight: 0.9990 chunk 387 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS F 138 HIS F 157 ASN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 142 GLN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS W 29 HIS X 16 ASN X 44 HIS Y 16 HIS ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 129 ASN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 84200 Z= 0.194 Angle : 0.620 23.260 122597 Z= 0.312 Chirality : 0.037 0.284 15214 Planarity : 0.005 0.055 8638 Dihedral : 23.619 179.858 34598 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.07 % Allowed : 2.04 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.12), residues: 4821 helix: 0.31 (0.13), residues: 1497 sheet: -1.35 (0.18), residues: 771 loop : -1.84 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 60 HIS 0.010 0.001 HIS U 91 PHE 0.018 0.002 PHE I 135 TYR 0.024 0.002 TYR G 188 ARG 0.012 0.001 ARG I 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 704 time to evaluate : 4.382 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: B 174 MET cc_start: 0.8053 (mmt) cc_final: 0.7834 (mmt) REVERT: B 177 MET cc_start: 0.8898 (mtm) cc_final: 0.8610 (mtp) REVERT: B 185 MET cc_start: 0.8364 (tpp) cc_final: 0.7763 (tpp) REVERT: B 205 ARG cc_start: 0.7470 (mpt-90) cc_final: 0.6536 (mmm-85) REVERT: C 26 SER cc_start: 0.7612 (p) cc_final: 0.7258 (m) REVERT: C 42 ARG cc_start: 0.5613 (mmm160) cc_final: 0.4558 (ttm-80) REVERT: C 68 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7153 (tm-30) REVERT: C 103 MET cc_start: 0.7908 (tmm) cc_final: 0.7676 (tmm) REVERT: C 110 MET cc_start: 0.5877 (mpp) cc_final: 0.5605 (mtp) REVERT: C 224 GLU cc_start: 0.5705 (tp30) cc_final: 0.3619 (pm20) REVERT: D 105 GLU cc_start: 0.7482 (pm20) cc_final: 0.5895 (mm-30) REVERT: D 117 ARG cc_start: 0.5729 (tpt170) cc_final: 0.5053 (mtp85) REVERT: D 263 LYS cc_start: 0.6842 (mtpt) cc_final: 0.6594 (tttm) REVERT: F 164 LEU cc_start: 0.8603 (mt) cc_final: 0.8054 (mm) REVERT: F 198 ARG cc_start: 0.7835 (ttt90) cc_final: 0.7568 (ttm-80) REVERT: F 212 ASP cc_start: 0.7893 (t70) cc_final: 0.7499 (t0) REVERT: G 88 MET cc_start: 0.7018 (ttt) cc_final: 0.6813 (ttt) REVERT: G 104 THR cc_start: 0.8647 (t) cc_final: 0.8424 (t) REVERT: H 32 MET cc_start: 0.7333 (tpp) cc_final: 0.7099 (tpp) REVERT: H 45 TRP cc_start: 0.6637 (m100) cc_final: 0.6137 (m100) REVERT: H 59 GLN cc_start: 0.7734 (tp40) cc_final: 0.7395 (mp10) REVERT: H 68 LEU cc_start: 0.8121 (mp) cc_final: 0.7427 (tt) REVERT: H 103 ASP cc_start: 0.6525 (m-30) cc_final: 0.6039 (m-30) REVERT: H 105 ASN cc_start: 0.8467 (t0) cc_final: 0.8158 (t0) REVERT: H 218 LYS cc_start: 0.5893 (tmmt) cc_final: 0.5322 (mmmt) REVERT: I 41 ARG cc_start: 0.6336 (mtm110) cc_final: 0.6053 (tpt170) REVERT: I 84 GLU cc_start: 0.6648 (tp30) cc_final: 0.6085 (tp30) REVERT: I 87 PHE cc_start: 0.5860 (t80) cc_final: 0.5609 (t80) REVERT: I 159 ASP cc_start: 0.5551 (t0) cc_final: 0.5170 (t0) REVERT: J 109 TYR cc_start: 0.6573 (m-80) cc_final: 0.6118 (m-80) REVERT: K 71 LEU cc_start: 0.8520 (pp) cc_final: 0.8178 (tp) REVERT: L 5 LYS cc_start: 0.6930 (tttp) cc_final: 0.6577 (tptt) REVERT: L 6 LYS cc_start: 0.6472 (tttp) cc_final: 0.6209 (mmtt) REVERT: L 34 GLU cc_start: 0.6276 (pm20) cc_final: 0.6027 (pm20) REVERT: L 49 MET cc_start: 0.5967 (mmp) cc_final: 0.5707 (mmp) REVERT: L 78 TYR cc_start: 0.4338 (t80) cc_final: 0.4014 (t80) REVERT: M 11 GLN cc_start: 0.7602 (mm110) cc_final: 0.7181 (mm-40) REVERT: M 49 GLU cc_start: 0.7278 (pp20) cc_final: 0.6920 (pm20) REVERT: M 59 LYS cc_start: 0.5362 (mtmt) cc_final: 0.5145 (mtmt) REVERT: O 4 MET cc_start: 0.8407 (tpp) cc_final: 0.7875 (tpp) REVERT: O 105 ASN cc_start: 0.6248 (m-40) cc_final: 0.5926 (m-40) REVERT: O 132 LYS cc_start: 0.8223 (tppt) cc_final: 0.7968 (tppt) REVERT: P 63 LYS cc_start: 0.5031 (mmtt) cc_final: 0.4340 (tmtt) REVERT: P 90 ILE cc_start: 0.7828 (mm) cc_final: 0.7436 (mm) REVERT: P 143 LYS cc_start: 0.5922 (tmtt) cc_final: 0.5571 (mmmm) REVERT: P 151 LEU cc_start: 0.4496 (pp) cc_final: 0.3679 (tp) REVERT: Q 83 MET cc_start: 0.7010 (tpt) cc_final: 0.6723 (tpp) REVERT: Q 88 GLU cc_start: 0.7795 (pt0) cc_final: 0.7136 (pm20) REVERT: R 8 GLN cc_start: 0.4844 (mp10) cc_final: 0.4504 (mm-40) REVERT: R 106 LYS cc_start: 0.6979 (tttt) cc_final: 0.6568 (mmmt) REVERT: T 61 GLU cc_start: 0.6867 (mp0) cc_final: 0.6577 (pp20) REVERT: T 73 ASN cc_start: 0.7459 (m-40) cc_final: 0.6868 (m-40) REVERT: T 101 ASN cc_start: 0.7290 (t0) cc_final: 0.6687 (t0) REVERT: T 134 GLN cc_start: 0.6975 (mp10) cc_final: 0.6727 (mp10) REVERT: U 45 LEU cc_start: 0.7216 (mm) cc_final: 0.6696 (tp) REVERT: V 56 MET cc_start: 0.5538 (mmm) cc_final: 0.5295 (tpt) REVERT: W 11 LEU cc_start: 0.5921 (pt) cc_final: 0.5681 (pt) REVERT: X 15 ASN cc_start: 0.8075 (t0) cc_final: 0.7798 (t0) REVERT: X 42 MET cc_start: 0.8584 (tmm) cc_final: 0.8335 (tmm) REVERT: X 71 LYS cc_start: 0.6504 (ptmm) cc_final: 0.5855 (tmtt) REVERT: X 94 LEU cc_start: 0.8719 (mt) cc_final: 0.8481 (mt) REVERT: X 105 THR cc_start: 0.7366 (p) cc_final: 0.6970 (p) REVERT: X 110 ILE cc_start: 0.7278 (mp) cc_final: 0.6799 (mt) REVERT: Y 114 ASP cc_start: 0.7971 (p0) cc_final: 0.7590 (p0) REVERT: Z 13 MET cc_start: 0.6162 (tmm) cc_final: 0.5738 (tmm) REVERT: Z 16 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6714 (mmm160) REVERT: Z 18 LEU cc_start: 0.7413 (mt) cc_final: 0.7006 (mt) REVERT: Z 40 ILE cc_start: 0.8455 (mm) cc_final: 0.8153 (tp) REVERT: Z 114 MET cc_start: 0.6617 (mmt) cc_final: 0.6100 (ttt) REVERT: a 108 ILE cc_start: 0.7619 (mp) cc_final: 0.7314 (mt) REVERT: b 42 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7180 (ttt-90) REVERT: b 43 ASN cc_start: 0.8302 (t0) cc_final: 0.8068 (t0) REVERT: b 55 GLU cc_start: 0.6481 (tm-30) cc_final: 0.5892 (tp30) REVERT: d 35 MET cc_start: 0.4934 (mpp) cc_final: 0.4524 (mtm) REVERT: e 27 ARG cc_start: 0.7703 (ptp-110) cc_final: 0.6982 (ptp-110) REVERT: f 107 ARG cc_start: 0.5376 (mtt90) cc_final: 0.4616 (ptp-170) REVERT: h 30 MET cc_start: 0.3972 (ptm) cc_final: 0.3546 (ptp) REVERT: h 302 TYR cc_start: 0.4498 (t80) cc_final: 0.3309 (t80) REVERT: h 304 ASP cc_start: 0.6044 (t0) cc_final: 0.4983 (p0) REVERT: E 96 LEU cc_start: 0.7834 (mm) cc_final: 0.7427 (mt) REVERT: E 189 MET cc_start: 0.6142 (ppp) cc_final: 0.5588 (ppp) REVERT: S 107 LYS cc_start: 0.7320 (mmtt) cc_final: 0.6848 (mtmm) outliers start: 3 outliers final: 1 residues processed: 706 average time/residue: 0.7481 time to fit residues: 909.2469 Evaluate side-chains 566 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 565 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 chunk 379 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 403 optimal weight: 2.9990 chunk 432 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 HIS ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 GLN O 58 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 142 GLN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS W 29 HIS X 16 ASN X 44 HIS Y 16 HIS ** Z 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 HIS ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN S 118 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 84200 Z= 0.211 Angle : 0.639 22.323 122597 Z= 0.322 Chirality : 0.038 0.244 15214 Planarity : 0.005 0.059 8638 Dihedral : 23.635 179.969 34598 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4821 helix: 0.27 (0.13), residues: 1496 sheet: -1.41 (0.18), residues: 776 loop : -1.83 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 112 HIS 0.011 0.001 HIS U 91 PHE 0.026 0.002 PHE D 241 TYR 0.020 0.002 TYR L 12 ARG 0.014 0.001 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 688 time to evaluate : 4.932 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: B 34 MET cc_start: 0.7265 (mmm) cc_final: 0.6532 (mtt) REVERT: B 57 LYS cc_start: 0.8860 (tptt) cc_final: 0.8423 (mmtt) REVERT: B 185 MET cc_start: 0.8302 (tpp) cc_final: 0.7956 (tpp) REVERT: C 26 SER cc_start: 0.7611 (p) cc_final: 0.7240 (m) REVERT: C 42 ARG cc_start: 0.5518 (mmm160) cc_final: 0.4446 (ttm-80) REVERT: C 103 MET cc_start: 0.7896 (tmm) cc_final: 0.7652 (tmm) REVERT: D 105 GLU cc_start: 0.7444 (pm20) cc_final: 0.6100 (mm-30) REVERT: D 117 ARG cc_start: 0.5758 (tpt170) cc_final: 0.5150 (mtp85) REVERT: D 263 LYS cc_start: 0.6828 (mtpt) cc_final: 0.6569 (tttm) REVERT: F 19 MET cc_start: 0.7359 (tpp) cc_final: 0.6938 (mtp) REVERT: F 164 LEU cc_start: 0.8663 (mt) cc_final: 0.8108 (mm) REVERT: F 198 ARG cc_start: 0.7884 (ttt90) cc_final: 0.7610 (ttm-80) REVERT: F 212 ASP cc_start: 0.7891 (t70) cc_final: 0.7651 (t0) REVERT: G 88 MET cc_start: 0.7136 (ttt) cc_final: 0.6936 (ttt) REVERT: G 104 THR cc_start: 0.8635 (t) cc_final: 0.8401 (t) REVERT: H 1 MET cc_start: 0.7338 (ttm) cc_final: 0.6956 (ttp) REVERT: H 32 MET cc_start: 0.7318 (tpp) cc_final: 0.7110 (tpp) REVERT: H 45 TRP cc_start: 0.6486 (m100) cc_final: 0.6243 (m100) REVERT: H 59 GLN cc_start: 0.7836 (tp40) cc_final: 0.7514 (mp10) REVERT: H 68 LEU cc_start: 0.8169 (mp) cc_final: 0.7471 (tt) REVERT: H 103 ASP cc_start: 0.6557 (m-30) cc_final: 0.6053 (m-30) REVERT: H 105 ASN cc_start: 0.8526 (t0) cc_final: 0.8002 (t0) REVERT: H 218 LYS cc_start: 0.6034 (tmmt) cc_final: 0.5415 (mmmt) REVERT: I 41 ARG cc_start: 0.6266 (mtm110) cc_final: 0.6024 (tpt170) REVERT: I 84 GLU cc_start: 0.6671 (tp30) cc_final: 0.6169 (tp30) REVERT: I 159 ASP cc_start: 0.5507 (t0) cc_final: 0.5209 (t0) REVERT: J 109 TYR cc_start: 0.6594 (m-80) cc_final: 0.6140 (m-80) REVERT: K 71 LEU cc_start: 0.8476 (pp) cc_final: 0.8272 (tp) REVERT: L 5 LYS cc_start: 0.6882 (tttp) cc_final: 0.6295 (tptp) REVERT: L 6 LYS cc_start: 0.6601 (tttp) cc_final: 0.6294 (mmtt) REVERT: L 12 TYR cc_start: 0.3832 (m-80) cc_final: 0.3423 (m-80) REVERT: L 65 ARG cc_start: 0.3997 (mpt180) cc_final: 0.3456 (mmt-90) REVERT: L 78 TYR cc_start: 0.4515 (t80) cc_final: 0.4180 (t80) REVERT: M 49 GLU cc_start: 0.7425 (pp20) cc_final: 0.7098 (pm20) REVERT: M 82 MET cc_start: 0.6517 (ptp) cc_final: 0.6222 (ptp) REVERT: O 4 MET cc_start: 0.8412 (tpp) cc_final: 0.8141 (tpp) REVERT: O 36 GLN cc_start: 0.8240 (tt0) cc_final: 0.8025 (tt0) REVERT: O 105 ASN cc_start: 0.6158 (m-40) cc_final: 0.5905 (m-40) REVERT: O 132 LYS cc_start: 0.8234 (tppt) cc_final: 0.7990 (tppt) REVERT: P 63 LYS cc_start: 0.5044 (mmtt) cc_final: 0.4522 (tmtt) REVERT: P 90 ILE cc_start: 0.7798 (mm) cc_final: 0.7509 (mm) REVERT: P 143 LYS cc_start: 0.5885 (tmtt) cc_final: 0.5580 (mmmm) REVERT: P 151 LEU cc_start: 0.4652 (pp) cc_final: 0.3836 (tp) REVERT: Q 83 MET cc_start: 0.7019 (tpt) cc_final: 0.6814 (tpp) REVERT: Q 88 GLU cc_start: 0.7795 (pt0) cc_final: 0.7248 (pm20) REVERT: R 106 LYS cc_start: 0.7014 (tttt) cc_final: 0.6595 (mmmt) REVERT: T 73 ASN cc_start: 0.7486 (m-40) cc_final: 0.6851 (m-40) REVERT: T 101 ASN cc_start: 0.7238 (t0) cc_final: 0.6640 (t0) REVERT: T 134 GLN cc_start: 0.6938 (mp10) cc_final: 0.6678 (mp10) REVERT: U 45 LEU cc_start: 0.7124 (mm) cc_final: 0.6579 (tp) REVERT: X 15 ASN cc_start: 0.8095 (t0) cc_final: 0.7810 (t0) REVERT: X 42 MET cc_start: 0.8636 (tmm) cc_final: 0.8358 (tmm) REVERT: X 70 ASN cc_start: 0.6767 (m110) cc_final: 0.6231 (m110) REVERT: X 71 LYS cc_start: 0.6507 (ptmm) cc_final: 0.5882 (tmtt) REVERT: X 94 LEU cc_start: 0.8757 (mt) cc_final: 0.8494 (mt) REVERT: X 105 THR cc_start: 0.7371 (p) cc_final: 0.6994 (p) REVERT: X 110 ILE cc_start: 0.7228 (mp) cc_final: 0.6796 (mt) REVERT: Y 114 ASP cc_start: 0.8017 (p0) cc_final: 0.7645 (p0) REVERT: Z 13 MET cc_start: 0.6195 (tmm) cc_final: 0.5899 (tmm) REVERT: Z 16 ARG cc_start: 0.6987 (mtm180) cc_final: 0.6673 (mmm160) REVERT: Z 40 ILE cc_start: 0.8457 (mm) cc_final: 0.8123 (tp) REVERT: Z 114 MET cc_start: 0.6632 (mmt) cc_final: 0.6062 (ttt) REVERT: a 108 ILE cc_start: 0.7576 (mp) cc_final: 0.7268 (mt) REVERT: b 42 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7191 (ttt-90) REVERT: b 43 ASN cc_start: 0.8324 (t0) cc_final: 0.8060 (t0) REVERT: b 55 GLU cc_start: 0.6599 (tm-30) cc_final: 0.5892 (tp30) REVERT: d 35 MET cc_start: 0.4924 (mpp) cc_final: 0.4556 (mtm) REVERT: e 27 ARG cc_start: 0.7774 (ptp-110) cc_final: 0.7042 (ptp-110) REVERT: f 107 ARG cc_start: 0.5493 (mtt90) cc_final: 0.4776 (ptp-170) REVERT: h 52 TYR cc_start: 0.6287 (t80) cc_final: 0.5805 (t80) REVERT: h 64 HIS cc_start: 0.6890 (t-170) cc_final: 0.6324 (t-170) REVERT: h 83 TRP cc_start: 0.6677 (m-10) cc_final: 0.6428 (m-10) REVERT: h 302 TYR cc_start: 0.4395 (t80) cc_final: 0.3280 (t80) REVERT: h 304 ASP cc_start: 0.6221 (t0) cc_final: 0.5000 (p0) REVERT: n 20 MET cc_start: 0.6707 (tpp) cc_final: 0.6422 (tpp) REVERT: E 96 LEU cc_start: 0.7852 (mm) cc_final: 0.7464 (mt) REVERT: E 189 MET cc_start: 0.6116 (ppp) cc_final: 0.5563 (ppp) REVERT: S 107 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6666 (mtmm) outliers start: 2 outliers final: 0 residues processed: 689 average time/residue: 0.8005 time to fit residues: 960.0799 Evaluate side-chains 563 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 3.9990 chunk 608 optimal weight: 0.0270 chunk 555 optimal weight: 5.9990 chunk 591 optimal weight: 9.9990 chunk 356 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 464 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 534 optimal weight: 7.9990 chunk 559 optimal weight: 0.5980 chunk 589 optimal weight: 10.0000 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS F 138 HIS F 157 ASN H 81 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 HIS K 111 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 142 GLN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS W 29 HIS X 16 ASN X 44 HIS ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 ASN E 57 ASN S 48 ASN S 118 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 84200 Z= 0.160 Angle : 0.595 20.898 122597 Z= 0.300 Chirality : 0.036 0.278 15214 Planarity : 0.004 0.054 8638 Dihedral : 23.582 179.889 34598 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.05 % Allowed : 0.95 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4821 helix: 0.38 (0.13), residues: 1500 sheet: -1.42 (0.18), residues: 773 loop : -1.75 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 112 HIS 0.010 0.001 HIS U 91 PHE 0.027 0.002 PHE Y 120 TYR 0.030 0.001 TYR G 188 ARG 0.018 0.000 ARG e 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 702 time to evaluate : 4.379 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: B 57 LYS cc_start: 0.8785 (tptt) cc_final: 0.8394 (mmtt) REVERT: B 110 ASN cc_start: 0.6894 (m-40) cc_final: 0.5150 (t0) REVERT: B 142 LEU cc_start: 0.7670 (tp) cc_final: 0.7430 (tp) REVERT: B 177 MET cc_start: 0.8761 (mtm) cc_final: 0.8480 (mtp) REVERT: B 185 MET cc_start: 0.8421 (tpp) cc_final: 0.7817 (tpp) REVERT: C 26 SER cc_start: 0.7612 (p) cc_final: 0.7217 (m) REVERT: C 42 ARG cc_start: 0.5577 (mmm160) cc_final: 0.4526 (ttm-80) REVERT: C 68 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 103 MET cc_start: 0.7945 (tmm) cc_final: 0.7649 (tmm) REVERT: C 168 MET cc_start: 0.8222 (ttp) cc_final: 0.7583 (tpt) REVERT: C 207 LEU cc_start: 0.7245 (pt) cc_final: 0.7029 (pt) REVERT: D 105 GLU cc_start: 0.7344 (pm20) cc_final: 0.6077 (mm-30) REVERT: D 117 ARG cc_start: 0.5886 (tpt170) cc_final: 0.5290 (mtp85) REVERT: F 62 LYS cc_start: 0.7925 (mmmm) cc_final: 0.7438 (tppt) REVERT: F 106 LYS cc_start: 0.6158 (ttpp) cc_final: 0.5928 (ttpt) REVERT: F 182 MET cc_start: 0.8682 (ttp) cc_final: 0.8391 (ptm) REVERT: F 198 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7061 (ttt180) REVERT: F 212 ASP cc_start: 0.7882 (t70) cc_final: 0.7600 (t0) REVERT: G 104 THR cc_start: 0.8605 (t) cc_final: 0.8363 (t) REVERT: H 1 MET cc_start: 0.7345 (ttm) cc_final: 0.6980 (ttp) REVERT: H 28 TYR cc_start: 0.7276 (m-80) cc_final: 0.6580 (m-80) REVERT: H 45 TRP cc_start: 0.6456 (m100) cc_final: 0.6234 (m100) REVERT: H 59 GLN cc_start: 0.7789 (tp40) cc_final: 0.7572 (mp10) REVERT: H 68 LEU cc_start: 0.8112 (mp) cc_final: 0.7369 (tt) REVERT: H 81 HIS cc_start: 0.8008 (m90) cc_final: 0.7117 (m-70) REVERT: H 103 ASP cc_start: 0.6545 (m-30) cc_final: 0.5857 (m-30) REVERT: H 105 ASN cc_start: 0.8492 (t0) cc_final: 0.7986 (t0) REVERT: H 218 LYS cc_start: 0.5841 (tmmt) cc_final: 0.5314 (mmmt) REVERT: I 41 ARG cc_start: 0.6509 (mtm110) cc_final: 0.6148 (tpt170) REVERT: I 84 GLU cc_start: 0.6667 (tp30) cc_final: 0.6160 (tp30) REVERT: I 159 ASP cc_start: 0.5557 (t0) cc_final: 0.5218 (t0) REVERT: J 109 TYR cc_start: 0.6572 (m-80) cc_final: 0.6107 (m-80) REVERT: K 27 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7935 (tp-100) REVERT: K 71 LEU cc_start: 0.8499 (pp) cc_final: 0.8245 (tp) REVERT: L 5 LYS cc_start: 0.6818 (tttp) cc_final: 0.6160 (tptp) REVERT: L 6 LYS cc_start: 0.6523 (tttp) cc_final: 0.6224 (mmtt) REVERT: L 65 ARG cc_start: 0.3980 (mpt180) cc_final: 0.3298 (mmt-90) REVERT: L 78 TYR cc_start: 0.4361 (t80) cc_final: 0.4031 (t80) REVERT: M 49 GLU cc_start: 0.7424 (pp20) cc_final: 0.7119 (pm20) REVERT: M 82 MET cc_start: 0.6473 (ptp) cc_final: 0.6195 (ptp) REVERT: O 132 LYS cc_start: 0.8223 (tppt) cc_final: 0.7963 (tppt) REVERT: P 63 LYS cc_start: 0.5107 (mmtt) cc_final: 0.4661 (tppt) REVERT: P 90 ILE cc_start: 0.7762 (mm) cc_final: 0.7353 (mm) REVERT: P 151 LEU cc_start: 0.4629 (pp) cc_final: 0.3819 (tp) REVERT: Q 88 GLU cc_start: 0.7724 (pt0) cc_final: 0.7231 (pm20) REVERT: R 106 LYS cc_start: 0.6959 (tttt) cc_final: 0.6585 (mmmt) REVERT: T 38 ARG cc_start: 0.6182 (mtt180) cc_final: 0.5877 (mtt180) REVERT: T 61 GLU cc_start: 0.6896 (mp0) cc_final: 0.6496 (pp20) REVERT: T 73 ASN cc_start: 0.7437 (m-40) cc_final: 0.6763 (m-40) REVERT: T 101 ASN cc_start: 0.7243 (t0) cc_final: 0.6626 (t0) REVERT: T 134 GLN cc_start: 0.6948 (mp10) cc_final: 0.6649 (mp10) REVERT: U 45 LEU cc_start: 0.7053 (mm) cc_final: 0.6714 (tp) REVERT: X 15 ASN cc_start: 0.8017 (t0) cc_final: 0.7752 (t0) REVERT: X 42 MET cc_start: 0.8663 (tmm) cc_final: 0.8442 (tmm) REVERT: X 71 LYS cc_start: 0.6467 (ptmm) cc_final: 0.5805 (tmtt) REVERT: X 92 ASN cc_start: 0.7976 (p0) cc_final: 0.7689 (t0) REVERT: X 94 LEU cc_start: 0.8687 (mt) cc_final: 0.8428 (mt) REVERT: X 105 THR cc_start: 0.7250 (p) cc_final: 0.6932 (p) REVERT: Y 114 ASP cc_start: 0.7993 (p0) cc_final: 0.7643 (p0) REVERT: Z 16 ARG cc_start: 0.7003 (mtm180) cc_final: 0.6674 (mmm160) REVERT: Z 40 ILE cc_start: 0.8371 (mm) cc_final: 0.8073 (tp) REVERT: Z 114 MET cc_start: 0.6542 (mmt) cc_final: 0.5975 (ttt) REVERT: a 108 ILE cc_start: 0.7719 (mp) cc_final: 0.7428 (mt) REVERT: b 42 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7113 (ttt-90) REVERT: b 43 ASN cc_start: 0.8210 (t0) cc_final: 0.7974 (t0) REVERT: b 55 GLU cc_start: 0.6584 (tm-30) cc_final: 0.5848 (tp30) REVERT: d 35 MET cc_start: 0.4862 (mpp) cc_final: 0.4430 (mtm) REVERT: e 27 ARG cc_start: 0.7762 (ptp-110) cc_final: 0.6907 (mtp85) REVERT: f 107 ARG cc_start: 0.5635 (mtt90) cc_final: 0.4893 (ptp-170) REVERT: h 52 TYR cc_start: 0.6400 (t80) cc_final: 0.6129 (t80) REVERT: h 64 HIS cc_start: 0.6882 (t-170) cc_final: 0.6388 (t-170) REVERT: h 83 TRP cc_start: 0.6940 (m-10) cc_final: 0.6669 (m-10) REVERT: h 304 ASP cc_start: 0.6132 (t0) cc_final: 0.5665 (p0) REVERT: n 20 MET cc_start: 0.6596 (tpp) cc_final: 0.6302 (tpp) REVERT: E 96 LEU cc_start: 0.7844 (mm) cc_final: 0.7475 (mt) REVERT: E 189 MET cc_start: 0.6004 (ppp) cc_final: 0.5497 (ppp) REVERT: S 121 GLN cc_start: 0.7656 (pm20) cc_final: 0.7360 (pm20) REVERT: S 126 MET cc_start: -0.0343 (mmm) cc_final: -0.0702 (mmm) outliers start: 2 outliers final: 1 residues processed: 703 average time/residue: 0.7368 time to fit residues: 894.6690 Evaluate side-chains 568 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 567 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 3.9990 chunk 625 optimal weight: 0.0040 chunk 382 optimal weight: 7.9990 chunk 296 optimal weight: 0.9980 chunk 435 optimal weight: 6.9990 chunk 656 optimal weight: 20.0000 chunk 604 optimal weight: 9.9990 chunk 522 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 142 GLN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS W 29 HIS X 16 ASN X 44 HIS ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN S 48 ASN S 118 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 84200 Z= 0.158 Angle : 0.592 19.404 122597 Z= 0.298 Chirality : 0.036 0.253 15214 Planarity : 0.004 0.065 8638 Dihedral : 23.540 179.795 34598 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.02 % Allowed : 0.50 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 4821 helix: 0.43 (0.13), residues: 1501 sheet: -1.37 (0.18), residues: 765 loop : -1.73 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 112 HIS 0.011 0.001 HIS U 91 PHE 0.020 0.002 PHE X 50 TYR 0.038 0.002 TYR D 248 ARG 0.014 0.000 ARG T 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 678 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8403 (tppt) cc_final: 0.8188 (tppt) REVERT: B 110 ASN cc_start: 0.7145 (m-40) cc_final: 0.5431 (t0) REVERT: B 126 ASP cc_start: 0.7767 (t70) cc_final: 0.7567 (t70) REVERT: B 185 MET cc_start: 0.8398 (tpp) cc_final: 0.7749 (tpp) REVERT: C 26 SER cc_start: 0.7633 (p) cc_final: 0.7230 (m) REVERT: C 42 ARG cc_start: 0.5546 (mmm160) cc_final: 0.4472 (ttm-80) REVERT: C 68 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 103 MET cc_start: 0.7907 (tmm) cc_final: 0.7622 (tmm) REVERT: C 207 LEU cc_start: 0.7316 (pt) cc_final: 0.7087 (pt) REVERT: D 61 LEU cc_start: 0.8134 (mp) cc_final: 0.7833 (mp) REVERT: D 73 MET cc_start: 0.8111 (mpp) cc_final: 0.7824 (mmm) REVERT: D 105 GLU cc_start: 0.7167 (pm20) cc_final: 0.6366 (mm-30) REVERT: D 117 ARG cc_start: 0.5780 (tpt170) cc_final: 0.5229 (mtp85) REVERT: D 263 LYS cc_start: 0.6619 (tttm) cc_final: 0.6415 (tttm) REVERT: F 62 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7414 (tppt) REVERT: F 164 LEU cc_start: 0.8516 (mp) cc_final: 0.8276 (mp) REVERT: F 182 MET cc_start: 0.8645 (ttp) cc_final: 0.8375 (ptm) REVERT: F 198 ARG cc_start: 0.7695 (ttt90) cc_final: 0.6888 (ttt180) REVERT: F 212 ASP cc_start: 0.7919 (t70) cc_final: 0.7466 (t0) REVERT: F 237 SER cc_start: 0.8131 (m) cc_final: 0.7924 (m) REVERT: G 104 THR cc_start: 0.8607 (t) cc_final: 0.8379 (t) REVERT: H 1 MET cc_start: 0.7420 (ttm) cc_final: 0.7042 (ttp) REVERT: H 28 TYR cc_start: 0.7204 (m-80) cc_final: 0.6502 (m-80) REVERT: H 45 TRP cc_start: 0.6414 (m100) cc_final: 0.6211 (m100) REVERT: H 59 GLN cc_start: 0.7811 (tp40) cc_final: 0.7586 (mp10) REVERT: H 68 LEU cc_start: 0.8088 (mp) cc_final: 0.7313 (tt) REVERT: H 81 HIS cc_start: 0.7952 (m90) cc_final: 0.7072 (m-70) REVERT: H 103 ASP cc_start: 0.6583 (m-30) cc_final: 0.5817 (m-30) REVERT: H 105 ASN cc_start: 0.8501 (t0) cc_final: 0.8014 (t0) REVERT: H 218 LYS cc_start: 0.5813 (tmmt) cc_final: 0.5318 (mmmt) REVERT: I 41 ARG cc_start: 0.6476 (mtm110) cc_final: 0.6164 (tpt170) REVERT: I 84 GLU cc_start: 0.6730 (tp30) cc_final: 0.6246 (tp30) REVERT: I 87 PHE cc_start: 0.5665 (t80) cc_final: 0.5415 (t80) REVERT: I 159 ASP cc_start: 0.5543 (t0) cc_final: 0.5233 (t0) REVERT: J 109 TYR cc_start: 0.6565 (m-80) cc_final: 0.6096 (m-80) REVERT: K 27 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7927 (tp-100) REVERT: L 5 LYS cc_start: 0.6865 (tttp) cc_final: 0.6241 (tptp) REVERT: L 6 LYS cc_start: 0.6547 (tttp) cc_final: 0.6263 (mmtt) REVERT: L 65 ARG cc_start: 0.4188 (mpt180) cc_final: 0.3641 (mmt-90) REVERT: L 78 TYR cc_start: 0.4452 (t80) cc_final: 0.4090 (t80) REVERT: M 49 GLU cc_start: 0.7501 (pp20) cc_final: 0.7229 (pm20) REVERT: M 82 MET cc_start: 0.6447 (ptp) cc_final: 0.6101 (ptp) REVERT: O 132 LYS cc_start: 0.8222 (tppt) cc_final: 0.7959 (tppt) REVERT: P 52 THR cc_start: 0.5767 (t) cc_final: 0.4945 (m) REVERT: P 63 LYS cc_start: 0.5057 (mmtt) cc_final: 0.4649 (tppt) REVERT: P 90 ILE cc_start: 0.7746 (mm) cc_final: 0.7323 (mm) REVERT: P 151 LEU cc_start: 0.4587 (pp) cc_final: 0.3778 (tp) REVERT: Q 83 MET cc_start: 0.7028 (tpt) cc_final: 0.6765 (tpp) REVERT: Q 88 GLU cc_start: 0.7710 (pt0) cc_final: 0.7228 (pm20) REVERT: Q 103 ASN cc_start: 0.7399 (m110) cc_final: 0.7104 (p0) REVERT: R 63 PHE cc_start: 0.7384 (m-80) cc_final: 0.5783 (m-80) REVERT: R 106 LYS cc_start: 0.6963 (tttt) cc_final: 0.6561 (mmmt) REVERT: T 58 GLU cc_start: 0.4314 (pt0) cc_final: 0.3719 (tt0) REVERT: T 65 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8379 (mm-30) REVERT: T 73 ASN cc_start: 0.7449 (m-40) cc_final: 0.6712 (m-40) REVERT: T 76 GLN cc_start: 0.5741 (pm20) cc_final: 0.5421 (pm20) REVERT: T 134 GLN cc_start: 0.6908 (mp10) cc_final: 0.6641 (mp10) REVERT: U 45 LEU cc_start: 0.6984 (mm) cc_final: 0.6360 (tp) REVERT: X 42 MET cc_start: 0.8682 (tmm) cc_final: 0.8474 (tmm) REVERT: X 43 LYS cc_start: 0.8165 (tppt) cc_final: 0.7885 (tmtt) REVERT: X 70 ASN cc_start: 0.6699 (m110) cc_final: 0.6068 (m110) REVERT: X 71 LYS cc_start: 0.5950 (ptmm) cc_final: 0.5676 (ptmm) REVERT: X 92 ASN cc_start: 0.7986 (p0) cc_final: 0.7690 (t0) REVERT: X 94 LEU cc_start: 0.8671 (mt) cc_final: 0.8424 (mt) REVERT: Y 114 ASP cc_start: 0.7949 (p0) cc_final: 0.7645 (p0) REVERT: Z 40 ILE cc_start: 0.8372 (mm) cc_final: 0.8077 (tp) REVERT: Z 114 MET cc_start: 0.6523 (mmt) cc_final: 0.5952 (ttt) REVERT: a 108 ILE cc_start: 0.7702 (mp) cc_final: 0.7429 (mt) REVERT: b 42 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7119 (ttt-90) REVERT: b 43 ASN cc_start: 0.8142 (t0) cc_final: 0.7891 (t0) REVERT: b 55 GLU cc_start: 0.6582 (tm-30) cc_final: 0.5816 (tp30) REVERT: d 35 MET cc_start: 0.4898 (mpp) cc_final: 0.4463 (mtm) REVERT: d 68 LEU cc_start: 0.4895 (mt) cc_final: 0.4634 (pt) REVERT: e 27 ARG cc_start: 0.7612 (ptp-110) cc_final: 0.6712 (mtp85) REVERT: f 107 ARG cc_start: 0.5598 (mtt90) cc_final: 0.4833 (ptp-170) REVERT: h 30 MET cc_start: 0.3972 (ptm) cc_final: 0.3511 (ptp) REVERT: h 52 TYR cc_start: 0.6429 (t80) cc_final: 0.6129 (t80) REVERT: h 64 HIS cc_start: 0.6893 (t-170) cc_final: 0.6382 (t-170) REVERT: h 83 TRP cc_start: 0.6930 (m-10) cc_final: 0.6713 (m-10) REVERT: h 241 PHE cc_start: 0.4008 (m-10) cc_final: 0.3289 (m-10) REVERT: h 261 LEU cc_start: 0.3640 (mt) cc_final: 0.3406 (mt) REVERT: h 302 TYR cc_start: 0.4282 (t80) cc_final: 0.3702 (t80) REVERT: n 20 MET cc_start: 0.6639 (tpp) cc_final: 0.6354 (tpp) REVERT: E 96 LEU cc_start: 0.7831 (mm) cc_final: 0.7445 (mt) REVERT: E 189 MET cc_start: 0.6053 (ppp) cc_final: 0.5507 (ppp) REVERT: S 121 GLN cc_start: 0.7574 (pm20) cc_final: 0.7295 (pm20) outliers start: 1 outliers final: 0 residues processed: 678 average time/residue: 0.7329 time to fit residues: 862.0625 Evaluate side-chains 558 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 4.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 1.9990 chunk 556 optimal weight: 2.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 0.4980 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 523 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 537 optimal weight: 0.1980 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS F 138 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 HIS O 101 HIS ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 142 GLN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS W 29 HIS X 16 ASN X 70 ASN ** a 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 ASN h 305 ASN E 57 ASN S 48 ASN S 118 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.094585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079455 restraints weight = 357098.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080790 restraints weight = 178137.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081733 restraints weight = 112151.723| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 84200 Z= 0.141 Angle : 0.572 18.329 122597 Z= 0.287 Chirality : 0.035 0.240 15214 Planarity : 0.004 0.057 8638 Dihedral : 23.481 179.346 34598 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4821 helix: 0.55 (0.13), residues: 1487 sheet: -1.21 (0.18), residues: 755 loop : -1.66 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 112 HIS 0.011 0.001 HIS U 91 PHE 0.028 0.002 PHE D 241 TYR 0.028 0.001 TYR G 188 ARG 0.015 0.000 ARG M 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15560.69 seconds wall clock time: 272 minutes 48.57 seconds (16368.57 seconds total)