Starting phenix.real_space_refine on Wed Sep 17 18:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5z_33629/09_2025/7y5z_33629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5z_33629/09_2025/7y5z_33629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y5z_33629/09_2025/7y5z_33629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5z_33629/09_2025/7y5z_33629.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5z_33629/09_2025/7y5z_33629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5z_33629/09_2025/7y5z_33629.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 6517 2.51 5 N 1576 2.21 5 O 1829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9962 Number of models: 1 Model: "" Number of chains: 13 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: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" 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: "F" 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: "G" 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.45, per 1000 atoms: 0.25 Number of scatterers: 9962 At special positions: 0 Unit cell: (110.415, 95.26, 132.065, 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 39 16.00 P 1 15.00 O 1829 8.00 N 1576 7.00 C 6517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 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=2.02 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 Atom "HETATM 9783 O5 NAG A 802 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 389.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 54.5% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.907A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.839A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.997A 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: 3.618A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.945A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.615A pdb=" N GLN A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.710A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.762A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.524A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.629A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.623A pdb=" N LEU A 546 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.578A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 91 through 110 removed outlier: 4.067A pdb=" N VAL B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 181 removed outlier: 3.791A pdb=" N MET B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.566A pdb=" N TYR B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 220 removed outlier: 3.509A pdb=" N LEU B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 213 " --> pdb=" O TRP B 209 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 247 removed outlier: 3.617A pdb=" N LEU B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.599A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.613A pdb=" N TYR B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 407 removed outlier: 4.136A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 395 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 4.229A pdb=" N SER B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 removed outlier: 4.264A pdb=" N PHE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 30 through 60 removed outlier: 3.826A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 100 removed outlier: 4.028A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 139 removed outlier: 3.520A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.707A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.564A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 214 through 233 removed outlier: 3.534A pdb=" N GLY C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 21 removed outlier: 4.143A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR D 19 " --> pdb=" O CYS D 15 " (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 37 removed outlier: 3.655A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 81 removed outlier: 3.633A pdb=" N VAL D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 4.156A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.557A pdb=" N ARG A 657 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 73 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR A 94 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.723A 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 412 through 414 removed outlier: 4.201A pdb=" N SER A 437 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 256 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.508A pdb=" N THR A 577 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 609 through 610 removed outlier: 4.086A pdb=" N ASP A 615 " --> pdb=" O HIS A 610 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1374 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: 1.62 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1794 1.32 - 1.45: 2727 1.45 - 1.57: 5638 1.57 - 1.70: 4 1.70 - 1.82: 60 Bond restraints: 10223 Sorted by residual: bond pdb=" C1 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.410 1.470 -0.060 2.00e-02 2.50e+03 8.96e+00 bond pdb=" N VAL B 374 " pdb=" CA VAL B 374 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.58e+00 bond pdb=" N VAL A 465 " pdb=" CA VAL A 465 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.22e-02 6.72e+03 8.58e+00 bond pdb=" N VAL B 261 " pdb=" CA VAL B 261 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.24e+00 bond pdb=" N ILE B 368 " pdb=" CA ILE B 368 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 7.98e+00 ... (remaining 10218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 13595 2.77 - 5.53: 307 5.53 - 8.30: 43 8.30 - 11.06: 7 11.06 - 13.83: 1 Bond angle restraints: 13953 Sorted by residual: angle pdb=" C PRO B 248 " pdb=" N GLU B 249 " pdb=" CA GLU B 249 " ideal model delta sigma weight residual 120.79 127.44 -6.65 1.39e+00 5.18e-01 2.29e+01 angle pdb=" N ARG D 16 " pdb=" CA ARG D 16 " pdb=" C ARG D 16 " ideal model delta sigma weight residual 113.43 107.65 5.78 1.26e+00 6.30e-01 2.11e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 109.81 119.54 -9.73 2.21e+00 2.05e-01 1.94e+01 angle pdb=" N VAL A 36 " pdb=" CA VAL A 36 " pdb=" C VAL A 36 " ideal model delta sigma weight residual 111.81 108.03 3.78 8.60e-01 1.35e+00 1.93e+01 angle pdb=" N GLU B 249 " pdb=" CA GLU B 249 " pdb=" C GLU B 249 " ideal model delta sigma weight residual 111.02 116.34 -5.32 1.22e+00 6.72e-01 1.90e+01 ... (remaining 13948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 6087 22.70 - 45.41: 210 45.41 - 68.11: 43 68.11 - 90.81: 19 90.81 - 113.52: 22 Dihedral angle restraints: 6381 sinusoidal: 2846 harmonic: 3535 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 -173.52 87.52 1 1.00e+01 1.00e-02 9.18e+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 -170.14 84.14 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual -180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1417 0.084 - 0.168: 230 0.168 - 0.253: 15 0.253 - 0.337: 5 0.337 - 0.421: 3 Chirality restraints: 1670 Sorted by residual: chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1667 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 464 " -0.034 2.00e-02 2.50e+03 7.85e-02 7.70e+01 pdb=" CG ASN A 464 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 464 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 464 " 0.142 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 201 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 202 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A 560 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.039 5.00e-02 4.00e+02 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1314 2.75 - 3.29: 9492 3.29 - 3.82: 15984 3.82 - 4.36: 18936 4.36 - 4.90: 33001 Nonbonded interactions: 78727 Sorted by model distance: nonbonded pdb=" O VAL B 374 " pdb=" N ALA B 377 " model vdw 2.210 3.120 nonbonded pdb=" O LEU B 433 " pdb=" OG SER C 50 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.295 3.040 nonbonded pdb=" O TRP C 227 " pdb=" OG1 THR C 231 " model vdw 2.303 3.040 ... (remaining 78722 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.009 0.163 10248 Z= 0.393 Angle : 1.232 48.831 14024 Z= 0.597 Chirality : 0.063 0.421 1670 Planarity : 0.007 0.069 1689 Dihedral : 14.621 113.516 4091 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.96 % Allowed : 3.08 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.63 (0.18), residues: 1202 helix: -2.78 (0.15), residues: 618 sheet: -2.90 (0.40), residues: 132 loop : -3.31 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 429 TYR 0.042 0.003 TYR A 565 PHE 0.034 0.003 PHE C 132 TRP 0.046 0.003 TRP D 36 HIS 0.016 0.003 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00847 (10223) covalent geometry : angle 1.03107 (13953) SS BOND : bond 0.00808 ( 4) SS BOND : angle 2.29264 ( 8) hydrogen bonds : bond 0.19375 ( 474) hydrogen bonds : angle 7.69969 ( 1374) link_BETA1-3 : bond 0.00435 ( 1) link_BETA1-3 : angle 0.49021 ( 3) link_BETA1-4 : bond 0.00405 ( 7) link_BETA1-4 : angle 2.63577 ( 21) link_BETA1-6 : bond 0.00506 ( 1) link_BETA1-6 : angle 1.15804 ( 3) link_NAG-ASN : bond 0.04769 ( 12) link_NAG-ASN : angle 13.17049 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 232 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7573 (mmm-85) REVERT: A 221 MET cc_start: 0.8783 (mmp) cc_final: 0.8547 (mmm) REVERT: A 476 ASP cc_start: 0.8774 (m-30) cc_final: 0.8528 (m-30) REVERT: A 639 GLN cc_start: 0.8282 (pt0) cc_final: 0.7772 (tm-30) REVERT: B 171 TRP cc_start: 0.4600 (t60) cc_final: 0.4173 (t60) REVERT: B 174 MET cc_start: 0.7699 (tmt) cc_final: 0.7155 (tmm) REVERT: B 180 LEU cc_start: 0.8818 (mt) cc_final: 0.8113 (mt) REVERT: B 190 GLU cc_start: 0.7989 (tp30) cc_final: 0.7779 (tp30) REVERT: C 12 VAL cc_start: 0.9367 (t) cc_final: 0.9055 (m) REVERT: C 215 LEU cc_start: 0.8744 (mm) cc_final: 0.8541 (mm) REVERT: D 85 TRP cc_start: 0.8421 (m-10) cc_final: 0.8064 (m100) REVERT: D 90 ASP cc_start: 0.8450 (t70) cc_final: 0.8096 (t0) REVERT: D 96 ILE cc_start: 0.8444 (mt) cc_final: 0.8121 (mt) outliers start: 10 outliers final: 6 residues processed: 239 average time/residue: 0.1054 time to fit residues: 35.1854 Evaluate side-chains 152 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 163 GLN A 305 GLN A 355 GLN A 358 ASN A 449 HIS A 540 GLN A 552 GLN A 606 GLN B 210 ASN B 386 ASN C 58 HIS D 13 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077454 restraints weight = 22979.490| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.89 r_work: 0.2967 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10248 Z= 0.151 Angle : 0.723 12.550 14024 Z= 0.348 Chirality : 0.046 0.254 1670 Planarity : 0.005 0.047 1689 Dihedral : 13.421 108.736 1979 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.60 % Allowed : 9.73 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.22), residues: 1202 helix: -0.76 (0.19), residues: 632 sheet: -2.46 (0.41), residues: 132 loop : -2.93 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 435 TYR 0.027 0.002 TYR B 262 PHE 0.029 0.002 PHE A 302 TRP 0.023 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00329 (10223) covalent geometry : angle 0.69843 (13953) SS BOND : bond 0.00791 ( 4) SS BOND : angle 1.05790 ( 8) hydrogen bonds : bond 0.04650 ( 474) hydrogen bonds : angle 4.79093 ( 1374) link_BETA1-3 : bond 0.01217 ( 1) link_BETA1-3 : angle 1.41534 ( 3) link_BETA1-4 : bond 0.00444 ( 7) link_BETA1-4 : angle 1.66321 ( 21) link_BETA1-6 : bond 0.01381 ( 1) link_BETA1-6 : angle 2.61055 ( 3) link_NAG-ASN : bond 0.00503 ( 12) link_NAG-ASN : angle 3.44380 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8390 (mtp180) cc_final: 0.7936 (mtp85) REVERT: A 114 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7576 (mmm-85) REVERT: A 476 ASP cc_start: 0.9052 (m-30) cc_final: 0.8735 (m-30) REVERT: B 171 TRP cc_start: 0.4316 (t60) cc_final: 0.3896 (t60) REVERT: B 174 MET cc_start: 0.7746 (tmt) cc_final: 0.7042 (tmm) REVERT: B 193 LYS cc_start: 0.8944 (mttm) cc_final: 0.8735 (mttt) REVERT: B 229 GLN cc_start: 0.9084 (mt0) cc_final: 0.8621 (mp10) REVERT: B 239 MET cc_start: 0.8477 (mmm) cc_final: 0.8134 (mmm) REVERT: B 424 LEU cc_start: 0.9404 (mt) cc_final: 0.8446 (pp) REVERT: B 435 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8143 (ttp80) REVERT: B 439 ASP cc_start: 0.8781 (m-30) cc_final: 0.8464 (m-30) REVERT: C 170 LEU cc_start: 0.9508 (mt) cc_final: 0.9250 (mt) REVERT: C 180 ASP cc_start: 0.8908 (t0) cc_final: 0.8699 (t0) REVERT: C 196 SER cc_start: 0.9197 (m) cc_final: 0.8957 (t) REVERT: D 47 TYR cc_start: 0.7527 (m-80) cc_final: 0.7317 (m-80) REVERT: D 50 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: D 85 TRP cc_start: 0.8596 (m-10) cc_final: 0.8273 (m100) REVERT: D 90 ASP cc_start: 0.8624 (t70) cc_final: 0.8313 (t0) outliers start: 27 outliers final: 20 residues processed: 184 average time/residue: 0.0888 time to fit residues: 24.1302 Evaluate side-chains 163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 237 GLN B 210 ASN C 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.095784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.074159 restraints weight = 23315.839| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.88 r_work: 0.2904 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10248 Z= 0.257 Angle : 0.768 11.061 14024 Z= 0.366 Chirality : 0.049 0.290 1670 Planarity : 0.005 0.044 1689 Dihedral : 11.782 106.697 1974 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.43 % Allowed : 10.89 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.24), residues: 1202 helix: 0.07 (0.20), residues: 641 sheet: -2.21 (0.42), residues: 132 loop : -2.62 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 52 TYR 0.025 0.002 TYR D 18 PHE 0.030 0.002 PHE A 302 TRP 0.025 0.002 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00596 (10223) covalent geometry : angle 0.74522 (13953) SS BOND : bond 0.00646 ( 4) SS BOND : angle 1.11127 ( 8) hydrogen bonds : bond 0.04395 ( 474) hydrogen bonds : angle 4.51308 ( 1374) link_BETA1-3 : bond 0.01008 ( 1) link_BETA1-3 : angle 1.05423 ( 3) link_BETA1-4 : bond 0.00189 ( 7) link_BETA1-4 : angle 1.73685 ( 21) link_BETA1-6 : bond 0.01758 ( 1) link_BETA1-6 : angle 2.36858 ( 3) link_NAG-ASN : bond 0.00517 ( 12) link_NAG-ASN : angle 3.42522 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7749 (mmm-85) REVERT: A 476 ASP cc_start: 0.9088 (m-30) cc_final: 0.8789 (m-30) REVERT: A 669 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 171 TRP cc_start: 0.4479 (t60) cc_final: 0.3975 (t60) REVERT: B 174 MET cc_start: 0.7838 (tmt) cc_final: 0.7203 (tmm) REVERT: B 224 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8224 (Cg_endo) REVERT: B 239 MET cc_start: 0.8345 (mmm) cc_final: 0.7917 (tpt) REVERT: B 424 LEU cc_start: 0.9470 (mt) cc_final: 0.8673 (pp) REVERT: B 435 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8237 (ttp80) REVERT: C 180 ASP cc_start: 0.8860 (t0) cc_final: 0.8587 (t0) REVERT: C 190 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9284 (mp) REVERT: D 85 TRP cc_start: 0.8688 (m-10) cc_final: 0.8214 (m100) outliers start: 46 outliers final: 36 residues processed: 175 average time/residue: 0.0898 time to fit residues: 23.1053 Evaluate side-chains 172 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076009 restraints weight = 23091.018| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.80 r_work: 0.2937 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10248 Z= 0.162 Angle : 0.683 10.807 14024 Z= 0.321 Chirality : 0.046 0.300 1670 Planarity : 0.004 0.042 1689 Dihedral : 10.819 104.166 1972 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.62 % Allowed : 12.24 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.25), residues: 1202 helix: 0.56 (0.21), residues: 644 sheet: -1.98 (0.43), residues: 135 loop : -2.39 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.023 0.002 TYR D 18 PHE 0.027 0.001 PHE A 302 TRP 0.016 0.001 TRP D 67 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00370 (10223) covalent geometry : angle 0.66232 (13953) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.86908 ( 8) hydrogen bonds : bond 0.03838 ( 474) hydrogen bonds : angle 4.27406 ( 1374) link_BETA1-3 : bond 0.01053 ( 1) link_BETA1-3 : angle 1.13336 ( 3) link_BETA1-4 : bond 0.00328 ( 7) link_BETA1-4 : angle 1.58239 ( 21) link_BETA1-6 : bond 0.01763 ( 1) link_BETA1-6 : angle 2.66006 ( 3) link_NAG-ASN : bond 0.00442 ( 12) link_NAG-ASN : angle 3.03301 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7697 (mmm-85) REVERT: A 476 ASP cc_start: 0.9012 (m-30) cc_final: 0.8734 (m-30) REVERT: A 669 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7779 (mt-10) REVERT: B 99 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8819 (mtt) REVERT: B 171 TRP cc_start: 0.4615 (t60) cc_final: 0.4078 (t60) REVERT: B 174 MET cc_start: 0.7783 (tmt) cc_final: 0.7178 (tmm) REVERT: B 175 SER cc_start: 0.5675 (t) cc_final: 0.5007 (t) REVERT: B 225 LEU cc_start: 0.8129 (tp) cc_final: 0.7885 (tp) REVERT: B 229 GLN cc_start: 0.8877 (mt0) cc_final: 0.8097 (mp10) REVERT: B 429 SER cc_start: 0.9518 (m) cc_final: 0.9133 (p) REVERT: B 435 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8202 (ttp80) REVERT: B 439 ASP cc_start: 0.8526 (m-30) cc_final: 0.8273 (m-30) REVERT: C 180 ASP cc_start: 0.8939 (t0) cc_final: 0.8636 (t0) REVERT: D 85 TRP cc_start: 0.8710 (m-10) cc_final: 0.8256 (m100) outliers start: 48 outliers final: 37 residues processed: 186 average time/residue: 0.0858 time to fit residues: 23.9836 Evaluate side-chains 182 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074474 restraints weight = 23222.652| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.88 r_work: 0.2909 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10248 Z= 0.206 Angle : 0.707 10.501 14024 Z= 0.333 Chirality : 0.047 0.287 1670 Planarity : 0.004 0.045 1689 Dihedral : 10.352 104.776 1971 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.62 % Allowed : 13.78 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.25), residues: 1202 helix: 0.72 (0.21), residues: 649 sheet: -1.86 (0.44), residues: 135 loop : -2.32 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 626 TYR 0.026 0.002 TYR D 18 PHE 0.028 0.002 PHE A 302 TRP 0.018 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00478 (10223) covalent geometry : angle 0.68616 (13953) SS BOND : bond 0.00464 ( 4) SS BOND : angle 1.04984 ( 8) hydrogen bonds : bond 0.03878 ( 474) hydrogen bonds : angle 4.22005 ( 1374) link_BETA1-3 : bond 0.01031 ( 1) link_BETA1-3 : angle 1.51637 ( 3) link_BETA1-4 : bond 0.00248 ( 7) link_BETA1-4 : angle 1.67177 ( 21) link_BETA1-6 : bond 0.01769 ( 1) link_BETA1-6 : angle 2.83491 ( 3) link_NAG-ASN : bond 0.00464 ( 12) link_NAG-ASN : angle 3.07462 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7968 (tpp80) cc_final: 0.7725 (mmm-85) REVERT: A 476 ASP cc_start: 0.9080 (m-30) cc_final: 0.8788 (m-30) REVERT: B 171 TRP cc_start: 0.4657 (t60) cc_final: 0.4100 (t60) REVERT: B 174 MET cc_start: 0.7881 (tmt) cc_final: 0.7285 (tmm) REVERT: B 175 SER cc_start: 0.5771 (t) cc_final: 0.5017 (t) REVERT: B 435 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8254 (ttp80) REVERT: B 439 ASP cc_start: 0.8620 (m-30) cc_final: 0.8398 (m-30) REVERT: C 136 ASN cc_start: 0.8776 (m-40) cc_final: 0.8513 (m-40) REVERT: C 180 ASP cc_start: 0.8970 (t0) cc_final: 0.8631 (t0) REVERT: D 85 TRP cc_start: 0.8798 (m-10) cc_final: 0.8282 (m100) outliers start: 48 outliers final: 41 residues processed: 174 average time/residue: 0.0852 time to fit residues: 22.2831 Evaluate side-chains 171 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 45 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078091 restraints weight = 22971.467| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.82 r_work: 0.2981 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10248 Z= 0.107 Angle : 0.628 10.198 14024 Z= 0.293 Chirality : 0.044 0.280 1670 Planarity : 0.004 0.040 1689 Dihedral : 9.760 104.660 1969 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.76 % Allowed : 15.51 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1202 helix: 1.02 (0.21), residues: 647 sheet: -1.70 (0.44), residues: 135 loop : -2.09 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 82 TYR 0.018 0.001 TYR C 119 PHE 0.028 0.001 PHE A 302 TRP 0.015 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00226 (10223) covalent geometry : angle 0.60998 (13953) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.66884 ( 8) hydrogen bonds : bond 0.03304 ( 474) hydrogen bonds : angle 3.94497 ( 1374) link_BETA1-3 : bond 0.01093 ( 1) link_BETA1-3 : angle 1.23338 ( 3) link_BETA1-4 : bond 0.00418 ( 7) link_BETA1-4 : angle 1.41587 ( 21) link_BETA1-6 : bond 0.01624 ( 1) link_BETA1-6 : angle 3.19881 ( 3) link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 2.69200 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7640 (mmm-85) REVERT: A 476 ASP cc_start: 0.8942 (m-30) cc_final: 0.8713 (m-30) REVERT: B 171 TRP cc_start: 0.4720 (t60) cc_final: 0.4144 (t60) REVERT: B 174 MET cc_start: 0.7896 (tmt) cc_final: 0.7303 (tmm) REVERT: B 435 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8228 (ttp80) REVERT: B 439 ASP cc_start: 0.8573 (m-30) cc_final: 0.8322 (m-30) REVERT: C 48 LEU cc_start: 0.9065 (tt) cc_final: 0.8840 (tt) REVERT: C 84 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8200 (mm-30) REVERT: C 180 ASP cc_start: 0.8967 (t0) cc_final: 0.8681 (t0) REVERT: C 240 GLN cc_start: 0.7305 (mt0) cc_final: 0.6298 (tp40) REVERT: D 66 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7447 (m-10) REVERT: D 67 TRP cc_start: 0.8816 (m100) cc_final: 0.8610 (m100) REVERT: D 85 TRP cc_start: 0.8694 (m-10) cc_final: 0.8247 (m100) REVERT: D 91 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7025 (m-80) outliers start: 39 outliers final: 30 residues processed: 177 average time/residue: 0.0896 time to fit residues: 23.6486 Evaluate side-chains 173 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076449 restraints weight = 23166.623| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.81 r_work: 0.2946 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10248 Z= 0.157 Angle : 0.671 11.085 14024 Z= 0.312 Chirality : 0.045 0.280 1670 Planarity : 0.004 0.042 1689 Dihedral : 9.497 104.796 1969 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.76 % Allowed : 16.09 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.26), residues: 1202 helix: 1.12 (0.21), residues: 646 sheet: -1.66 (0.44), residues: 135 loop : -2.02 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.019 0.002 TYR C 119 PHE 0.029 0.001 PHE A 302 TRP 0.012 0.001 TRP B 253 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00366 (10223) covalent geometry : angle 0.65274 (13953) SS BOND : bond 0.00363 ( 4) SS BOND : angle 0.90371 ( 8) hydrogen bonds : bond 0.03478 ( 474) hydrogen bonds : angle 4.01173 ( 1374) link_BETA1-3 : bond 0.01099 ( 1) link_BETA1-3 : angle 1.47407 ( 3) link_BETA1-4 : bond 0.00229 ( 7) link_BETA1-4 : angle 1.48537 ( 21) link_BETA1-6 : bond 0.01539 ( 1) link_BETA1-6 : angle 3.37811 ( 3) link_NAG-ASN : bond 0.00432 ( 12) link_NAG-ASN : angle 2.77151 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7667 (mmm-85) REVERT: A 476 ASP cc_start: 0.8967 (m-30) cc_final: 0.8729 (m-30) REVERT: B 99 MET cc_start: 0.9049 (mtm) cc_final: 0.8788 (mtm) REVERT: B 171 TRP cc_start: 0.4784 (t60) cc_final: 0.4142 (t60) REVERT: B 174 MET cc_start: 0.7920 (tmt) cc_final: 0.7318 (tmm) REVERT: B 435 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8274 (ttp80) REVERT: B 439 ASP cc_start: 0.8624 (m-30) cc_final: 0.8416 (m-30) REVERT: C 48 LEU cc_start: 0.9089 (tt) cc_final: 0.8861 (tt) REVERT: C 84 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8216 (mm-30) REVERT: C 90 TYR cc_start: 0.9131 (t80) cc_final: 0.8687 (t80) REVERT: C 180 ASP cc_start: 0.8951 (t0) cc_final: 0.8628 (t0) REVERT: C 221 THR cc_start: 0.8783 (m) cc_final: 0.8347 (m) REVERT: C 240 GLN cc_start: 0.7336 (mt0) cc_final: 0.6354 (tp40) REVERT: D 85 TRP cc_start: 0.8752 (m-10) cc_final: 0.8259 (m100) REVERT: D 91 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.7016 (m-80) outliers start: 39 outliers final: 36 residues processed: 163 average time/residue: 0.0838 time to fit residues: 20.7054 Evaluate side-chains 170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075046 restraints weight = 23130.991| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.79 r_work: 0.2925 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10248 Z= 0.201 Angle : 0.695 11.870 14024 Z= 0.326 Chirality : 0.046 0.280 1670 Planarity : 0.004 0.044 1689 Dihedral : 9.326 105.242 1969 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.05 % Allowed : 15.99 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.25), residues: 1202 helix: 1.09 (0.21), residues: 648 sheet: -1.71 (0.44), residues: 135 loop : -2.11 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 626 TYR 0.021 0.002 TYR D 18 PHE 0.028 0.002 PHE A 302 TRP 0.024 0.001 TRP D 67 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00470 (10223) covalent geometry : angle 0.67624 (13953) SS BOND : bond 0.00430 ( 4) SS BOND : angle 1.05828 ( 8) hydrogen bonds : bond 0.03721 ( 474) hydrogen bonds : angle 4.07859 ( 1374) link_BETA1-3 : bond 0.01126 ( 1) link_BETA1-3 : angle 1.69051 ( 3) link_BETA1-4 : bond 0.00204 ( 7) link_BETA1-4 : angle 1.52185 ( 21) link_BETA1-6 : bond 0.01427 ( 1) link_BETA1-6 : angle 3.60196 ( 3) link_NAG-ASN : bond 0.00435 ( 12) link_NAG-ASN : angle 2.85211 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7925 (tpp80) cc_final: 0.7718 (mmm-85) REVERT: A 476 ASP cc_start: 0.9040 (m-30) cc_final: 0.8780 (m-30) REVERT: B 99 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8795 (mtm) REVERT: B 171 TRP cc_start: 0.4846 (t60) cc_final: 0.4232 (t60) REVERT: B 174 MET cc_start: 0.8011 (tmt) cc_final: 0.7422 (tmm) REVERT: B 262 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6876 (p90) REVERT: B 435 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8320 (ttp80) REVERT: C 84 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8307 (mm-30) REVERT: C 90 TYR cc_start: 0.9170 (t80) cc_final: 0.8775 (t80) REVERT: C 180 ASP cc_start: 0.8914 (t0) cc_final: 0.8554 (t0) REVERT: C 240 GLN cc_start: 0.7333 (mt0) cc_final: 0.6332 (tp40) REVERT: D 85 TRP cc_start: 0.8771 (m-10) cc_final: 0.8337 (m100) outliers start: 42 outliers final: 36 residues processed: 163 average time/residue: 0.0883 time to fit residues: 21.3519 Evaluate side-chains 169 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 17 optimal weight: 0.0020 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077516 restraints weight = 22869.019| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.79 r_work: 0.2970 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10248 Z= 0.116 Angle : 0.653 12.368 14024 Z= 0.302 Chirality : 0.044 0.272 1670 Planarity : 0.004 0.041 1689 Dihedral : 8.899 104.974 1969 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.18 % Allowed : 17.24 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1202 helix: 1.22 (0.21), residues: 648 sheet: -1.60 (0.44), residues: 135 loop : -1.99 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 82 TYR 0.018 0.001 TYR C 119 PHE 0.029 0.001 PHE A 302 TRP 0.024 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00260 (10223) covalent geometry : angle 0.63608 (13953) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.73586 ( 8) hydrogen bonds : bond 0.03343 ( 474) hydrogen bonds : angle 3.93915 ( 1374) link_BETA1-3 : bond 0.01149 ( 1) link_BETA1-3 : angle 1.40159 ( 3) link_BETA1-4 : bond 0.00342 ( 7) link_BETA1-4 : angle 1.28400 ( 21) link_BETA1-6 : bond 0.01253 ( 1) link_BETA1-6 : angle 3.94053 ( 3) link_NAG-ASN : bond 0.00419 ( 12) link_NAG-ASN : angle 2.57996 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7616 (mmm-85) REVERT: A 476 ASP cc_start: 0.8970 (m-30) cc_final: 0.8716 (m-30) REVERT: B 99 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8743 (mtm) REVERT: B 171 TRP cc_start: 0.4824 (t60) cc_final: 0.4194 (t60) REVERT: B 174 MET cc_start: 0.7961 (tmt) cc_final: 0.7368 (tmm) REVERT: B 435 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8188 (ttp80) REVERT: B 439 ASP cc_start: 0.8536 (m-30) cc_final: 0.8294 (m-30) REVERT: C 84 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8217 (mm-30) REVERT: C 90 TYR cc_start: 0.9115 (t80) cc_final: 0.8834 (t80) REVERT: C 136 ASN cc_start: 0.8741 (m-40) cc_final: 0.8507 (m-40) REVERT: C 180 ASP cc_start: 0.8907 (t0) cc_final: 0.8604 (t0) REVERT: C 221 THR cc_start: 0.8737 (m) cc_final: 0.8333 (m) REVERT: C 240 GLN cc_start: 0.7374 (mt0) cc_final: 0.6380 (tp40) REVERT: D 66 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: D 85 TRP cc_start: 0.8759 (m-10) cc_final: 0.8337 (m100) outliers start: 33 outliers final: 30 residues processed: 157 average time/residue: 0.0819 time to fit residues: 19.6714 Evaluate side-chains 164 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 84 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.100076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078920 restraints weight = 22643.589| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.81 r_work: 0.3001 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10248 Z= 0.106 Angle : 0.630 12.860 14024 Z= 0.291 Chirality : 0.044 0.265 1670 Planarity : 0.004 0.040 1689 Dihedral : 8.391 104.764 1969 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.08 % Allowed : 17.15 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1202 helix: 1.38 (0.21), residues: 645 sheet: -1.52 (0.44), residues: 135 loop : -1.78 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 82 TYR 0.019 0.001 TYR C 119 PHE 0.030 0.001 PHE A 302 TRP 0.019 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00232 (10223) covalent geometry : angle 0.61312 (13953) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.68605 ( 8) hydrogen bonds : bond 0.03129 ( 474) hydrogen bonds : angle 3.85802 ( 1374) link_BETA1-3 : bond 0.01227 ( 1) link_BETA1-3 : angle 1.51068 ( 3) link_BETA1-4 : bond 0.00329 ( 7) link_BETA1-4 : angle 1.22454 ( 21) link_BETA1-6 : bond 0.00853 ( 1) link_BETA1-6 : angle 4.13225 ( 3) link_NAG-ASN : bond 0.00413 ( 12) link_NAG-ASN : angle 2.47487 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9260 (mmt) cc_final: 0.8993 (mmm) REVERT: A 114 ARG cc_start: 0.7956 (tpp80) cc_final: 0.7686 (mmm-85) REVERT: A 476 ASP cc_start: 0.8947 (m-30) cc_final: 0.8705 (m-30) REVERT: B 99 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8705 (mtm) REVERT: B 103 VAL cc_start: 0.9290 (t) cc_final: 0.9050 (p) REVERT: B 171 TRP cc_start: 0.4853 (t60) cc_final: 0.4220 (t60) REVERT: B 174 MET cc_start: 0.7959 (tmt) cc_final: 0.7374 (tmm) REVERT: B 222 LYS cc_start: 0.9302 (mptt) cc_final: 0.8784 (mptt) REVERT: B 262 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6951 (p90) REVERT: B 435 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8271 (ttp80) REVERT: C 84 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8161 (mm-30) REVERT: C 90 TYR cc_start: 0.9098 (t80) cc_final: 0.8830 (t80) REVERT: C 136 ASN cc_start: 0.8733 (m-40) cc_final: 0.8406 (m-40) REVERT: C 180 ASP cc_start: 0.8943 (t0) cc_final: 0.8630 (t0) REVERT: C 221 THR cc_start: 0.8737 (m) cc_final: 0.8345 (m) REVERT: C 240 GLN cc_start: 0.7362 (mt0) cc_final: 0.6370 (tp40) REVERT: D 66 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7520 (m-10) REVERT: D 85 TRP cc_start: 0.8742 (m-10) cc_final: 0.8284 (m100) outliers start: 32 outliers final: 24 residues processed: 166 average time/residue: 0.0823 time to fit residues: 20.5561 Evaluate side-chains 163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075041 restraints weight = 23491.464| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.80 r_work: 0.2918 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10248 Z= 0.238 Angle : 0.738 13.197 14024 Z= 0.344 Chirality : 0.048 0.281 1670 Planarity : 0.004 0.045 1689 Dihedral : 8.463 105.073 1969 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.28 % Allowed : 16.96 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.26), residues: 1202 helix: 1.19 (0.21), residues: 650 sheet: -1.53 (0.45), residues: 133 loop : -1.92 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 82 TYR 0.019 0.002 TYR C 119 PHE 0.027 0.002 PHE A 302 TRP 0.036 0.002 TRP D 67 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00558 (10223) covalent geometry : angle 0.71948 (13953) SS BOND : bond 0.00480 ( 4) SS BOND : angle 1.18387 ( 8) hydrogen bonds : bond 0.03785 ( 474) hydrogen bonds : angle 4.09430 ( 1374) link_BETA1-3 : bond 0.01132 ( 1) link_BETA1-3 : angle 1.96093 ( 3) link_BETA1-4 : bond 0.00322 ( 7) link_BETA1-4 : angle 1.51716 ( 21) link_BETA1-6 : bond 0.00587 ( 1) link_BETA1-6 : angle 4.25322 ( 3) link_NAG-ASN : bond 0.00481 ( 12) link_NAG-ASN : angle 2.79888 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.69 seconds wall clock time: 39 minutes 18.57 seconds (2358.57 seconds total)