Starting phenix.real_space_refine on Thu Sep 26 01:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/09_2024/6idf_9648.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/09_2024/6idf_9648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/09_2024/6idf_9648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/09_2024/6idf_9648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/09_2024/6idf_9648.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6idf_9648/09_2024/6idf_9648.cif" } resolution = 2.7 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 7344 2.51 5 N 1762 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11188 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 263 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 8.65, per 1000 atoms: 0.77 Number of scatterers: 11188 At special positions: 0 Unit cell: (110.191, 94.917, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 4 15.00 O 2034 8.00 N 1762 7.00 C 7344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS E 9 " distance=2.03 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=1, symmetry=0 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 817 " - " ASN A 464 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 57.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.563A pdb=" N ILE A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.137A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.170A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.934A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.524A pdb=" N TYR A 173 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 174' Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.737A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.998A pdb=" N ARG A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.901A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 removed outlier: 3.572A pdb=" N ARG A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 405 removed outlier: 3.561A pdb=" N ASP A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.712A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.677A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.743A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.560A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 74 through 103 removed outlier: 3.902A pdb=" N HIS B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 154 removed outlier: 3.881A pdb=" N HIS B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.920A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 4.334A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.609A pdb=" N TYR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 removed outlier: 3.764A pdb=" N TRP B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 240 removed outlier: 4.081A pdb=" N GLN B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.552A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.864A pdb=" N MET B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.871A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 429 removed outlier: 3.511A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.306A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.564A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 28 through 60 removed outlier: 4.256A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 107 removed outlier: 3.712A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 139 removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.785A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.929A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 removed outlier: 3.819A pdb=" N ASN C 207 " --> pdb=" O THR C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.756A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'D' and resid 7 through 21 removed outlier: 4.058A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 26 through 42 removed outlier: 3.845A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 removed outlier: 3.570A pdb=" N TYR D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 81 removed outlier: 4.050A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.675A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.661A pdb=" N THR E 6 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 7 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 8 " --> pdb=" O GLU E 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 8' Processing helix chain 'E' and resid 16 through 23 removed outlier: 4.278A pdb=" N VAL E 20 " --> pdb=" O HIS E 16 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.497A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 74 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 222 removed outlier: 4.029A pdb=" N ARG A 652 " --> pdb=" O HIS A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 8.976A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.299A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.661A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.517A pdb=" N LEU E 36 " --> pdb=" O GLY B 382 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1572 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: 3.43 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1680 1.31 - 1.44: 3232 1.44 - 1.57: 6471 1.57 - 1.70: 13 1.70 - 1.83: 66 Bond restraints: 11462 Sorted by residual: bond pdb=" C29 PC1 C 301 " pdb=" C2A PC1 C 301 " ideal model delta sigma weight residual 1.524 1.347 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C29 PC1 B 501 " pdb=" C2A PC1 B 501 " ideal model delta sigma weight residual 1.524 1.348 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C29 PC1 B 502 " pdb=" C2A PC1 B 502 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C29 PC1 D 201 " pdb=" C2A PC1 D 201 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C31 PC1 B 502 " pdb=" O31 PC1 B 502 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 11457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 15463 4.70 - 9.39: 143 9.39 - 14.09: 5 14.09 - 18.78: 0 18.78 - 23.48: 4 Bond angle restraints: 15615 Sorted by residual: angle pdb=" O12 PC1 C 301 " pdb=" P PC1 C 301 " pdb=" O14 PC1 C 301 " ideal model delta sigma weight residual 123.67 100.19 23.48 3.00e+00 1.11e-01 6.12e+01 angle pdb=" O12 PC1 B 501 " pdb=" P PC1 B 501 " pdb=" O14 PC1 B 501 " ideal model delta sigma weight residual 123.67 101.07 22.60 3.00e+00 1.11e-01 5.68e+01 angle pdb=" O12 PC1 D 201 " pdb=" P PC1 D 201 " pdb=" O14 PC1 D 201 " ideal model delta sigma weight residual 123.67 101.14 22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" O12 PC1 B 502 " pdb=" P PC1 B 502 " pdb=" O14 PC1 B 502 " ideal model delta sigma weight residual 123.67 101.17 22.50 3.00e+00 1.11e-01 5.62e+01 angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" CB PRO B 117 " ideal model delta sigma weight residual 103.25 110.99 -7.74 1.05e+00 9.07e-01 5.44e+01 ... (remaining 15610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 6779 23.33 - 46.66: 269 46.66 - 69.98: 75 69.98 - 93.31: 33 93.31 - 116.64: 14 Dihedral angle restraints: 7170 sinusoidal: 3193 harmonic: 3977 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -169.97 83.97 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.97 78.97 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 180.00 137.02 42.98 0 5.00e+00 4.00e-02 7.39e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1707 0.097 - 0.194: 146 0.194 - 0.291: 10 0.291 - 0.388: 3 0.388 - 0.485: 2 Chirality restraints: 1868 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.01 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG A 819 " pdb=" ND2 ASN A 264 " pdb=" C2 NAG A 819 " pdb=" O5 NAG A 819 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1865 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 211 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP C 227 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 560 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.036 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2836 2.80 - 3.33: 9763 3.33 - 3.85: 17960 3.85 - 4.38: 20803 4.38 - 4.90: 36230 Nonbonded interactions: 87592 Sorted by model distance: nonbonded pdb=" O VAL A 383 " pdb=" O6 NAG H 1 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.285 3.040 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.318 3.040 nonbonded pdb=" O PHE C 162 " pdb=" OH TYR C 218 " model vdw 2.323 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.329 3.040 ... (remaining 87587 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 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 7.890 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: 0.000 Extract box with map and model: 1.510 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.770 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.008 0.177 11462 Z= 0.512 Angle : 1.173 23.476 15615 Z= 0.557 Chirality : 0.059 0.485 1868 Planarity : 0.007 0.084 1877 Dihedral : 15.399 116.639 4589 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.81 % Favored : 93.04 % Rotamer: Outliers : 0.44 % Allowed : 2.99 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.08 % 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: -4.02 (0.17), residues: 1351 helix: -2.36 (0.14), residues: 697 sheet: -1.88 (0.43), residues: 125 loop : -3.14 (0.21), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP C 227 HIS 0.012 0.003 HIS C 197 PHE 0.041 0.003 PHE C 132 TYR 0.030 0.002 TYR A 565 ARG 0.013 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 PHE cc_start: 0.8577 (m-80) cc_final: 0.8260 (m-80) REVERT: B 165 TRP cc_start: 0.7314 (t60) cc_final: 0.6977 (t60) REVERT: B 248 LEU cc_start: 0.8061 (mt) cc_final: 0.7522 (tm) REVERT: B 259 VAL cc_start: 0.7387 (p) cc_final: 0.7093 (m) REVERT: C 117 MET cc_start: 0.8093 (mtm) cc_final: 0.7874 (mtt) outliers start: 5 outliers final: 2 residues processed: 222 average time/residue: 1.1897 time to fit residues: 286.0964 Evaluate side-chains 128 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain C residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 158 HIS A 305 GLN A 331 GLN A 358 ASN A 454 GLN A 531 ASN A 587 GLN A 606 GLN B 81 HIS B 135 ASN D 50 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11462 Z= 0.200 Angle : 0.681 10.006 15615 Z= 0.332 Chirality : 0.045 0.254 1868 Planarity : 0.005 0.097 1877 Dihedral : 13.949 111.260 2264 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 3.69 % Allowed : 9.66 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.21), residues: 1351 helix: -0.46 (0.19), residues: 704 sheet: -1.63 (0.42), residues: 131 loop : -2.85 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 227 HIS 0.006 0.001 HIS C 197 PHE 0.038 0.002 PHE A 302 TYR 0.018 0.002 TYR D 91 ARG 0.005 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7553 (t0) cc_final: 0.7249 (t0) REVERT: A 186 GLU cc_start: 0.6791 (tp30) cc_final: 0.6465 (tm-30) REVERT: A 231 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8394 (mmm) REVERT: A 601 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: A 657 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8417 (ptt-90) REVERT: B 165 TRP cc_start: 0.7130 (t60) cc_final: 0.6926 (t60) REVERT: B 248 LEU cc_start: 0.7885 (mt) cc_final: 0.7496 (tm) REVERT: B 259 VAL cc_start: 0.7431 (p) cc_final: 0.7104 (m) REVERT: B 287 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7949 (mp) REVERT: C 240 GLN cc_start: 0.7811 (mt0) cc_final: 0.7585 (mt0) REVERT: D 54 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7474 (ttmm) outliers start: 42 outliers final: 16 residues processed: 159 average time/residue: 1.2070 time to fit residues: 207.4561 Evaluate side-chains 126 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 0.0870 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 142 ASN A 169 ASN A 194 GLN A 222 HIS A 553 HIS A 587 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11462 Z= 0.408 Angle : 0.791 12.223 15615 Z= 0.388 Chirality : 0.049 0.267 1868 Planarity : 0.006 0.102 1877 Dihedral : 12.859 114.137 2264 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.09 % Allowed : 11.85 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.67 (0.22), residues: 1351 helix: 0.02 (0.19), residues: 721 sheet: -1.51 (0.40), residues: 134 loop : -2.66 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 209 HIS 0.014 0.002 HIS A 449 PHE 0.040 0.003 PHE A 302 TYR 0.023 0.003 TYR B 225 ARG 0.008 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 116 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 601 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: A 657 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8406 (ptt-90) REVERT: B 248 LEU cc_start: 0.7921 (mt) cc_final: 0.7548 (tm) REVERT: B 259 VAL cc_start: 0.7514 (p) cc_final: 0.7220 (m) REVERT: C 180 ASP cc_start: 0.8241 (t70) cc_final: 0.7939 (t0) outliers start: 58 outliers final: 27 residues processed: 156 average time/residue: 1.2924 time to fit residues: 217.6494 Evaluate side-chains 143 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 102 HIS A 587 GLN B 222 GLN C 240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11462 Z= 0.177 Angle : 0.612 11.404 15615 Z= 0.301 Chirality : 0.043 0.254 1868 Planarity : 0.004 0.081 1877 Dihedral : 11.876 117.903 2264 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.99 % Allowed : 14.93 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.89 (0.23), residues: 1351 helix: 0.66 (0.20), residues: 715 sheet: -1.13 (0.42), residues: 135 loop : -2.30 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 165 HIS 0.005 0.001 HIS A 449 PHE 0.034 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.010 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7455 (t0) cc_final: 0.7247 (t0) REVERT: A 75 VAL cc_start: 0.9164 (m) cc_final: 0.8914 (t) REVERT: A 186 GLU cc_start: 0.6676 (tp30) cc_final: 0.6372 (tm-30) REVERT: A 231 MET cc_start: 0.8789 (tpt) cc_final: 0.8378 (mmm) REVERT: A 237 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: A 364 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: A 408 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7794 (p) REVERT: A 601 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: A 657 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8375 (ptt-90) REVERT: B 248 LEU cc_start: 0.7836 (mt) cc_final: 0.7489 (tm) REVERT: B 255 VAL cc_start: 0.8746 (t) cc_final: 0.8464 (m) REVERT: B 259 VAL cc_start: 0.7381 (p) cc_final: 0.7049 (m) REVERT: D 54 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7282 (ttpt) outliers start: 34 outliers final: 17 residues processed: 148 average time/residue: 1.2541 time to fit residues: 200.7331 Evaluate side-chains 135 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 222 HIS A 587 GLN C 240 GLN D 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11462 Z= 0.193 Angle : 0.613 12.080 15615 Z= 0.300 Chirality : 0.044 0.253 1868 Planarity : 0.004 0.084 1877 Dihedral : 11.456 114.215 2264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.25 % Allowed : 15.89 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.64 (0.23), residues: 1351 helix: 0.86 (0.20), residues: 722 sheet: -1.00 (0.42), residues: 135 loop : -2.21 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 165 HIS 0.005 0.001 HIS A 449 PHE 0.033 0.001 PHE A 302 TYR 0.013 0.001 TYR B 225 ARG 0.009 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7508 (t0) cc_final: 0.7302 (t0) REVERT: A 75 VAL cc_start: 0.9135 (m) cc_final: 0.8904 (t) REVERT: A 186 GLU cc_start: 0.6678 (tp30) cc_final: 0.6366 (tm-30) REVERT: A 231 MET cc_start: 0.8846 (tpt) cc_final: 0.8394 (mmm) REVERT: A 237 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: A 343 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8256 (tpt) REVERT: A 408 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 601 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: A 657 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8391 (ptt-90) REVERT: B 165 TRP cc_start: 0.7155 (t60) cc_final: 0.6890 (t60) REVERT: B 248 LEU cc_start: 0.7805 (mt) cc_final: 0.7463 (tm) REVERT: B 255 VAL cc_start: 0.8745 (t) cc_final: 0.8460 (m) REVERT: B 259 VAL cc_start: 0.7371 (p) cc_final: 0.7038 (m) REVERT: E 36 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7630 (pp) outliers start: 37 outliers final: 16 residues processed: 148 average time/residue: 1.2270 time to fit residues: 196.9169 Evaluate side-chains 136 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 36 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 222 HIS A 587 GLN C 240 GLN D 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11462 Z= 0.227 Angle : 0.632 12.582 15615 Z= 0.308 Chirality : 0.044 0.253 1868 Planarity : 0.004 0.078 1877 Dihedral : 11.298 111.621 2264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.42 % Allowed : 16.59 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.47 (0.23), residues: 1351 helix: 0.98 (0.20), residues: 720 sheet: -0.90 (0.42), residues: 134 loop : -2.10 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 165 HIS 0.006 0.001 HIS A 449 PHE 0.035 0.002 PHE A 302 TYR 0.016 0.002 TYR D 47 ARG 0.011 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7589 (t0) cc_final: 0.7358 (t0) REVERT: A 75 VAL cc_start: 0.9129 (m) cc_final: 0.8895 (t) REVERT: A 186 GLU cc_start: 0.6683 (tp30) cc_final: 0.6367 (tm-30) REVERT: A 231 MET cc_start: 0.8857 (tpt) cc_final: 0.8383 (mmm) REVERT: A 237 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: A 343 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8297 (tpt) REVERT: A 601 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7081 (tt0) REVERT: A 657 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8395 (ptt-90) REVERT: B 165 TRP cc_start: 0.7188 (t60) cc_final: 0.6975 (t60) REVERT: B 248 LEU cc_start: 0.7832 (mt) cc_final: 0.7512 (tm) REVERT: B 259 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7013 (m) REVERT: C 237 ARG cc_start: 0.6990 (mmm160) cc_final: 0.6737 (mmm-85) REVERT: D 54 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7305 (ttpt) REVERT: E 36 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7639 (pp) outliers start: 39 outliers final: 23 residues processed: 147 average time/residue: 1.2635 time to fit residues: 201.1426 Evaluate side-chains 143 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 36 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN C 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11462 Z= 0.192 Angle : 0.611 12.467 15615 Z= 0.298 Chirality : 0.044 0.251 1868 Planarity : 0.004 0.079 1877 Dihedral : 10.983 108.477 2264 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.07 % Allowed : 16.94 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.35 (0.23), residues: 1351 helix: 1.07 (0.20), residues: 726 sheet: -0.77 (0.43), residues: 134 loop : -2.10 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 165 HIS 0.005 0.001 HIS A 449 PHE 0.032 0.001 PHE A 302 TYR 0.017 0.001 TYR D 19 ARG 0.009 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7504 (t0) cc_final: 0.7298 (t0) REVERT: A 75 VAL cc_start: 0.9079 (m) cc_final: 0.8842 (t) REVERT: A 186 GLU cc_start: 0.6649 (tp30) cc_final: 0.6338 (tm-30) REVERT: A 231 MET cc_start: 0.8840 (tpt) cc_final: 0.8388 (mmm) REVERT: A 343 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8280 (tpt) REVERT: A 601 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: A 657 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8367 (ptt-90) REVERT: B 165 TRP cc_start: 0.7163 (t60) cc_final: 0.6924 (t60) REVERT: B 248 LEU cc_start: 0.7844 (mt) cc_final: 0.7522 (tm) REVERT: B 259 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.6984 (m) REVERT: C 237 ARG cc_start: 0.6976 (mmm160) cc_final: 0.6744 (mmm-85) outliers start: 35 outliers final: 24 residues processed: 147 average time/residue: 1.2455 time to fit residues: 198.3066 Evaluate side-chains 143 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain E residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 0.0020 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS C 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11462 Z= 0.286 Angle : 0.683 13.688 15615 Z= 0.332 Chirality : 0.046 0.256 1868 Planarity : 0.005 0.080 1877 Dihedral : 11.151 106.961 2264 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.78 % Allowed : 17.03 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.45 (0.23), residues: 1351 helix: 1.00 (0.20), residues: 719 sheet: -0.82 (0.43), residues: 134 loop : -2.12 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 165 HIS 0.008 0.001 HIS A 449 PHE 0.037 0.002 PHE A 302 TYR 0.019 0.002 TYR D 19 ARG 0.007 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7766 (t0) cc_final: 0.7518 (t0) REVERT: A 75 VAL cc_start: 0.9134 (m) cc_final: 0.8897 (t) REVERT: A 237 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: A 601 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: A 657 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8393 (ptt-90) REVERT: B 165 TRP cc_start: 0.7206 (t60) cc_final: 0.6986 (t60) REVERT: B 248 LEU cc_start: 0.7875 (mt) cc_final: 0.7550 (tm) REVERT: B 259 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7001 (m) REVERT: D 84 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6337 (mtm180) outliers start: 43 outliers final: 27 residues processed: 139 average time/residue: 1.2943 time to fit residues: 194.0881 Evaluate side-chains 142 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS C 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11462 Z= 0.449 Angle : 0.801 15.430 15615 Z= 0.390 Chirality : 0.051 0.254 1868 Planarity : 0.006 0.086 1877 Dihedral : 11.841 109.200 2264 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.25 % Allowed : 17.73 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.81 (0.23), residues: 1351 helix: 0.68 (0.20), residues: 724 sheet: -0.97 (0.42), residues: 135 loop : -2.28 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 36 HIS 0.012 0.002 HIS A 449 PHE 0.043 0.003 PHE A 302 TYR 0.024 0.002 TYR B 466 ARG 0.014 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 75 VAL cc_start: 0.9149 (m) cc_final: 0.8916 (t) REVERT: A 114 ARG cc_start: 0.7219 (mtp85) cc_final: 0.6940 (mtp180) REVERT: A 601 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: A 657 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8391 (ptt-90) REVERT: B 248 LEU cc_start: 0.7921 (mt) cc_final: 0.7577 (tm) REVERT: B 259 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.7105 (m) REVERT: D 84 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6321 (mtm180) outliers start: 37 outliers final: 27 residues processed: 136 average time/residue: 1.3009 time to fit residues: 191.2403 Evaluate side-chains 139 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 11 optimal weight: 0.0170 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 355 GLN A 385 GLN B 222 GLN C 240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11462 Z= 0.179 Angle : 0.635 13.538 15615 Z= 0.309 Chirality : 0.043 0.260 1868 Planarity : 0.004 0.076 1877 Dihedral : 11.080 105.918 2264 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.55 % Allowed : 18.53 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.40 (0.23), residues: 1351 helix: 1.03 (0.20), residues: 724 sheet: -0.84 (0.42), residues: 136 loop : -2.11 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 165 HIS 0.007 0.001 HIS A 222 PHE 0.033 0.001 PHE A 302 TYR 0.017 0.001 TYR D 19 ARG 0.014 0.001 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7416 (t0) cc_final: 0.7182 (t0) REVERT: A 75 VAL cc_start: 0.9149 (m) cc_final: 0.8910 (t) REVERT: A 114 ARG cc_start: 0.7382 (mtp85) cc_final: 0.7155 (mtp180) REVERT: A 186 GLU cc_start: 0.6487 (tp30) cc_final: 0.6201 (tm-30) REVERT: A 343 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8239 (tpt) REVERT: A 601 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: A 657 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8339 (ptt-90) REVERT: B 248 LEU cc_start: 0.7904 (mt) cc_final: 0.7574 (tm) REVERT: B 259 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6907 (m) outliers start: 29 outliers final: 22 residues processed: 133 average time/residue: 1.2153 time to fit residues: 175.6324 Evaluate side-chains 136 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 44 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 691 ASN C 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107834 restraints weight = 14231.925| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.27 r_work: 0.3079 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11462 Z= 0.180 Angle : 0.632 12.922 15615 Z= 0.306 Chirality : 0.043 0.251 1868 Planarity : 0.004 0.080 1877 Dihedral : 10.576 101.243 2264 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.19 % Allowed : 19.40 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.15 (0.24), residues: 1351 helix: 1.23 (0.20), residues: 720 sheet: -0.72 (0.43), residues: 135 loop : -1.94 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 165 HIS 0.006 0.001 HIS A 222 PHE 0.030 0.001 PHE A 302 TYR 0.019 0.001 TYR D 19 ARG 0.015 0.001 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4040.77 seconds wall clock time: 81 minutes 7.65 seconds (4867.65 seconds total)