Starting phenix.real_space_refine on Tue Jul 29 21:35:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6idf_9648/07_2025/6idf_9648.cif Found real_map, /net/cci-nas-00/data/ceres_data/6idf_9648/07_2025/6idf_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/cci-nas-00/data/ceres_data/6idf_9648/07_2025/6idf_9648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6idf_9648/07_2025/6idf_9648.map" model { file = "/net/cci-nas-00/data/ceres_data/6idf_9648/07_2025/6idf_9648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6idf_9648/07_2025/6idf_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.94, per 1000 atoms: 0.71 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: 3.05 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: 1.26 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: 3.81 Time building geometry restraints manager: 3.60 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: 2.190 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.340 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:14.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.320 ------------------------------------------------------------------------------- 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 11488 Z= 0.380 Angle : 1.201 23.476 15685 Z= 0.563 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01034 ( 11) link_NAG-ASN : angle 4.91600 ( 33) link_BETA1-4 : bond 0.01683 ( 7) link_BETA1-4 : angle 3.56597 ( 21) hydrogen bonds : bond 0.15547 ( 545) hydrogen bonds : angle 6.64183 ( 1572) link_BETA1-6 : bond 0.00663 ( 1) link_BETA1-6 : angle 1.33488 ( 3) SS BOND : bond 0.00505 ( 5) SS BOND : angle 2.42310 ( 10) link_BETA1-3 : bond 0.00608 ( 1) link_BETA1-3 : angle 1.96120 ( 3) covalent geometry : bond 0.00776 (11462) covalent geometry : angle 1.17263 (15615) Misc. bond : bond 0.00363 ( 1) *********************** 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 to be fit. rotamer outliers: 5 poor density : 217 time to evaluate : 1.213 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: 1.5952 time to fit residues: 386.4605 Evaluate side-chains 128 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114967 restraints weight = 14294.552| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.14 r_work: 0.3194 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11488 Z= 0.137 Angle : 0.702 10.260 15685 Z= 0.335 Chirality : 0.045 0.262 1868 Planarity : 0.005 0.097 1877 Dihedral : 13.826 111.654 2264 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 3.78 % Allowed : 9.66 % Favored : 86.57 % 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: -2.19 (0.21), residues: 1351 helix: -0.45 (0.19), residues: 704 sheet: -1.61 (0.42), residues: 130 loop : -2.81 (0.23), residues: 517 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 0.020 0.002 TYR D 91 ARG 0.005 0.001 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 11) link_NAG-ASN : angle 3.43804 ( 33) link_BETA1-4 : bond 0.00745 ( 7) link_BETA1-4 : angle 2.30047 ( 21) hydrogen bonds : bond 0.04441 ( 545) hydrogen bonds : angle 4.65836 ( 1572) link_BETA1-6 : bond 0.01627 ( 1) link_BETA1-6 : angle 2.65109 ( 3) SS BOND : bond 0.00837 ( 5) SS BOND : angle 1.96515 ( 10) link_BETA1-3 : bond 0.01150 ( 1) link_BETA1-3 : angle 1.84325 ( 3) covalent geometry : bond 0.00302 (11462) covalent geometry : angle 0.67660 (15615) Misc. bond : bond 0.00175 ( 1) *********************** 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 177 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8788 (mptm) cc_final: 0.8481 (mppt) REVERT: A 55 ASN cc_start: 0.8105 (t0) cc_final: 0.7826 (t0) REVERT: A 78 LYS cc_start: 0.8285 (ptpt) cc_final: 0.7980 (pttt) REVERT: A 80 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7641 (tp30) REVERT: A 186 GLU cc_start: 0.7350 (tp30) cc_final: 0.6828 (tm-30) REVERT: A 231 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8524 (mmm) REVERT: A 474 GLU cc_start: 0.8162 (tp30) cc_final: 0.7961 (tp30) REVERT: A 601 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 657 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8601 (ptt-90) REVERT: B 165 TRP cc_start: 0.7277 (t60) cc_final: 0.7067 (t60) REVERT: B 248 LEU cc_start: 0.7703 (mt) cc_final: 0.7290 (tm) REVERT: B 255 VAL cc_start: 0.8581 (t) cc_final: 0.8271 (m) REVERT: B 259 VAL cc_start: 0.7249 (p) cc_final: 0.6889 (m) REVERT: C 240 GLN cc_start: 0.7780 (mt0) cc_final: 0.7475 (mt0) outliers start: 43 outliers final: 16 residues processed: 162 average time/residue: 1.2261 time to fit residues: 215.2253 Evaluate side-chains 131 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 63 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 131 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 169 ASN A 194 GLN A 222 HIS A 553 HIS A 587 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107835 restraints weight = 14320.007| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.06 r_work: 0.3049 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11488 Z= 0.219 Angle : 0.759 11.427 15685 Z= 0.367 Chirality : 0.048 0.255 1868 Planarity : 0.005 0.097 1877 Dihedral : 12.636 114.078 2264 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.57 % Allowed : 11.94 % Favored : 83.49 % 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: -1.51 (0.22), residues: 1351 helix: 0.18 (0.20), residues: 715 sheet: -1.46 (0.41), residues: 134 loop : -2.61 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 209 HIS 0.013 0.002 HIS A 449 PHE 0.040 0.003 PHE A 302 TYR 0.021 0.002 TYR B 225 ARG 0.006 0.001 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 11) link_NAG-ASN : angle 3.31136 ( 33) link_BETA1-4 : bond 0.00786 ( 7) link_BETA1-4 : angle 2.44722 ( 21) hydrogen bonds : bond 0.05105 ( 545) hydrogen bonds : angle 4.42691 ( 1572) link_BETA1-6 : bond 0.01085 ( 1) link_BETA1-6 : angle 2.12389 ( 3) SS BOND : bond 0.00515 ( 5) SS BOND : angle 1.82235 ( 10) link_BETA1-3 : bond 0.01166 ( 1) link_BETA1-3 : angle 1.19905 ( 3) covalent geometry : bond 0.00528 (11462) covalent geometry : angle 0.73751 (15615) Misc. bond : bond 0.00219 ( 1) *********************** 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 170 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8800 (mptm) cc_final: 0.8418 (mppt) REVERT: A 75 VAL cc_start: 0.9250 (m) cc_final: 0.8924 (t) REVERT: A 78 LYS cc_start: 0.8324 (ptpt) cc_final: 0.8077 (pttt) REVERT: A 80 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7657 (tp30) REVERT: A 85 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8833 (m) REVERT: A 474 GLU cc_start: 0.8128 (tp30) cc_final: 0.7905 (tp30) REVERT: A 583 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6811 (ttt180) REVERT: A 601 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: A 657 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8657 (ptt-90) REVERT: A 669 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: B 248 LEU cc_start: 0.7747 (mt) cc_final: 0.7361 (tm) REVERT: B 259 VAL cc_start: 0.7305 (p) cc_final: 0.6950 (m) REVERT: C 211 GLU cc_start: 0.8597 (pt0) cc_final: 0.8376 (pm20) REVERT: D 54 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6952 (ttpt) outliers start: 52 outliers final: 24 residues processed: 153 average time/residue: 1.2453 time to fit residues: 205.6932 Evaluate side-chains 144 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 85 VAL 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 643 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU 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 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 54 LYS 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 45 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 587 GLN B 222 GLN C 240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107376 restraints weight = 14182.684| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.20 r_work: 0.3078 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11488 Z= 0.141 Angle : 0.650 11.854 15685 Z= 0.315 Chirality : 0.044 0.264 1868 Planarity : 0.004 0.081 1877 Dihedral : 11.973 117.407 2264 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.51 % Allowed : 14.05 % Favored : 82.44 % 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: -0.95 (0.23), residues: 1351 helix: 0.63 (0.20), residues: 716 sheet: -1.18 (0.41), residues: 134 loop : -2.36 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 165 HIS 0.007 0.001 HIS A 449 PHE 0.035 0.002 PHE A 302 TYR 0.015 0.002 TYR B 225 ARG 0.010 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 11) link_NAG-ASN : angle 2.67108 ( 33) link_BETA1-4 : bond 0.00740 ( 7) link_BETA1-4 : angle 2.20774 ( 21) hydrogen bonds : bond 0.04136 ( 545) hydrogen bonds : angle 4.23266 ( 1572) link_BETA1-6 : bond 0.01233 ( 1) link_BETA1-6 : angle 1.73176 ( 3) SS BOND : bond 0.00342 ( 5) SS BOND : angle 1.27863 ( 10) link_BETA1-3 : bond 0.01160 ( 1) link_BETA1-3 : angle 0.85846 ( 3) covalent geometry : bond 0.00326 (11462) covalent geometry : angle 0.63285 (15615) Misc. bond : bond 0.00195 ( 1) *********************** 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 161 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8733 (mptm) cc_final: 0.8352 (mppt) REVERT: A 55 ASN cc_start: 0.8119 (t0) cc_final: 0.7913 (t0) REVERT: A 75 VAL cc_start: 0.9229 (m) cc_final: 0.8880 (t) REVERT: A 78 LYS cc_start: 0.8275 (ptpt) cc_final: 0.8008 (pttt) REVERT: A 80 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7654 (tp30) REVERT: A 186 GLU cc_start: 0.7321 (tp30) cc_final: 0.6801 (tm-30) REVERT: A 231 MET cc_start: 0.8901 (tpt) cc_final: 0.8500 (mmm) REVERT: A 237 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: A 364 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: A 507 PHE cc_start: 0.8621 (m-80) cc_final: 0.8408 (m-80) REVERT: A 583 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.6920 (ttt90) REVERT: A 601 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: A 657 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8570 (ptt-90) REVERT: A 669 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: B 165 TRP cc_start: 0.7350 (t60) cc_final: 0.7141 (t60) REVERT: B 248 LEU cc_start: 0.7629 (mt) cc_final: 0.7258 (tm) REVERT: B 259 VAL cc_start: 0.7236 (p) cc_final: 0.6844 (m) REVERT: C 211 GLU cc_start: 0.8556 (pt0) cc_final: 0.8339 (pm20) REVERT: E 36 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7620 (pp) outliers start: 40 outliers final: 22 residues processed: 150 average time/residue: 1.3105 time to fit residues: 211.9688 Evaluate side-chains 142 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 HIS 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 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 669 GLU 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 C residue 236 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 36 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 overall best weight: 1.7344 ------------------------------------------------------------------------------- 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 222 HIS A 587 GLN C 240 GLN D 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103684 restraints weight = 14145.739| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.18 r_work: 0.3019 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11488 Z= 0.223 Angle : 0.735 13.325 15685 Z= 0.355 Chirality : 0.048 0.259 1868 Planarity : 0.005 0.090 1877 Dihedral : 12.019 115.639 2264 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.48 % Allowed : 14.31 % Favored : 81.21 % 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: -0.94 (0.23), residues: 1351 helix: 0.60 (0.20), residues: 722 sheet: -1.17 (0.41), residues: 134 loop : -2.33 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 165 HIS 0.011 0.002 HIS A 449 PHE 0.038 0.002 PHE A 302 TYR 0.021 0.002 TYR D 18 ARG 0.009 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 11) link_NAG-ASN : angle 3.04514 ( 33) link_BETA1-4 : bond 0.00756 ( 7) link_BETA1-4 : angle 2.46987 ( 21) hydrogen bonds : bond 0.04905 ( 545) hydrogen bonds : angle 4.26181 ( 1572) link_BETA1-6 : bond 0.01049 ( 1) link_BETA1-6 : angle 1.81413 ( 3) SS BOND : bond 0.00448 ( 5) SS BOND : angle 1.57608 ( 10) link_BETA1-3 : bond 0.01085 ( 1) link_BETA1-3 : angle 0.81592 ( 3) covalent geometry : bond 0.00542 (11462) covalent geometry : angle 0.71629 (15615) Misc. bond : bond 0.00221 ( 1) *********************** 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 167 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8834 (mptm) cc_final: 0.8402 (mppt) REVERT: A 55 ASN cc_start: 0.8339 (t0) cc_final: 0.8098 (t0) REVERT: A 78 LYS cc_start: 0.8233 (ptpt) cc_final: 0.7939 (pttt) REVERT: A 80 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7625 (tp30) REVERT: A 85 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8844 (m) REVERT: A 237 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: A 364 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: A 583 ARG cc_start: 0.7292 (ttp-110) cc_final: 0.6890 (ttt90) REVERT: A 601 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: A 657 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8590 (ptt-90) REVERT: A 667 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7307 (tt0) REVERT: A 669 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: B 165 TRP cc_start: 0.7430 (t60) cc_final: 0.7229 (t60) REVERT: B 248 LEU cc_start: 0.7639 (mt) cc_final: 0.7269 (tm) REVERT: B 259 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6866 (m) REVERT: C 180 ASP cc_start: 0.8649 (t70) cc_final: 0.8342 (t0) REVERT: C 211 GLU cc_start: 0.8600 (pt0) cc_final: 0.8373 (pm20) REVERT: C 237 ARG cc_start: 0.7077 (mmm160) cc_final: 0.6835 (mmm160) REVERT: D 54 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7318 (ttpt) outliers start: 51 outliers final: 28 residues processed: 154 average time/residue: 1.2800 time to fit residues: 212.9684 Evaluate side-chains 149 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 85 VAL 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 201 LEU 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 364 GLU 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 598 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU 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 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 optimal weight: 0.6980 chunk 37 optimal weight: 0.0020 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 587 GLN C 240 GLN D 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107388 restraints weight = 14207.310| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.22 r_work: 0.3075 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11488 Z= 0.121 Angle : 0.617 12.491 15685 Z= 0.298 Chirality : 0.043 0.257 1868 Planarity : 0.004 0.076 1877 Dihedral : 11.397 113.262 2264 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.90 % Allowed : 16.24 % 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: -0.49 (0.23), residues: 1351 helix: 0.98 (0.20), residues: 719 sheet: -0.81 (0.42), residues: 130 loop : -2.17 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 165 HIS 0.004 0.001 HIS A 222 PHE 0.032 0.001 PHE A 302 TYR 0.015 0.001 TYR D 47 ARG 0.009 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 11) link_NAG-ASN : angle 2.36447 ( 33) link_BETA1-4 : bond 0.00786 ( 7) link_BETA1-4 : angle 2.17435 ( 21) hydrogen bonds : bond 0.03767 ( 545) hydrogen bonds : angle 4.08434 ( 1572) link_BETA1-6 : bond 0.01177 ( 1) link_BETA1-6 : angle 1.90027 ( 3) SS BOND : bond 0.00265 ( 5) SS BOND : angle 0.99798 ( 10) link_BETA1-3 : bond 0.01100 ( 1) link_BETA1-3 : angle 0.70637 ( 3) covalent geometry : bond 0.00274 (11462) covalent geometry : angle 0.60249 (15615) Misc. bond : bond 0.00174 ( 1) *********************** 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 154 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8723 (mptm) cc_final: 0.8312 (mppt) REVERT: A 75 VAL cc_start: 0.9211 (m) cc_final: 0.8856 (t) REVERT: A 78 LYS cc_start: 0.8256 (ptpt) cc_final: 0.7892 (pttp) REVERT: A 80 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7618 (tp30) REVERT: A 174 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8771 (mm-30) REVERT: A 186 GLU cc_start: 0.7083 (tp30) cc_final: 0.6580 (tm-30) REVERT: A 237 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: A 364 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: A 408 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 507 PHE cc_start: 0.8605 (m-80) cc_final: 0.8353 (m-80) REVERT: A 583 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6863 (ttt90) REVERT: A 601 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 657 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8532 (ptt-90) REVERT: A 669 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: B 165 TRP cc_start: 0.7427 (t60) cc_final: 0.7219 (t60) REVERT: B 248 LEU cc_start: 0.7592 (mt) cc_final: 0.7248 (tm) REVERT: B 259 VAL cc_start: 0.7150 (OUTLIER) cc_final: 0.6777 (m) REVERT: C 211 GLU cc_start: 0.8610 (pt0) cc_final: 0.8379 (pm20) REVERT: C 237 ARG cc_start: 0.7004 (mmm160) cc_final: 0.6509 (mmm160) REVERT: D 54 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7343 (ttpt) outliers start: 33 outliers final: 17 residues processed: 145 average time/residue: 1.4118 time to fit residues: 221.3769 Evaluate side-chains 139 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 318 VAL Chi-restraints excluded: chain A residue 364 GLU 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 601 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 259 VAL 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 226 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 C 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102359 restraints weight = 14258.321| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.12 r_work: 0.2989 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11488 Z= 0.269 Angle : 0.781 14.402 15685 Z= 0.377 Chirality : 0.050 0.253 1868 Planarity : 0.005 0.089 1877 Dihedral : 11.892 113.092 2264 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.78 % Allowed : 15.98 % Favored : 80.25 % 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: -0.87 (0.23), residues: 1351 helix: 0.64 (0.20), residues: 726 sheet: -1.00 (0.41), residues: 134 loop : -2.32 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 36 HIS 0.011 0.002 HIS A 449 PHE 0.038 0.002 PHE A 302 TYR 0.023 0.002 TYR B 466 ARG 0.008 0.001 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 11) link_NAG-ASN : angle 3.08414 ( 33) link_BETA1-4 : bond 0.00761 ( 7) link_BETA1-4 : angle 2.58035 ( 21) hydrogen bonds : bond 0.05222 ( 545) hydrogen bonds : angle 4.26314 ( 1572) link_BETA1-6 : bond 0.00985 ( 1) link_BETA1-6 : angle 2.02498 ( 3) SS BOND : bond 0.00505 ( 5) SS BOND : angle 1.66749 ( 10) link_BETA1-3 : bond 0.01063 ( 1) link_BETA1-3 : angle 0.75790 ( 3) covalent geometry : bond 0.00659 (11462) covalent geometry : angle 0.76244 (15615) Misc. bond : bond 0.00244 ( 1) *********************** 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 160 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8831 (mptm) cc_final: 0.8411 (mppt) REVERT: A 75 VAL cc_start: 0.9240 (m) cc_final: 0.8896 (t) REVERT: A 80 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7625 (tp30) REVERT: A 237 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: A 583 ARG cc_start: 0.7344 (ttp-110) cc_final: 0.6905 (ttt90) REVERT: A 601 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 626 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8504 (ptp90) REVERT: A 657 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8606 (ptt-90) REVERT: A 667 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7365 (tt0) REVERT: A 669 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: B 248 LEU cc_start: 0.7639 (mt) cc_final: 0.7272 (tm) REVERT: B 259 VAL cc_start: 0.7210 (OUTLIER) cc_final: 0.6857 (m) REVERT: C 180 ASP cc_start: 0.8578 (t70) cc_final: 0.8333 (t0) REVERT: C 211 GLU cc_start: 0.8616 (pt0) cc_final: 0.8403 (pm20) REVERT: C 237 ARG cc_start: 0.7017 (mmm160) cc_final: 0.6511 (mmm160) REVERT: D 54 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7373 (ttpt) outliers start: 43 outliers final: 24 residues processed: 151 average time/residue: 1.4424 time to fit residues: 236.1929 Evaluate side-chains 145 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 82 LEU 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 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 318 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 A residue 669 GLU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 84 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 385 GLN C 240 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107235 restraints weight = 14229.569| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.27 r_work: 0.3086 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11488 Z= 0.118 Angle : 0.637 13.472 15685 Z= 0.308 Chirality : 0.043 0.258 1868 Planarity : 0.004 0.075 1877 Dihedral : 11.305 110.490 2264 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.99 % Allowed : 16.68 % Favored : 80.33 % 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: -0.41 (0.23), residues: 1351 helix: 1.06 (0.20), residues: 716 sheet: -0.85 (0.42), residues: 135 loop : -2.12 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 165 HIS 0.006 0.001 HIS A 222 PHE 0.031 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.008 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 11) link_NAG-ASN : angle 2.37601 ( 33) link_BETA1-4 : bond 0.00791 ( 7) link_BETA1-4 : angle 2.19756 ( 21) hydrogen bonds : bond 0.03826 ( 545) hydrogen bonds : angle 4.07275 ( 1572) link_BETA1-6 : bond 0.01194 ( 1) link_BETA1-6 : angle 2.05017 ( 3) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.94298 ( 10) link_BETA1-3 : bond 0.01155 ( 1) link_BETA1-3 : angle 0.84685 ( 3) covalent geometry : bond 0.00259 (11462) covalent geometry : angle 0.62243 (15615) Misc. bond : bond 0.00157 ( 1) *********************** 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 to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8694 (mptm) cc_final: 0.8307 (mppt) REVERT: A 75 VAL cc_start: 0.9232 (m) cc_final: 0.8896 (t) REVERT: A 80 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7671 (tp30) REVERT: A 174 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8794 (mm-30) REVERT: A 186 GLU cc_start: 0.6982 (tp30) cc_final: 0.6478 (tm-30) REVERT: A 231 MET cc_start: 0.8916 (tpt) cc_final: 0.8546 (mmm) REVERT: A 583 ARG cc_start: 0.7300 (ttp-110) cc_final: 0.6934 (ttt90) REVERT: A 601 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: A 657 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8565 (ptt-90) REVERT: B 165 TRP cc_start: 0.7359 (t60) cc_final: 0.7068 (t60) REVERT: B 248 LEU cc_start: 0.7661 (mt) cc_final: 0.7312 (tm) REVERT: B 259 VAL cc_start: 0.7093 (OUTLIER) cc_final: 0.6709 (m) REVERT: C 237 ARG cc_start: 0.6938 (mmm160) cc_final: 0.6437 (mmm160) REVERT: D 54 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7413 (ttpt) outliers start: 34 outliers final: 18 residues processed: 144 average time/residue: 1.7828 time to fit residues: 276.4677 Evaluate side-chains 138 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 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 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 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 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 C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 91 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 97 optimal weight: 0.0370 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 C 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108090 restraints weight = 14209.450| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.13 r_work: 0.3073 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11488 Z= 0.117 Angle : 0.632 12.951 15685 Z= 0.302 Chirality : 0.043 0.252 1868 Planarity : 0.004 0.081 1877 Dihedral : 10.854 105.651 2264 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.63 % Allowed : 17.65 % Favored : 79.72 % 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: -0.24 (0.23), residues: 1351 helix: 1.16 (0.20), residues: 723 sheet: -0.72 (0.43), residues: 133 loop : -2.03 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 165 HIS 0.005 0.001 HIS A 222 PHE 0.030 0.001 PHE A 302 TYR 0.017 0.001 TYR D 19 ARG 0.008 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 11) link_NAG-ASN : angle 2.43608 ( 33) link_BETA1-4 : bond 0.00732 ( 7) link_BETA1-4 : angle 2.10823 ( 21) hydrogen bonds : bond 0.03614 ( 545) hydrogen bonds : angle 4.00095 ( 1572) link_BETA1-6 : bond 0.01274 ( 1) link_BETA1-6 : angle 2.29934 ( 3) SS BOND : bond 0.00252 ( 5) SS BOND : angle 0.87178 ( 10) link_BETA1-3 : bond 0.01096 ( 1) link_BETA1-3 : angle 0.77173 ( 3) covalent geometry : bond 0.00261 (11462) covalent geometry : angle 0.61757 (15615) Misc. bond : bond 0.00156 ( 1) *********************** 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 149 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8669 (mptm) cc_final: 0.8259 (mppt) REVERT: A 72 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8673 (t) REVERT: A 75 VAL cc_start: 0.9180 (m) cc_final: 0.8841 (t) REVERT: A 80 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7647 (tp30) REVERT: A 186 GLU cc_start: 0.6878 (tp30) cc_final: 0.6440 (tm-30) REVERT: A 231 MET cc_start: 0.8872 (tpt) cc_final: 0.8456 (mmm) REVERT: A 237 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: A 364 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: A 583 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6870 (ttt90) REVERT: A 601 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 657 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8573 (ptt-90) REVERT: B 165 TRP cc_start: 0.7254 (t60) cc_final: 0.6941 (t60) REVERT: B 210 MET cc_start: 0.8026 (mmm) cc_final: 0.7712 (mmm) REVERT: B 248 LEU cc_start: 0.7599 (mt) cc_final: 0.7260 (tm) REVERT: B 259 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6653 (m) REVERT: C 237 ARG cc_start: 0.6980 (mmm160) cc_final: 0.6465 (mmm160) REVERT: D 54 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7319 (ttpt) outliers start: 30 outliers final: 16 residues processed: 141 average time/residue: 1.3161 time to fit residues: 200.4560 Evaluate side-chains 137 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 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 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 487 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 385 GLN C 240 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102864 restraints weight = 14256.105| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.26 r_work: 0.3009 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11488 Z= 0.256 Angle : 0.780 14.739 15685 Z= 0.376 Chirality : 0.050 0.256 1868 Planarity : 0.005 0.083 1877 Dihedral : 11.486 106.298 2264 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.63 % Allowed : 18.00 % Favored : 79.37 % 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: -0.58 (0.23), residues: 1351 helix: 0.89 (0.20), residues: 719 sheet: -0.87 (0.42), residues: 134 loop : -2.18 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 165 HIS 0.010 0.002 HIS A 449 PHE 0.041 0.002 PHE A 302 TYR 0.020 0.002 TYR B 466 ARG 0.008 0.001 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 11) link_NAG-ASN : angle 3.00752 ( 33) link_BETA1-4 : bond 0.00724 ( 7) link_BETA1-4 : angle 2.55258 ( 21) hydrogen bonds : bond 0.05112 ( 545) hydrogen bonds : angle 4.23352 ( 1572) link_BETA1-6 : bond 0.01175 ( 1) link_BETA1-6 : angle 2.27715 ( 3) SS BOND : bond 0.00462 ( 5) SS BOND : angle 1.54966 ( 10) link_BETA1-3 : bond 0.01159 ( 1) link_BETA1-3 : angle 0.66956 ( 3) covalent geometry : bond 0.00621 (11462) covalent geometry : angle 0.76151 (15615) Misc. bond : bond 0.00238 ( 1) ********************** 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 144 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 2.177 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8787 (mptm) cc_final: 0.8370 (mppt) REVERT: A 75 VAL cc_start: 0.9191 (m) cc_final: 0.8852 (t) REVERT: A 80 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7599 (tp30) REVERT: A 237 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7660 (tp40) REVERT: A 364 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: A 583 ARG cc_start: 0.7381 (ttp-110) cc_final: 0.6981 (ttt90) REVERT: A 601 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 626 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8031 (ptp90) REVERT: A 657 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8595 (ptt-90) REVERT: A 667 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7425 (tt0) REVERT: B 165 TRP cc_start: 0.7335 (t60) cc_final: 0.7131 (t60) REVERT: B 210 MET cc_start: 0.8118 (mmm) cc_final: 0.7818 (mmm) REVERT: B 248 LEU cc_start: 0.7696 (mt) cc_final: 0.7328 (tm) REVERT: B 259 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6787 (m) REVERT: C 180 ASP cc_start: 0.8603 (t70) cc_final: 0.8381 (t0) REVERT: C 237 ARG cc_start: 0.6986 (mmm160) cc_final: 0.6470 (mmm160) REVERT: D 54 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7356 (ttpt) outliers start: 30 outliers final: 20 residues processed: 138 average time/residue: 1.8427 time to fit residues: 275.9683 Evaluate side-chains 139 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 82 LEU 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 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 487 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 385 GLN C 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106572 restraints weight = 14205.052| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.34 r_work: 0.3059 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11488 Z= 0.133 Angle : 0.657 13.582 15685 Z= 0.315 Chirality : 0.044 0.258 1868 Planarity : 0.004 0.078 1877 Dihedral : 10.960 104.190 2264 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.19 % Allowed : 18.53 % Favored : 79.28 % 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: -0.29 (0.23), residues: 1351 helix: 1.14 (0.20), residues: 716 sheet: -0.72 (0.42), residues: 133 loop : -2.05 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 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 0.009 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 11) link_NAG-ASN : angle 2.44763 ( 33) link_BETA1-4 : bond 0.00773 ( 7) link_BETA1-4 : angle 2.23092 ( 21) hydrogen bonds : bond 0.03942 ( 545) hydrogen bonds : angle 4.08758 ( 1572) link_BETA1-6 : bond 0.01278 ( 1) link_BETA1-6 : angle 2.31068 ( 3) SS BOND : bond 0.00288 ( 5) SS BOND : angle 0.99830 ( 10) link_BETA1-3 : bond 0.01090 ( 1) link_BETA1-3 : angle 0.75139 ( 3) covalent geometry : bond 0.00304 (11462) covalent geometry : angle 0.64227 (15615) Misc. bond : bond 0.00173 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10425.44 seconds wall clock time: 188 minutes 8.32 seconds (11288.32 seconds total)