Starting phenix.real_space_refine on Fri Feb 14 16:30:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5z_33629/02_2025/7y5z_33629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5z_33629/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y5z_33629/02_2025/7y5z_33629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5z_33629/02_2025/7y5z_33629.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5z_33629/02_2025/7y5z_33629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5z_33629/02_2025/7y5z_33629.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.29, per 1000 atoms: 0.53 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: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 3.14 Time building geometry restraints manager: 2.95 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: 1.050 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- 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 : 0.008 0.085 10223 Z= 0.544 Angle : 1.031 13.829 13953 Z= 0.554 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 : 4.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (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 TRP 0.046 0.003 TRP D 36 HIS 0.016 0.003 HIS C 197 PHE 0.034 0.003 PHE C 132 TYR 0.042 0.003 TYR A 565 ARG 0.009 0.001 ARG A 429 *********************** 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 : 1.099 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: 0.2221 time to fit residues: 73.5173 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 : 1.172 ------------------------------------------------------------------------------- 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 100 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3493 r_free = 0.3493 target = 0.099874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078577 restraints weight = 22693.006| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.86 r_work: 0.2988 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10223 Z= 0.173 Angle : 0.678 10.308 13953 Z= 0.332 Chirality : 0.045 0.320 1670 Planarity : 0.005 0.045 1689 Dihedral : 13.394 108.640 1979 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.22 % Allowed : 10.02 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.22), residues: 1202 helix: -0.69 (0.19), residues: 632 sheet: -2.48 (0.40), residues: 130 loop : -2.94 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 PHE 0.029 0.002 PHE A 302 TYR 0.030 0.001 TYR B 262 ARG 0.004 0.001 ARG D 82 *********************** 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 197 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7889 (mtp85) REVERT: A 114 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7609 (mmm-85) REVERT: A 476 ASP cc_start: 0.9011 (m-30) cc_final: 0.8705 (m-30) REVERT: B 171 TRP cc_start: 0.4352 (t60) cc_final: 0.3962 (t60) REVERT: B 174 MET cc_start: 0.7734 (tmt) cc_final: 0.7030 (tmm) REVERT: B 193 LYS cc_start: 0.8935 (mttm) cc_final: 0.8732 (mttt) REVERT: B 229 GLN cc_start: 0.9066 (mt0) cc_final: 0.8613 (mp10) REVERT: B 239 MET cc_start: 0.8479 (mmm) cc_final: 0.8164 (mmm) REVERT: B 424 LEU cc_start: 0.9404 (mt) cc_final: 0.8441 (pp) REVERT: B 435 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8274 (ttp80) REVERT: B 439 ASP cc_start: 0.8749 (m-30) cc_final: 0.8475 (m-30) REVERT: C 170 LEU cc_start: 0.9493 (mt) cc_final: 0.9234 (mt) REVERT: C 180 ASP cc_start: 0.8891 (t0) cc_final: 0.8675 (t0) REVERT: C 196 SER cc_start: 0.9245 (m) cc_final: 0.9034 (t) REVERT: D 50 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: D 85 TRP cc_start: 0.8577 (m-10) cc_final: 0.8253 (m100) REVERT: D 90 ASP cc_start: 0.8606 (t70) cc_final: 0.8290 (t0) outliers start: 23 outliers final: 18 residues processed: 187 average time/residue: 0.1947 time to fit residues: 53.0366 Evaluate side-chains 161 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 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 60 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 19 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN B 210 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073603 restraints weight = 23368.774| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.87 r_work: 0.2895 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10223 Z= 0.422 Angle : 0.779 10.904 13953 Z= 0.377 Chirality : 0.050 0.284 1670 Planarity : 0.005 0.045 1689 Dihedral : 11.760 106.569 1974 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.72 % Allowed : 11.18 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.24), residues: 1202 helix: 0.04 (0.20), residues: 642 sheet: -2.19 (0.42), residues: 132 loop : -2.58 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 36 HIS 0.005 0.002 HIS A 553 PHE 0.032 0.002 PHE A 302 TYR 0.023 0.002 TYR A 173 ARG 0.004 0.001 ARG A 52 *********************** 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: 49 poor density : 142 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7789 (mmm-85) REVERT: A 476 ASP cc_start: 0.9086 (m-30) cc_final: 0.8794 (m-30) REVERT: A 669 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 171 TRP cc_start: 0.4480 (t60) cc_final: 0.3974 (t60) REVERT: B 174 MET cc_start: 0.7838 (tmt) cc_final: 0.7206 (tmm) REVERT: B 193 LYS cc_start: 0.8999 (mttm) cc_final: 0.8782 (mttt) REVERT: B 224 PRO cc_start: 0.8634 (Cg_exo) cc_final: 0.8177 (Cg_endo) REVERT: B 239 MET cc_start: 0.8300 (mmm) cc_final: 0.7904 (tpt) REVERT: B 424 LEU cc_start: 0.9469 (mt) cc_final: 0.8678 (pp) REVERT: B 435 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8249 (ttp80) REVERT: C 180 ASP cc_start: 0.8859 (t0) cc_final: 0.8587 (t0) REVERT: C 190 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9302 (mp) REVERT: D 85 TRP cc_start: 0.8710 (m-10) cc_final: 0.8253 (m100) outliers start: 49 outliers final: 37 residues processed: 175 average time/residue: 0.2065 time to fit residues: 53.0195 Evaluate side-chains 160 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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 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 16 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 237 GLN A 385 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076862 restraints weight = 22766.115| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.87 r_work: 0.2960 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10223 Z= 0.167 Angle : 0.648 10.451 13953 Z= 0.309 Chirality : 0.045 0.306 1670 Planarity : 0.004 0.041 1689 Dihedral : 10.761 103.981 1972 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.85 % Allowed : 13.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1202 helix: 0.63 (0.21), residues: 640 sheet: -1.91 (0.44), residues: 135 loop : -2.31 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.027 0.001 PHE A 302 TYR 0.022 0.001 TYR D 18 ARG 0.002 0.000 ARG D 82 *********************** 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 202 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7957 (tpp80) cc_final: 0.7711 (mmm-85) REVERT: A 476 ASP cc_start: 0.9001 (m-30) cc_final: 0.8713 (m-30) REVERT: A 669 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7754 (mt-10) REVERT: B 99 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8867 (mtt) REVERT: B 171 TRP cc_start: 0.4510 (t60) cc_final: 0.3979 (t60) REVERT: B 174 MET cc_start: 0.7764 (tmt) cc_final: 0.7163 (tmm) REVERT: B 175 SER cc_start: 0.5657 (t) cc_final: 0.5011 (t) REVERT: B 225 LEU cc_start: 0.8133 (tp) cc_final: 0.7778 (tp) REVERT: B 229 GLN cc_start: 0.8865 (mt0) cc_final: 0.8069 (mp10) REVERT: B 239 MET cc_start: 0.8153 (mmm) cc_final: 0.7831 (tpt) REVERT: B 424 LEU cc_start: 0.9467 (mt) cc_final: 0.8633 (pp) REVERT: B 429 SER cc_start: 0.9508 (m) cc_final: 0.9182 (p) REVERT: B 435 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8094 (ttp80) REVERT: B 439 ASP cc_start: 0.8517 (m-30) cc_final: 0.8252 (m-30) REVERT: C 84 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8319 (mm-30) REVERT: C 170 LEU cc_start: 0.9482 (mt) cc_final: 0.9225 (mt) REVERT: C 180 ASP cc_start: 0.8933 (t0) cc_final: 0.8620 (t0) REVERT: D 85 TRP cc_start: 0.8708 (m-10) cc_final: 0.8251 (m100) outliers start: 40 outliers final: 29 residues processed: 187 average time/residue: 0.1877 time to fit residues: 51.8166 Evaluate side-chains 175 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 481 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.073345 restraints weight = 22990.497| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.84 r_work: 0.2889 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10223 Z= 0.395 Angle : 0.741 10.755 13953 Z= 0.356 Chirality : 0.049 0.290 1670 Planarity : 0.004 0.046 1689 Dihedral : 10.430 104.522 1971 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.53 % Allowed : 13.97 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1202 helix: 0.68 (0.21), residues: 648 sheet: -1.87 (0.44), residues: 135 loop : -2.29 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 36 HIS 0.006 0.001 HIS A 553 PHE 0.030 0.002 PHE A 302 TYR 0.031 0.002 TYR D 18 ARG 0.004 0.001 ARG A 626 *********************** 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 186 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7798 (mmm-85) REVERT: A 476 ASP cc_start: 0.9118 (m-30) cc_final: 0.8834 (m-30) REVERT: B 171 TRP cc_start: 0.4693 (t60) cc_final: 0.4127 (t60) REVERT: B 174 MET cc_start: 0.7946 (tmt) cc_final: 0.7322 (tmm) REVERT: B 175 SER cc_start: 0.5787 (t) cc_final: 0.5039 (t) REVERT: B 435 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8275 (ttp80) REVERT: B 439 ASP cc_start: 0.8630 (m-30) cc_final: 0.8417 (m-30) REVERT: C 136 ASN cc_start: 0.8856 (m-40) cc_final: 0.8608 (m-40) REVERT: C 180 ASP cc_start: 0.8961 (t0) cc_final: 0.8620 (t0) REVERT: D 85 TRP cc_start: 0.8782 (m-10) cc_final: 0.8281 (m100) REVERT: D 91 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7103 (m-80) outliers start: 47 outliers final: 39 residues processed: 169 average time/residue: 0.1941 time to fit residues: 48.6588 Evaluate side-chains 167 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 247 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 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 397 ILE Chi-restraints excluded: chain B residue 433 LEU 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 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 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 Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 204 ASN A 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.098189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.076649 restraints weight = 22925.746| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.88 r_work: 0.2955 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10223 Z= 0.154 Angle : 0.622 10.319 13953 Z= 0.296 Chirality : 0.044 0.284 1670 Planarity : 0.004 0.042 1689 Dihedral : 9.862 104.629 1969 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.47 % Allowed : 15.90 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1202 helix: 0.98 (0.21), residues: 648 sheet: -1.67 (0.44), residues: 135 loop : -2.04 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.027 0.001 PHE A 302 TYR 0.019 0.001 TYR C 119 ARG 0.006 0.000 ARG D 82 *********************** 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 187 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7720 (mmm-85) REVERT: A 476 ASP cc_start: 0.8993 (m-30) cc_final: 0.8712 (m-30) REVERT: B 171 TRP cc_start: 0.4677 (t60) cc_final: 0.4116 (t60) REVERT: B 174 MET cc_start: 0.7880 (tmt) cc_final: 0.7256 (tmm) REVERT: B 239 MET cc_start: 0.8395 (mmm) cc_final: 0.7976 (tpt) REVERT: B 435 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8232 (ttp80) REVERT: B 439 ASP cc_start: 0.8606 (m-30) cc_final: 0.8364 (m-30) REVERT: C 84 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8299 (mm-30) REVERT: C 180 ASP cc_start: 0.8996 (t0) cc_final: 0.8639 (t0) REVERT: C 240 GLN cc_start: 0.7322 (mt0) cc_final: 0.6316 (tp40) REVERT: D 85 TRP cc_start: 0.8787 (m-10) cc_final: 0.8275 (m100) REVERT: D 91 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7008 (m-80) outliers start: 36 outliers final: 30 residues processed: 171 average time/residue: 0.1873 time to fit residues: 47.3147 Evaluate side-chains 173 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 80 GLU 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 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 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 397 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 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 91 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 107 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.097268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075859 restraints weight = 23227.551| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.82 r_work: 0.2940 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10223 Z= 0.236 Angle : 0.655 11.166 13953 Z= 0.310 Chirality : 0.046 0.281 1670 Planarity : 0.004 0.042 1689 Dihedral : 9.636 104.851 1969 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.85 % Allowed : 16.28 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1202 helix: 1.09 (0.21), residues: 646 sheet: -1.68 (0.44), residues: 135 loop : -1.98 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.022 0.002 TYR D 18 ARG 0.002 0.000 ARG D 82 *********************** 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 176 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.8968 (m-30) cc_final: 0.8722 (m-30) REVERT: B 171 TRP cc_start: 0.4947 (t60) cc_final: 0.4213 (t60) REVERT: B 174 MET cc_start: 0.7997 (tmt) cc_final: 0.7413 (tmm) REVERT: B 239 MET cc_start: 0.8378 (mmm) cc_final: 0.7985 (tpt) REVERT: B 435 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8314 (ttp80) REVERT: B 439 ASP cc_start: 0.8602 (m-30) cc_final: 0.8381 (m-30) REVERT: C 84 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8275 (mm-30) REVERT: C 136 ASN cc_start: 0.8746 (m-40) cc_final: 0.8503 (m-40) REVERT: C 180 ASP cc_start: 0.9001 (t0) cc_final: 0.8618 (t0) REVERT: C 240 GLN cc_start: 0.7307 (mt0) cc_final: 0.6319 (tp40) REVERT: D 85 TRP cc_start: 0.8765 (m-10) cc_final: 0.8267 (m100) REVERT: D 91 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.7003 (m-80) outliers start: 40 outliers final: 38 residues processed: 160 average time/residue: 0.1909 time to fit residues: 45.6394 Evaluate side-chains 172 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 80 GLU 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 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 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 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 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 29 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 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 71 optimal weight: 0.0270 chunk 69 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.094238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.072722 restraints weight = 23514.432| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.82 r_work: 0.2882 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10223 Z= 0.442 Angle : 0.755 11.808 13953 Z= 0.362 Chirality : 0.050 0.280 1670 Planarity : 0.004 0.046 1689 Dihedral : 9.716 105.583 1969 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.82 % Allowed : 15.51 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1202 helix: 0.91 (0.21), residues: 646 sheet: -1.71 (0.45), residues: 135 loop : -2.01 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 36 HIS 0.006 0.001 HIS A 553 PHE 0.026 0.002 PHE A 302 TYR 0.031 0.002 TYR D 18 ARG 0.004 0.001 ARG A 626 *********************** 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 171 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: B 99 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8764 (mtm) REVERT: B 171 TRP cc_start: 0.4931 (t60) cc_final: 0.4329 (t60) REVERT: B 174 MET cc_start: 0.8037 (tmt) cc_final: 0.7443 (tmm) REVERT: B 239 MET cc_start: 0.8463 (mmm) cc_final: 0.8029 (tpt) REVERT: B 262 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6904 (p90) REVERT: B 435 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8343 (ttp80) REVERT: C 180 ASP cc_start: 0.8979 (t0) cc_final: 0.8598 (t0) REVERT: C 224 MET cc_start: 0.8988 (tpp) cc_final: 0.8391 (mmp) REVERT: C 240 GLN cc_start: 0.7355 (mt0) cc_final: 0.6351 (tp40) REVERT: D 85 TRP cc_start: 0.8816 (m-10) cc_final: 0.8314 (m100) outliers start: 50 outliers final: 46 residues processed: 157 average time/residue: 0.1862 time to fit residues: 43.8811 Evaluate side-chains 165 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 GLU 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 247 VAL 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 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 97 LEU 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 253 TRP Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 51 VAL 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.097796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076237 restraints weight = 23015.613| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.88 r_work: 0.2944 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10223 Z= 0.170 Angle : 0.648 12.277 13953 Z= 0.305 Chirality : 0.045 0.268 1670 Planarity : 0.004 0.042 1689 Dihedral : 9.235 105.471 1969 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.85 % Allowed : 16.47 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1202 helix: 1.12 (0.21), residues: 650 sheet: -1.51 (0.45), residues: 133 loop : -1.93 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.019 0.001 TYR A 602 ARG 0.003 0.000 ARG D 82 *********************** 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 178 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.9033 (m-30) cc_final: 0.8714 (m-30) REVERT: B 171 TRP cc_start: 0.4782 (t60) cc_final: 0.4213 (t60) REVERT: B 174 MET cc_start: 0.8054 (tmt) cc_final: 0.7428 (tmm) REVERT: B 222 LYS cc_start: 0.9309 (mptt) cc_final: 0.8774 (mptt) REVERT: B 239 MET cc_start: 0.8467 (mmm) cc_final: 0.8172 (mmm) REVERT: B 262 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.6980 (p90) REVERT: B 435 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8270 (ttp80) REVERT: C 84 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8288 (mm-30) REVERT: C 90 TYR cc_start: 0.9245 (t80) cc_final: 0.8991 (t80) REVERT: C 180 ASP cc_start: 0.8974 (t0) cc_final: 0.8603 (t0) REVERT: C 192 LEU cc_start: 0.8789 (mt) cc_final: 0.8505 (mt) REVERT: C 221 THR cc_start: 0.8778 (m) cc_final: 0.8361 (m) REVERT: C 240 GLN cc_start: 0.7388 (mt0) cc_final: 0.6353 (tp40) REVERT: D 66 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7392 (m-10) REVERT: D 85 TRP cc_start: 0.8790 (m-10) cc_final: 0.8345 (m100) REVERT: D 91 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6962 (m-80) outliers start: 40 outliers final: 34 residues processed: 163 average time/residue: 0.1922 time to fit residues: 46.3974 Evaluate side-chains 168 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 80 GLU 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 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 413 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 226 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 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 Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN C 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.074318 restraints weight = 23228.093| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.79 r_work: 0.2913 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10223 Z= 0.307 Angle : 0.698 13.103 13953 Z= 0.330 Chirality : 0.047 0.274 1670 Planarity : 0.004 0.044 1689 Dihedral : 9.110 105.848 1969 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.66 % Allowed : 16.86 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1202 helix: 1.09 (0.21), residues: 650 sheet: -1.55 (0.45), residues: 133 loop : -1.95 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.029 0.002 PHE A 302 TYR 0.023 0.002 TYR D 18 ARG 0.003 0.000 ARG D 82 ********************** 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 164 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.9053 (m-30) cc_final: 0.8768 (m-30) REVERT: B 171 TRP cc_start: 0.4896 (t60) cc_final: 0.4298 (t60) REVERT: B 174 MET cc_start: 0.8077 (tmt) cc_final: 0.7461 (tmm) REVERT: B 239 MET cc_start: 0.8407 (mmm) cc_final: 0.8135 (mmm) REVERT: B 262 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6950 (p90) REVERT: B 435 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8295 (ttp80) REVERT: C 90 TYR cc_start: 0.9252 (t80) cc_final: 0.8892 (t80) REVERT: C 180 ASP cc_start: 0.8984 (t0) cc_final: 0.8597 (t0) REVERT: C 240 GLN cc_start: 0.7383 (mt0) cc_final: 0.6344 (tp40) REVERT: D 85 TRP cc_start: 0.8769 (m-10) cc_final: 0.8320 (m100) outliers start: 38 outliers final: 37 residues processed: 154 average time/residue: 0.1834 time to fit residues: 42.5041 Evaluate side-chains 161 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 80 GLU 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 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 262 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 413 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 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 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 5 optimal weight: 0.0470 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.097708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076247 restraints weight = 23104.276| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.88 r_work: 0.2941 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10223 Z= 0.183 Angle : 0.640 12.822 13953 Z= 0.302 Chirality : 0.045 0.262 1670 Planarity : 0.004 0.042 1689 Dihedral : 8.717 105.780 1969 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.95 % Allowed : 16.76 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1202 helix: 1.18 (0.21), residues: 652 sheet: -1.48 (0.45), residues: 133 loop : -1.81 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.019 0.001 TYR C 119 ARG 0.003 0.000 ARG D 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.08 seconds wall clock time: 72 minutes 51.77 seconds (4371.77 seconds total)