Starting phenix.real_space_refine on Sat Sep 28 06:33:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/09_2024/8j0n_35906.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/09_2024/8j0n_35906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/09_2024/8j0n_35906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/09_2024/8j0n_35906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/09_2024/8j0n_35906.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/09_2024/8j0n_35906.cif" } resolution = 3.47 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11829 2.51 5 N 3152 2.21 5 O 3406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18475 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7544 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 43, 'TRANS': 905} Chain breaks: 2 Chain: "B" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2438 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 4, 'TRANS': 291} Chain: "C" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain breaks: 1 Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1222 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain breaks: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "H" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1559 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain breaks: 1 Chain: "J" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1146 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.45, per 1000 atoms: 0.57 Number of scatterers: 18475 At special positions: 0 Unit cell: (131.89, 212.55, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3406 8.00 N 3152 7.00 C 11829 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 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG L 1 " - " ASN A 818 " " NAG M 1 " - " ASN A 913 " " NAG N 1 " - " ASN J 182 " Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.5 seconds 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 26 sheets defined 39.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 479 through 510 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.628A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 993 removed outlier: 3.908A pdb=" N ILE A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 removed outlier: 3.511A pdb=" N ASP B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.199A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.828A pdb=" N ILE B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.873A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.595A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.827A pdb=" N ALA B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.519A pdb=" N TRP B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.586A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.668A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.571A pdb=" N LYS B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 246 through 270 Processing helix chain 'B' and resid 277 through 297 removed outlier: 3.909A pdb=" N SER B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.535A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'C' and resid 45 through 64 Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.858A pdb=" N LYS C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 removed outlier: 3.660A pdb=" N MET C 121 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.843A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 187 removed outlier: 4.209A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 209 removed outlier: 3.748A pdb=" N MET C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.711A pdb=" N LEU C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.645A pdb=" N GLY C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.984A pdb=" N VAL D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 95 through 113 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.751A pdb=" N THR D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 155 removed outlier: 3.562A pdb=" N PHE D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 134 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 140 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.523A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 34 removed outlier: 3.505A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 64 removed outlier: 3.568A pdb=" N VAL E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 61 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.671A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 101 removed outlier: 3.931A pdb=" N VAL E 99 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 45 removed outlier: 3.528A pdb=" N VAL F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.511A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.993A pdb=" N TYR F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.671A pdb=" N LEU F 98 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.671A pdb=" N SER G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.624A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 83 removed outlier: 3.685A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 119 removed outlier: 3.997A pdb=" N GLY H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 177 Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 199 through 210 Processing helix chain 'J' and resid 91 through 104 Processing helix chain 'J' and resid 133 through 140 removed outlier: 4.072A pdb=" N LEU J 137 " --> pdb=" O PRO J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 207 removed outlier: 3.675A pdb=" N PHE J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.523A pdb=" N CYS A 933 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 44 removed outlier: 3.639A pdb=" N SER A 44 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 55 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.598A pdb=" N THR A 99 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 108 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET A 107 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU A 120 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER A 109 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 135 removed outlier: 4.040A pdb=" N TRP A 163 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.654A pdb=" N LYS A 201 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN A 211 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 230 removed outlier: 3.901A pdb=" N GLY A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 236 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 275 through 278 removed outlier: 3.809A pdb=" N ARG A 275 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 292 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 291 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 303 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 293 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 301 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 313 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 405 through 412 removed outlier: 3.505A pdb=" N GLY A 418 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 412 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 430 through 433 removed outlier: 4.351A pdb=" N TRP A 443 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 458 removed outlier: 3.932A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 545 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 558 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 547 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 569 through 574 Processing sheet with id=AB5, first strand: chain 'A' and resid 625 through 633 removed outlier: 3.501A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 641 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 639 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 631 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 637 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 692 through 699 removed outlier: 5.846A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP A 696 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 682 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 670 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY D 180 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR A 672 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 705 through 711 removed outlier: 7.047A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 757 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 771 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR J 191 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=AB9, first strand: chain 'A' and resid 778 through 786 removed outlier: 5.080A pdb=" N TRP A 796 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 802 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 821 through 822 removed outlier: 3.578A pdb=" N PHE A 822 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 847 through 849 Processing sheet with id=AC3, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.849A pdb=" N THR C 138 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 84 through 89 removed outlier: 3.779A pdb=" N ASP G 88 " --> pdb=" O PHE G 45 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE G 45 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU G 138 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET G 140 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 77 removed outlier: 3.558A pdb=" N ARG G 66 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY G 92 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.857A pdb=" N GLY H 3 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE H 54 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS H 5 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL H 31 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS H 57 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU H 29 " --> pdb=" O CYS H 57 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN H 27 " --> pdb=" O PRO H 59 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE H 61 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA H 25 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 26 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY H 91 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ALA H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 92 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 125 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 127 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS H 153 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 83 through 87 removed outlier: 6.106A pdb=" N LYS J 70 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS J 58 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 72 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU J 56 " --> pdb=" O GLY J 72 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU J 55 " --> pdb=" O PRO J 113 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG J 109 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 128 " --> pdb=" O ILE J 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 156 through 162 removed outlier: 6.746A pdb=" N HIS J 149 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL J 159 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR J 147 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL J 161 " --> pdb=" O GLN J 145 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN J 145 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL J 150 " --> pdb=" O GLN J 188 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 1 1.04 - 1.23: 356 1.23 - 1.43: 7585 1.43 - 1.62: 10795 1.62 - 1.82: 153 Bond restraints: 18890 Sorted by residual: bond pdb=" CG PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 1.503 0.841 0.662 3.40e-02 8.65e+02 3.79e+02 bond pdb=" N PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 1.473 1.592 -0.119 1.40e-02 5.10e+03 7.24e+01 bond pdb=" CB PRO A 582 " pdb=" CG PRO A 582 " ideal model delta sigma weight residual 1.492 1.797 -0.305 5.00e-02 4.00e+02 3.72e+01 bond pdb=" CA LEU A 690 " pdb=" CB LEU A 690 " ideal model delta sigma weight residual 1.521 1.598 -0.077 1.48e-02 4.57e+03 2.73e+01 bond pdb=" CB PRO E 103 " pdb=" CG PRO E 103 " ideal model delta sigma weight residual 1.492 1.671 -0.179 5.00e-02 4.00e+02 1.28e+01 ... (remaining 18885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 25522 5.29 - 10.58: 61 10.58 - 15.87: 5 15.87 - 21.17: 2 21.17 - 26.46: 1 Bond angle restraints: 25591 Sorted by residual: angle pdb=" N PRO A 582 " pdb=" CD PRO A 582 " pdb=" CG PRO A 582 " ideal model delta sigma weight residual 103.20 76.74 26.46 1.50e+00 4.44e-01 3.11e+02 angle pdb=" CA PRO C 69 " pdb=" N PRO C 69 " pdb=" CD PRO C 69 " ideal model delta sigma weight residual 112.00 95.66 16.34 1.40e+00 5.10e-01 1.36e+02 angle pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" CD PRO E 103 " ideal model delta sigma weight residual 112.00 97.35 14.65 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO A 582 " pdb=" N PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 112.00 97.77 14.23 1.40e+00 5.10e-01 1.03e+02 angle pdb=" N PRO A 582 " pdb=" CA PRO A 582 " pdb=" CB PRO A 582 " ideal model delta sigma weight residual 103.48 94.38 9.10 1.00e+00 1.00e+00 8.28e+01 ... (remaining 25586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 10034 21.59 - 43.19: 1131 43.19 - 64.78: 195 64.78 - 86.37: 45 86.37 - 107.96: 17 Dihedral angle restraints: 11422 sinusoidal: 4720 harmonic: 6702 Sorted by residual: dihedral pdb=" CA LEU A 929 " pdb=" C LEU A 929 " pdb=" N GLU A 930 " pdb=" CA GLU A 930 " ideal model delta harmonic sigma weight residual 180.00 147.11 32.89 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA MET C 151 " pdb=" C MET C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLY B 67 " pdb=" C GLY B 67 " pdb=" N ARG B 68 " pdb=" CA ARG B 68 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 11419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2625 0.078 - 0.157: 256 0.157 - 0.235: 1 0.235 - 0.314: 5 0.314 - 0.392: 2 Chirality restraints: 2889 Sorted by residual: chirality pdb=" CA PRO A 582 " pdb=" N PRO A 582 " pdb=" C PRO A 582 " pdb=" CB PRO A 582 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" C PRO E 103 " pdb=" CB PRO E 103 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2886 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 68 " 0.110 5.00e-02 4.00e+02 1.52e-01 3.71e+01 pdb=" N PRO C 69 " -0.263 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 581 " -0.098 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO A 582 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 102 " 0.079 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 103 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " 0.059 5.00e-02 4.00e+02 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 351 2.69 - 3.24: 16640 3.24 - 3.79: 27210 3.79 - 4.35: 33688 4.35 - 4.90: 56091 Nonbonded interactions: 133980 Sorted by model distance: nonbonded pdb=" OD1 ASP B 104 " pdb=" NE2 GLN B 108 " model vdw 2.136 3.120 nonbonded pdb=" OG1 THR H 52 " pdb=" OD2 ASP H 121 " model vdw 2.140 3.040 nonbonded pdb=" OG SER A 747 " pdb=" OD1 ASP A 749 " model vdw 2.176 3.040 nonbonded pdb=" NZ LYS H 20 " pdb=" O LEU H 183 " model vdw 2.282 3.120 nonbonded pdb=" OG SER A 787 " pdb=" N GLU A 788 " model vdw 2.292 3.120 ... (remaining 133975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.010 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2400 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 : 0.007 0.662 18890 Z= 0.416 Angle : 0.833 26.457 25591 Z= 0.463 Chirality : 0.044 0.392 2889 Planarity : 0.006 0.152 3236 Dihedral : 18.252 107.964 7094 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.23 % Favored : 91.50 % Rotamer: Outliers : 0.75 % Allowed : 28.06 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.04 (0.17), residues: 2271 helix: 1.46 (0.19), residues: 836 sheet: 0.27 (0.24), residues: 444 loop : -3.25 (0.16), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 219 HIS 0.008 0.001 HIS A 306 PHE 0.019 0.001 PHE C 252 TYR 0.021 0.001 TYR A 305 ARG 0.010 0.000 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 448 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ILE cc_start: 0.4595 (mt) cc_final: 0.4198 (mt) REVERT: B 107 ILE cc_start: 0.4035 (mm) cc_final: 0.3611 (mm) REVERT: B 183 MET cc_start: 0.0394 (OUTLIER) cc_final: -0.0118 (mmt) REVERT: C 81 ASN cc_start: 0.4450 (m110) cc_final: 0.3554 (t0) REVERT: C 121 MET cc_start: 0.4674 (ppp) cc_final: 0.4261 (tpp) REVERT: C 232 TRP cc_start: 0.1901 (t60) cc_final: 0.1362 (t60) REVERT: E 31 MET cc_start: 0.6029 (tpt) cc_final: 0.5370 (ttt) REVERT: H 110 LYS cc_start: 0.5931 (mttt) cc_final: 0.5726 (tptp) outliers start: 15 outliers final: 2 residues processed: 460 average time/residue: 0.3951 time to fit residues: 252.4363 Evaluate side-chains 243 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain D residue 43 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 8.9990 chunk 171 optimal weight: 0.0870 chunk 95 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 102 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 188 ASN B 193 GLN B 194 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2978 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18890 Z= 0.266 Angle : 0.777 12.254 25591 Z= 0.385 Chirality : 0.045 0.254 2889 Planarity : 0.006 0.102 3236 Dihedral : 7.460 65.447 2691 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.23 % Favored : 91.46 % Rotamer: Outliers : 4.79 % Allowed : 27.86 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.87 (0.17), residues: 2271 helix: 1.46 (0.18), residues: 862 sheet: 0.34 (0.24), residues: 458 loop : -3.18 (0.16), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 557 HIS 0.010 0.002 HIS E 62 PHE 0.028 0.002 PHE B 230 TYR 0.024 0.002 TYR C 67 ARG 0.009 0.001 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 265 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7292 (tmm) cc_final: 0.6971 (tmm) REVERT: A 174 HIS cc_start: 0.8266 (t-170) cc_final: 0.8066 (t70) REVERT: A 248 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6629 (mp) REVERT: A 294 HIS cc_start: 0.5015 (t-170) cc_final: 0.4702 (t-170) REVERT: A 375 ILE cc_start: 0.6481 (mt) cc_final: 0.5394 (mt) REVERT: A 847 MET cc_start: 0.0820 (mmt) cc_final: -0.0453 (mtm) REVERT: B 39 GLU cc_start: 0.3959 (OUTLIER) cc_final: 0.3689 (tp30) REVERT: B 64 LEU cc_start: 0.2951 (OUTLIER) cc_final: 0.2553 (tp) REVERT: B 183 MET cc_start: 0.1780 (OUTLIER) cc_final: 0.1546 (mmt) REVERT: C 36 ILE cc_start: 0.4654 (OUTLIER) cc_final: 0.4391 (mt) REVERT: C 121 MET cc_start: 0.4993 (ppp) cc_final: 0.4685 (tpp) REVERT: C 232 TRP cc_start: 0.2399 (t60) cc_final: 0.1588 (t60) REVERT: E 31 MET cc_start: 0.6087 (tpt) cc_final: 0.5470 (ttt) REVERT: H 166 GLU cc_start: 0.8008 (mp0) cc_final: 0.7771 (mm-30) REVERT: H 209 LEU cc_start: 0.2978 (OUTLIER) cc_final: 0.2638 (mt) outliers start: 96 outliers final: 23 residues processed: 348 average time/residue: 0.3334 time to fit residues: 174.3821 Evaluate side-chains 246 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 217 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN A 836 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3393 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18890 Z= 0.247 Angle : 0.787 13.258 25591 Z= 0.381 Chirality : 0.045 0.240 2889 Planarity : 0.005 0.065 3236 Dihedral : 5.605 58.105 2689 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.37 % Favored : 91.33 % Rotamer: Outliers : 4.49 % Allowed : 26.91 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.85 (0.17), residues: 2271 helix: 1.35 (0.18), residues: 861 sheet: 0.36 (0.23), residues: 465 loop : -3.05 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 158 HIS 0.010 0.001 HIS E 62 PHE 0.045 0.002 PHE B 230 TYR 0.015 0.002 TYR A 923 ARG 0.008 0.001 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 250 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.8214 (t-170) cc_final: 0.7996 (t-90) REVERT: A 177 MET cc_start: 0.6349 (mtt) cc_final: 0.5281 (ptp) REVERT: A 248 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6643 (mp) REVERT: A 375 ILE cc_start: 0.6545 (mt) cc_final: 0.5756 (mt) REVERT: A 442 LEU cc_start: 0.2641 (OUTLIER) cc_final: 0.2243 (mp) REVERT: B 32 GLN cc_start: 0.7020 (pp30) cc_final: 0.6728 (pp30) REVERT: B 183 MET cc_start: 0.1973 (mtp) cc_final: 0.1645 (mmt) REVERT: C 36 ILE cc_start: 0.4986 (OUTLIER) cc_final: 0.4725 (mt) REVERT: C 111 MET cc_start: 0.3750 (mpp) cc_final: 0.3340 (tpp) REVERT: C 121 MET cc_start: 0.5729 (ppp) cc_final: 0.5196 (tpp) REVERT: C 208 MET cc_start: 0.6624 (ppp) cc_final: 0.6368 (ppp) REVERT: E 31 MET cc_start: 0.6271 (tpt) cc_final: 0.5675 (ttt) REVERT: J 70 LYS cc_start: 0.4718 (tmtt) cc_final: 0.4475 (mmmt) REVERT: J 77 ASN cc_start: 0.5857 (t0) cc_final: 0.5046 (t0) REVERT: J 192 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6733 (t) outliers start: 90 outliers final: 40 residues processed: 329 average time/residue: 0.2943 time to fit residues: 148.5684 Evaluate side-chains 273 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 229 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 167 ASN C 64 ASN D 140 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4093 moved from start: 0.7546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 18890 Z= 0.304 Angle : 0.829 13.923 25591 Z= 0.410 Chirality : 0.048 0.345 2889 Planarity : 0.006 0.064 3236 Dihedral : 5.073 59.693 2686 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.41 % Favored : 91.24 % Rotamer: Outliers : 5.84 % Allowed : 26.61 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.04 (0.17), residues: 2271 helix: 1.05 (0.17), residues: 853 sheet: 0.22 (0.24), residues: 460 loop : -2.92 (0.17), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 232 HIS 0.019 0.002 HIS A 751 PHE 0.040 0.003 PHE B 230 TYR 0.019 0.002 TYR A 733 ARG 0.010 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 275 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6967 (mtt) cc_final: 0.6041 (mtt) REVERT: A 248 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6851 (mp) REVERT: B 32 GLN cc_start: 0.7229 (pp30) cc_final: 0.6808 (pp30) REVERT: C 121 MET cc_start: 0.6022 (ppp) cc_final: 0.5466 (tpp) REVERT: E 31 MET cc_start: 0.6567 (tpt) cc_final: 0.5941 (ttt) REVERT: F 84 LEU cc_start: 0.3510 (mp) cc_final: 0.3165 (mm) REVERT: F 85 PHE cc_start: 0.0290 (OUTLIER) cc_final: 0.0022 (t80) REVERT: H 209 LEU cc_start: 0.3120 (OUTLIER) cc_final: 0.2889 (mm) REVERT: J 90 LEU cc_start: -0.0613 (OUTLIER) cc_final: -0.0968 (mp) REVERT: J 151 ASP cc_start: 0.4344 (m-30) cc_final: 0.3781 (t0) outliers start: 117 outliers final: 58 residues processed: 369 average time/residue: 0.2968 time to fit residues: 167.1428 Evaluate side-chains 298 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 236 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 162 optimal weight: 0.0070 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 169 HIS B 238 HIS ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN E 94 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 158 HIS J 141 HIS J 149 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4917 moved from start: 1.0090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 18890 Z= 0.395 Angle : 0.926 15.539 25591 Z= 0.468 Chirality : 0.051 0.367 2889 Planarity : 0.007 0.085 3236 Dihedral : 5.803 58.457 2686 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.41 % Favored : 91.24 % Rotamer: Outliers : 6.09 % Allowed : 28.26 % Favored : 65.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.48 (0.17), residues: 2271 helix: 0.62 (0.17), residues: 849 sheet: -0.32 (0.23), residues: 483 loop : -2.96 (0.17), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 110 HIS 0.019 0.002 HIS A 428 PHE 0.050 0.003 PHE B 230 TYR 0.029 0.003 TYR B 165 ARG 0.030 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 328 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7059 (mtt) cc_final: 0.5631 (mtt) REVERT: A 248 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7171 (mp) REVERT: A 336 MET cc_start: 0.6824 (mmm) cc_final: 0.6447 (mmm) REVERT: A 375 ILE cc_start: 0.6633 (mp) cc_final: 0.6291 (mp) REVERT: A 898 TYR cc_start: 0.4928 (t80) cc_final: 0.4086 (t80) REVERT: B 167 ASN cc_start: 0.3349 (OUTLIER) cc_final: 0.3066 (p0) REVERT: C 147 ARG cc_start: 0.2958 (mtt180) cc_final: 0.2641 (mtm180) REVERT: E 31 MET cc_start: 0.6589 (tpt) cc_final: 0.6087 (ttt) REVERT: F 84 LEU cc_start: 0.4092 (mp) cc_final: 0.3802 (mm) REVERT: G 133 ARG cc_start: 0.4510 (tpt170) cc_final: 0.4217 (tpt170) REVERT: H 13 LYS cc_start: 0.6402 (mtmt) cc_final: 0.5887 (mtmt) REVERT: H 175 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6501 (pp) REVERT: H 183 LEU cc_start: 0.3783 (OUTLIER) cc_final: 0.3580 (pp) REVERT: H 209 LEU cc_start: 0.3211 (OUTLIER) cc_final: 0.2658 (mt) REVERT: J 77 ASN cc_start: 0.7193 (t0) cc_final: 0.5676 (t0) outliers start: 122 outliers final: 70 residues processed: 423 average time/residue: 0.2786 time to fit residues: 182.0535 Evaluate side-chains 338 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 263 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 171 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 62 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 moved from start: 1.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18890 Z= 0.255 Angle : 0.839 15.882 25591 Z= 0.401 Chirality : 0.046 0.315 2889 Planarity : 0.005 0.069 3236 Dihedral : 5.296 59.393 2686 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.28 % Favored : 91.33 % Rotamer: Outliers : 5.14 % Allowed : 31.35 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.17), residues: 2271 helix: 0.92 (0.17), residues: 847 sheet: -0.14 (0.23), residues: 485 loop : -3.06 (0.17), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 232 HIS 0.018 0.002 HIS A 196 PHE 0.059 0.002 PHE B 230 TYR 0.020 0.002 TYR A 419 ARG 0.011 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 294 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6753 (mtt) cc_final: 0.5761 (mtt) REVERT: A 248 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7373 (mp) REVERT: A 336 MET cc_start: 0.7345 (mmm) cc_final: 0.6816 (mmm) REVERT: A 456 GLU cc_start: 0.5581 (tt0) cc_final: 0.5331 (tt0) REVERT: A 505 MET cc_start: 0.7227 (mmp) cc_final: 0.6865 (mmp) REVERT: A 862 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7524 (tp) REVERT: B 181 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.4361 (mm) REVERT: C 51 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8168 (p0) REVERT: C 121 MET cc_start: 0.6669 (ttp) cc_final: 0.5762 (tpp) REVERT: C 147 ARG cc_start: 0.2852 (mtt180) cc_final: 0.2454 (mtm110) REVERT: E 31 MET cc_start: 0.6548 (tpt) cc_final: 0.6124 (ttt) REVERT: H 14 MET cc_start: 0.6905 (tmm) cc_final: 0.6662 (tmm) REVERT: H 203 ASN cc_start: 0.7696 (m-40) cc_final: 0.7468 (m110) REVERT: H 209 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.2753 (mt) REVERT: J 77 ASN cc_start: 0.6903 (t0) cc_final: 0.5786 (t0) REVERT: J 107 LEU cc_start: -0.0515 (OUTLIER) cc_final: -0.0859 (tt) outliers start: 103 outliers final: 65 residues processed: 371 average time/residue: 0.2723 time to fit residues: 158.4843 Evaluate side-chains 332 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 261 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 0.4980 chunk 24 optimal weight: 0.0270 chunk 124 optimal weight: 0.0980 chunk 159 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 132 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 1.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18890 Z= 0.219 Angle : 0.821 14.922 25591 Z= 0.388 Chirality : 0.045 0.349 2889 Planarity : 0.005 0.062 3236 Dihedral : 5.125 59.586 2686 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.35 % Favored : 92.25 % Rotamer: Outliers : 4.14 % Allowed : 32.60 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.12 (0.17), residues: 2271 helix: 1.09 (0.18), residues: 847 sheet: -0.02 (0.22), residues: 483 loop : -3.00 (0.17), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 232 HIS 0.029 0.001 HIS H 62 PHE 0.060 0.002 PHE B 230 TYR 0.019 0.001 TYR F 96 ARG 0.014 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 280 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.8643 (t70) cc_final: 0.8324 (t70) REVERT: A 177 MET cc_start: 0.7003 (mtt) cc_final: 0.6037 (mtt) REVERT: A 248 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7397 (mp) REVERT: C 51 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8061 (p0) REVERT: C 121 MET cc_start: 0.6701 (ttp) cc_final: 0.5690 (tpp) REVERT: E 31 MET cc_start: 0.6483 (tpt) cc_final: 0.6076 (ttt) REVERT: H 27 ASN cc_start: 0.6457 (OUTLIER) cc_final: 0.6129 (m110) REVERT: H 170 ILE cc_start: 0.7182 (tt) cc_final: 0.6739 (tp) REVERT: J 77 ASN cc_start: 0.6252 (t0) cc_final: 0.5755 (t0) outliers start: 83 outliers final: 54 residues processed: 339 average time/residue: 0.2776 time to fit residues: 149.3917 Evaluate side-chains 319 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 262 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 27 ASN Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 155 HIS A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 145 ASN B 167 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 140 ASN D 160 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS H 188 ASN H 189 HIS H 203 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 1.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18890 Z= 0.357 Angle : 0.976 19.771 25591 Z= 0.483 Chirality : 0.052 0.393 2889 Planarity : 0.007 0.067 3236 Dihedral : 5.719 57.575 2686 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.38 % Favored : 90.22 % Rotamer: Outliers : 5.19 % Allowed : 32.05 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.17), residues: 2271 helix: 0.66 (0.18), residues: 842 sheet: -0.26 (0.23), residues: 488 loop : -3.13 (0.17), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 992 HIS 0.065 0.003 HIS D 160 PHE 0.063 0.003 PHE C 252 TYR 0.026 0.003 TYR A 672 ARG 0.012 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 311 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7252 (mtt) cc_final: 0.6343 (mtt) REVERT: A 248 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7508 (mp) REVERT: A 336 MET cc_start: 0.7170 (mmm) cc_final: 0.6762 (mmm) REVERT: A 536 MET cc_start: 0.7499 (ppp) cc_final: 0.6717 (ptt) REVERT: B 32 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8140 (pp30) REVERT: B 75 CYS cc_start: 0.7345 (m) cc_final: 0.7119 (m) REVERT: B 98 GLU cc_start: 0.6496 (tt0) cc_final: 0.6284 (pt0) REVERT: B 100 MET cc_start: 0.6486 (ptm) cc_final: 0.5629 (ttp) REVERT: C 121 MET cc_start: 0.7537 (ttp) cc_final: 0.6846 (tpp) REVERT: D 95 SER cc_start: -0.0165 (OUTLIER) cc_final: -0.0514 (t) REVERT: D 120 PHE cc_start: 0.2828 (OUTLIER) cc_final: 0.1795 (m-80) REVERT: H 14 MET cc_start: 0.7613 (tmm) cc_final: 0.7296 (tmm) REVERT: H 168 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6452 (mp10) REVERT: H 203 ASN cc_start: 0.8095 (m-40) cc_final: 0.7345 (p0) REVERT: J 77 ASN cc_start: 0.6830 (t0) cc_final: 0.6566 (t0) REVERT: J 99 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6541 (tpp-160) outliers start: 104 outliers final: 58 residues processed: 385 average time/residue: 0.2755 time to fit residues: 166.5983 Evaluate side-chains 336 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 272 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 172 TYR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 171 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 191 optimal weight: 0.0570 chunk 133 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 273 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN J 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 1.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18890 Z= 0.237 Angle : 0.881 19.080 25591 Z= 0.419 Chirality : 0.046 0.328 2889 Planarity : 0.005 0.061 3236 Dihedral : 5.249 59.997 2684 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.13 % Favored : 92.47 % Rotamer: Outliers : 3.15 % Allowed : 34.85 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.17), residues: 2271 helix: 0.92 (0.18), residues: 841 sheet: -0.07 (0.23), residues: 487 loop : -3.02 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 254 HIS 0.029 0.002 HIS A 222 PHE 0.060 0.002 PHE B 230 TYR 0.042 0.002 TYR E 30 ARG 0.007 0.001 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 294 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.8566 (t70) cc_final: 0.8015 (t70) REVERT: A 222 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.6402 (p90) REVERT: A 248 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7335 (mp) REVERT: A 610 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5635 (mmtm) REVERT: A 856 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5079 (mm) REVERT: C 121 MET cc_start: 0.7705 (ttp) cc_final: 0.6908 (tpp) REVERT: D 80 ILE cc_start: 0.5874 (mm) cc_final: 0.5585 (mm) REVERT: D 120 PHE cc_start: 0.2843 (OUTLIER) cc_final: 0.1821 (m-80) REVERT: E 31 MET cc_start: 0.6320 (ttt) cc_final: 0.5892 (ttt) REVERT: H 168 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6275 (mp10) REVERT: J 77 ASN cc_start: 0.6487 (t0) cc_final: 0.6105 (t0) REVERT: J 80 ASP cc_start: 0.5540 (p0) cc_final: 0.5298 (p0) outliers start: 63 outliers final: 42 residues processed: 341 average time/residue: 0.2649 time to fit residues: 144.6440 Evaluate side-chains 322 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 274 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 171 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 207 optimal weight: 0.0770 chunk 179 optimal weight: 0.0170 chunk 18 optimal weight: 0.0000 chunk 138 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 190 optimal weight: 0.0000 overall best weight: 0.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN B 155 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 1.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18890 Z= 0.218 Angle : 0.870 13.598 25591 Z= 0.414 Chirality : 0.046 0.325 2889 Planarity : 0.005 0.069 3236 Dihedral : 5.086 59.760 2684 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.66 % Favored : 91.99 % Rotamer: Outliers : 2.55 % Allowed : 35.10 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.17), residues: 2271 helix: 0.97 (0.18), residues: 844 sheet: 0.05 (0.23), residues: 479 loop : -2.97 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 197 HIS 0.023 0.002 HIS A 222 PHE 0.060 0.002 PHE B 230 TYR 0.027 0.001 TYR E 30 ARG 0.009 0.001 ARG G 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 297 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.8536 (t70) cc_final: 0.7891 (t70) REVERT: A 222 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.5948 (p-80) REVERT: A 248 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7307 (mp) REVERT: A 856 ILE cc_start: 0.5887 (tp) cc_final: 0.5352 (mm) REVERT: B 98 GLU cc_start: 0.6914 (pt0) cc_final: 0.6497 (pt0) REVERT: C 121 MET cc_start: 0.7707 (ttp) cc_final: 0.6868 (tpp) REVERT: D 80 ILE cc_start: 0.5954 (mm) cc_final: 0.5738 (mm) REVERT: D 120 PHE cc_start: 0.2728 (OUTLIER) cc_final: 0.1697 (m-80) REVERT: E 31 MET cc_start: 0.6355 (ttt) cc_final: 0.5860 (ttt) REVERT: F 89 LEU cc_start: 0.8361 (mm) cc_final: 0.8095 (mm) REVERT: H 168 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.6252 (mp10) REVERT: J 77 ASN cc_start: 0.6516 (t0) cc_final: 0.6136 (t0) REVERT: J 80 ASP cc_start: 0.5366 (p0) cc_final: 0.5128 (p0) outliers start: 51 outliers final: 37 residues processed: 334 average time/residue: 0.2578 time to fit residues: 138.7287 Evaluate side-chains 311 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 222 HIS ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.090350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.070999 restraints weight = 86972.658| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 6.15 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 1.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18890 Z= 0.430 Angle : 1.128 21.137 25591 Z= 0.570 Chirality : 0.058 0.326 2889 Planarity : 0.010 0.260 3236 Dihedral : 6.371 57.553 2684 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.86 % Favored : 89.74 % Rotamer: Outliers : 3.15 % Allowed : 35.05 % Favored : 61.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.01 (0.16), residues: 2271 helix: 0.21 (0.17), residues: 840 sheet: -0.64 (0.22), residues: 465 loop : -3.20 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 992 HIS 0.062 0.004 HIS A 196 PHE 0.063 0.004 PHE B 230 TYR 0.039 0.004 TYR A 733 ARG 0.027 0.002 ARG D 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4356.49 seconds wall clock time: 79 minutes 38.14 seconds (4778.14 seconds total)