Starting phenix.real_space_refine on Mon Jul 28 14:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5z_33629/07_2025/7y5z_33629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5z_33629/07_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_33629/07_2025/7y5z_33629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5z_33629/07_2025/7y5z_33629.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5z_33629/07_2025/7y5z_33629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5z_33629/07_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-5711/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: 6.59, per 1000 atoms: 0.66 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 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: 0.98 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: 2.70 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1794 1.32 - 1.45: 2727 1.45 - 1.57: 5638 1.57 - 1.70: 4 1.70 - 1.82: 60 Bond restraints: 10223 Sorted by residual: bond pdb=" C1 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.410 1.470 -0.060 2.00e-02 2.50e+03 8.96e+00 bond pdb=" N VAL B 374 " pdb=" CA VAL B 374 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.58e+00 bond pdb=" N VAL A 465 " pdb=" CA VAL A 465 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.22e-02 6.72e+03 8.58e+00 bond pdb=" N VAL B 261 " pdb=" CA VAL B 261 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.24e+00 bond pdb=" N ILE B 368 " pdb=" CA ILE B 368 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 7.98e+00 ... (remaining 10218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 13595 2.77 - 5.53: 307 5.53 - 8.30: 43 8.30 - 11.06: 7 11.06 - 13.83: 1 Bond angle restraints: 13953 Sorted by residual: angle pdb=" C PRO B 248 " pdb=" N GLU B 249 " pdb=" CA GLU B 249 " ideal model delta sigma weight residual 120.79 127.44 -6.65 1.39e+00 5.18e-01 2.29e+01 angle pdb=" N ARG D 16 " pdb=" CA ARG D 16 " pdb=" C ARG D 16 " ideal model delta sigma weight residual 113.43 107.65 5.78 1.26e+00 6.30e-01 2.11e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 109.81 119.54 -9.73 2.21e+00 2.05e-01 1.94e+01 angle pdb=" N VAL A 36 " pdb=" CA VAL A 36 " pdb=" C VAL A 36 " ideal model delta sigma weight residual 111.81 108.03 3.78 8.60e-01 1.35e+00 1.93e+01 angle pdb=" N GLU B 249 " pdb=" CA GLU B 249 " pdb=" C GLU B 249 " ideal model delta sigma weight residual 111.02 116.34 -5.32 1.22e+00 6.72e-01 1.90e+01 ... (remaining 13948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 6087 22.70 - 45.41: 210 45.41 - 68.11: 43 68.11 - 90.81: 19 90.81 - 113.52: 22 Dihedral angle restraints: 6381 sinusoidal: 2846 harmonic: 3535 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -173.52 87.52 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -170.14 84.14 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual -180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1417 0.084 - 0.168: 230 0.168 - 0.253: 15 0.253 - 0.337: 5 0.337 - 0.421: 3 Chirality restraints: 1670 Sorted by residual: chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1667 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 464 " -0.034 2.00e-02 2.50e+03 7.85e-02 7.70e+01 pdb=" CG ASN A 464 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 464 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 464 " 0.142 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 201 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 202 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A 560 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.039 5.00e-02 4.00e+02 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1314 2.75 - 3.29: 9492 3.29 - 3.82: 15984 3.82 - 4.36: 18936 4.36 - 4.90: 33001 Nonbonded interactions: 78727 Sorted by model distance: nonbonded pdb=" O VAL B 374 " pdb=" N ALA B 377 " model vdw 2.210 3.120 nonbonded pdb=" O LEU B 433 " pdb=" OG SER C 50 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.295 3.040 nonbonded pdb=" O TRP C 227 " pdb=" OG1 THR C 231 " model vdw 2.303 3.040 ... (remaining 78722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.260 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.163 10248 Z= 0.393 Angle : 1.232 48.831 14024 Z= 0.597 Chirality : 0.063 0.421 1670 Planarity : 0.007 0.069 1689 Dihedral : 14.621 113.516 4091 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.56 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 Details of bonding type rmsd link_NAG-ASN : bond 0.04769 ( 12) link_NAG-ASN : angle 13.17049 ( 36) link_BETA1-4 : bond 0.00405 ( 7) link_BETA1-4 : angle 2.63577 ( 21) hydrogen bonds : bond 0.19375 ( 474) hydrogen bonds : angle 7.69969 ( 1374) link_BETA1-6 : bond 0.00506 ( 1) link_BETA1-6 : angle 1.15804 ( 3) SS BOND : bond 0.00808 ( 4) SS BOND : angle 2.29264 ( 8) link_BETA1-3 : bond 0.00435 ( 1) link_BETA1-3 : angle 0.49021 ( 3) covalent geometry : bond 0.00847 (10223) covalent geometry : angle 1.03107 (13953) *********************** 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 : 1.131 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: 0.2316 time to fit residues: 77.5382 Evaluate side-chains 152 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9584 ------------------------------------------------------------------------------- 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 A 305 GLN A 355 GLN A 358 ASN A 385 GLN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078619 restraints weight = 22704.994| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.88 r_work: 0.2989 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10248 Z= 0.134 Angle : 0.698 10.337 14024 Z= 0.336 Chirality : 0.046 0.385 1670 Planarity : 0.005 0.045 1689 Dihedral : 13.296 108.979 1979 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.41 % Allowed : 9.83 % 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: -2.58 (0.22), residues: 1202 helix: -0.67 (0.19), residues: 632 sheet: -2.48 (0.40), residues: 130 loop : -2.92 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.029 0.002 PHE A 302 TYR 0.028 0.001 TYR B 262 ARG 0.004 0.000 ARG A 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 12) link_NAG-ASN : angle 3.16867 ( 36) link_BETA1-4 : bond 0.00584 ( 7) link_BETA1-4 : angle 1.66772 ( 21) hydrogen bonds : bond 0.04399 ( 474) hydrogen bonds : angle 4.72091 ( 1374) link_BETA1-6 : bond 0.01198 ( 1) link_BETA1-6 : angle 2.51085 ( 3) SS BOND : bond 0.00635 ( 4) SS BOND : angle 0.86237 ( 8) link_BETA1-3 : bond 0.01391 ( 1) link_BETA1-3 : angle 1.57512 ( 3) covalent geometry : bond 0.00274 (10223) covalent geometry : angle 0.67656 (13953) *********************** 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: 25 poor density : 172 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7883 (mtp85) REVERT: A 114 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7606 (mmm-85) REVERT: A 476 ASP cc_start: 0.9020 (m-30) cc_final: 0.8705 (m-30) REVERT: B 171 TRP cc_start: 0.4330 (t60) cc_final: 0.3942 (t60) REVERT: B 174 MET cc_start: 0.7734 (tmt) cc_final: 0.7031 (tmm) REVERT: B 229 GLN cc_start: 0.9069 (mt0) cc_final: 0.8609 (mp10) REVERT: B 239 MET cc_start: 0.8486 (mmm) cc_final: 0.8179 (mmm) REVERT: B 424 LEU cc_start: 0.9396 (mt) cc_final: 0.8422 (pp) REVERT: B 435 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8161 (ttp80) REVERT: B 439 ASP cc_start: 0.8751 (m-30) cc_final: 0.8422 (m-30) REVERT: C 170 LEU cc_start: 0.9493 (mt) cc_final: 0.9235 (mt) REVERT: C 180 ASP cc_start: 0.8893 (t0) cc_final: 0.8654 (t0) REVERT: C 196 SER cc_start: 0.9255 (m) cc_final: 0.9043 (t) REVERT: D 47 TYR cc_start: 0.7535 (m-80) cc_final: 0.7333 (m-80) REVERT: D 50 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: D 85 TRP cc_start: 0.8586 (m-10) cc_final: 0.8256 (m100) outliers start: 25 outliers final: 18 residues processed: 186 average time/residue: 0.2157 time to fit residues: 59.2940 Evaluate side-chains 162 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 204 ASN B 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.095941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074391 restraints weight = 23336.957| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.88 r_work: 0.2908 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10248 Z= 0.266 Angle : 0.769 11.215 14024 Z= 0.366 Chirality : 0.049 0.297 1670 Planarity : 0.004 0.043 1689 Dihedral : 11.921 106.857 1974 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.53 % Allowed : 10.98 % Favored : 84.49 % 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: -1.69 (0.24), residues: 1202 helix: 0.09 (0.20), residues: 640 sheet: -2.20 (0.42), residues: 132 loop : -2.58 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.002 PHE A 302 TYR 0.026 0.002 TYR D 18 ARG 0.003 0.001 ARG D 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 12) link_NAG-ASN : angle 3.41562 ( 36) link_BETA1-4 : bond 0.00224 ( 7) link_BETA1-4 : angle 1.73771 ( 21) hydrogen bonds : bond 0.04354 ( 474) hydrogen bonds : angle 4.50565 ( 1374) link_BETA1-6 : bond 0.01543 ( 1) link_BETA1-6 : angle 2.36799 ( 3) SS BOND : bond 0.00568 ( 4) SS BOND : angle 1.06237 ( 8) link_BETA1-3 : bond 0.01571 ( 1) link_BETA1-3 : angle 1.39870 ( 3) covalent geometry : bond 0.00615 (10223) covalent geometry : angle 0.74661 (13953) *********************** 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 192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7795 (mmm-85) REVERT: A 476 ASP cc_start: 0.9069 (m-30) cc_final: 0.8775 (m-30) REVERT: A 669 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 171 TRP cc_start: 0.4460 (t60) cc_final: 0.3937 (t60) REVERT: B 174 MET cc_start: 0.7826 (tmt) cc_final: 0.7188 (tmm) REVERT: B 224 PRO cc_start: 0.8662 (Cg_exo) cc_final: 0.8275 (Cg_endo) REVERT: B 229 GLN cc_start: 0.9027 (mt0) cc_final: 0.8478 (mp10) REVERT: B 239 MET cc_start: 0.8328 (mmm) cc_final: 0.7924 (tpt) REVERT: B 424 LEU cc_start: 0.9426 (mt) cc_final: 0.8541 (pp) REVERT: B 435 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8262 (ttp80) REVERT: C 180 ASP cc_start: 0.8961 (t0) cc_final: 0.8702 (t0) outliers start: 47 outliers final: 35 residues processed: 176 average time/residue: 0.1921 time to fit residues: 49.5516 Evaluate side-chains 172 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 LEU 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 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: 7.9990 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 114 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.078309 restraints weight = 22624.135| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.87 r_work: 0.2989 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10248 Z= 0.110 Angle : 0.657 10.803 14024 Z= 0.307 Chirality : 0.044 0.306 1670 Planarity : 0.004 0.039 1689 Dihedral : 10.735 104.315 1972 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.47 % Allowed : 12.81 % Favored : 83.72 % 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: -1.07 (0.25), residues: 1202 helix: 0.63 (0.21), residues: 639 sheet: -1.86 (0.44), residues: 135 loop : -2.37 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 85 HIS 0.004 0.001 HIS A 553 PHE 0.027 0.001 PHE A 302 TYR 0.021 0.001 TYR D 18 ARG 0.002 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 12) link_NAG-ASN : angle 2.89995 ( 36) link_BETA1-4 : bond 0.00490 ( 7) link_BETA1-4 : angle 1.46178 ( 21) hydrogen bonds : bond 0.03554 ( 474) hydrogen bonds : angle 4.19158 ( 1374) link_BETA1-6 : bond 0.01835 ( 1) link_BETA1-6 : angle 2.79706 ( 3) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.64930 ( 8) link_BETA1-3 : bond 0.01032 ( 1) link_BETA1-3 : angle 1.02832 ( 3) covalent geometry : bond 0.00228 (10223) covalent geometry : angle 0.63805 (13953) *********************** 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 199 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7663 (mmm-85) REVERT: A 476 ASP cc_start: 0.8977 (m-30) cc_final: 0.8707 (m-30) REVERT: B 99 MET cc_start: 0.9066 (mtt) cc_final: 0.8818 (mtt) REVERT: B 171 TRP cc_start: 0.4510 (t60) cc_final: 0.3988 (t60) REVERT: B 174 MET cc_start: 0.7764 (tmt) cc_final: 0.7159 (tmm) REVERT: B 175 SER cc_start: 0.5644 (t) cc_final: 0.5018 (t) REVERT: B 239 MET cc_start: 0.8177 (mmm) cc_final: 0.7895 (tpt) REVERT: B 429 SER cc_start: 0.9477 (m) cc_final: 0.9166 (p) REVERT: B 435 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8118 (ttp80) REVERT: B 439 ASP cc_start: 0.8483 (m-30) cc_final: 0.8166 (m-30) REVERT: C 83 GLN cc_start: 0.9146 (mt0) cc_final: 0.8941 (mt0) REVERT: C 84 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8252 (mm-30) REVERT: C 180 ASP cc_start: 0.8941 (t0) cc_final: 0.8637 (t0) REVERT: C 196 SER cc_start: 0.9247 (m) cc_final: 0.8998 (t) REVERT: D 85 TRP cc_start: 0.8137 (m-10) cc_final: 0.7157 (m100) REVERT: D 91 TYR cc_start: 0.8090 (m-80) cc_final: 0.7838 (t80) outliers start: 36 outliers final: 26 residues processed: 187 average time/residue: 0.1792 time to fit residues: 50.4437 Evaluate side-chains 164 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 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 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: 6.9990 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 0.0030 chunk 23 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.098269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076795 restraints weight = 22786.030| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.88 r_work: 0.2958 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10248 Z= 0.151 Angle : 0.665 10.489 14024 Z= 0.312 Chirality : 0.046 0.295 1670 Planarity : 0.004 0.042 1689 Dihedral : 10.147 103.450 1971 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.76 % Allowed : 14.35 % Favored : 81.89 % 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: -0.74 (0.25), residues: 1202 helix: 0.86 (0.21), residues: 646 sheet: -1.73 (0.44), residues: 135 loop : -2.21 (0.30), 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 0.029 0.001 PHE A 302 TYR 0.021 0.002 TYR D 18 ARG 0.003 0.000 ARG D 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 12) link_NAG-ASN : angle 2.90155 ( 36) link_BETA1-4 : bond 0.00292 ( 7) link_BETA1-4 : angle 1.58552 ( 21) hydrogen bonds : bond 0.03590 ( 474) hydrogen bonds : angle 4.10089 ( 1374) link_BETA1-6 : bond 0.01938 ( 1) link_BETA1-6 : angle 2.95122 ( 3) SS BOND : bond 0.00358 ( 4) SS BOND : angle 0.84497 ( 8) link_BETA1-3 : bond 0.01053 ( 1) link_BETA1-3 : angle 1.38208 ( 3) covalent geometry : bond 0.00344 (10223) covalent geometry : angle 0.64477 (13953) *********************** 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 185 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7734 (mmm-85) REVERT: A 476 ASP cc_start: 0.9042 (m-30) cc_final: 0.8762 (m-30) REVERT: B 171 TRP cc_start: 0.4614 (t60) cc_final: 0.4084 (t60) REVERT: B 174 MET cc_start: 0.7795 (tmt) cc_final: 0.7169 (tmm) REVERT: B 175 SER cc_start: 0.5728 (t) cc_final: 0.4986 (t) REVERT: B 435 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8076 (ttp80) REVERT: B 439 ASP cc_start: 0.8606 (m-30) cc_final: 0.8387 (m-30) REVERT: C 83 GLN cc_start: 0.9250 (mt0) cc_final: 0.9006 (mt0) REVERT: C 84 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8321 (mm-30) REVERT: C 90 TYR cc_start: 0.9148 (t80) cc_final: 0.8907 (t80) REVERT: C 180 ASP cc_start: 0.8914 (t0) cc_final: 0.8565 (t0) REVERT: C 196 SER cc_start: 0.9229 (m) cc_final: 0.8975 (t) REVERT: C 221 THR cc_start: 0.8707 (m) cc_final: 0.8410 (m) REVERT: D 85 TRP cc_start: 0.8228 (m-10) cc_final: 0.7201 (m100) outliers start: 39 outliers final: 35 residues processed: 169 average time/residue: 0.1714 time to fit residues: 44.4103 Evaluate side-chains 163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 146 VAL 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 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 0.4980 chunk 114 optimal weight: 10.0000 chunk 51 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.099776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.078304 restraints weight = 22875.621| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.90 r_work: 0.2982 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10248 Z= 0.109 Angle : 0.621 10.200 14024 Z= 0.290 Chirality : 0.044 0.287 1670 Planarity : 0.004 0.040 1689 Dihedral : 9.664 103.498 1969 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.95 % Allowed : 14.55 % 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: -0.47 (0.25), residues: 1202 helix: 1.06 (0.21), residues: 646 sheet: -1.59 (0.45), residues: 135 loop : -2.05 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.017 0.001 TYR D 18 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 12) link_NAG-ASN : angle 2.69370 ( 36) link_BETA1-4 : bond 0.00396 ( 7) link_BETA1-4 : angle 1.43636 ( 21) hydrogen bonds : bond 0.03269 ( 474) hydrogen bonds : angle 3.92119 ( 1374) link_BETA1-6 : bond 0.01520 ( 1) link_BETA1-6 : angle 3.07629 ( 3) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.67140 ( 8) link_BETA1-3 : bond 0.01179 ( 1) link_BETA1-3 : angle 1.35184 ( 3) covalent geometry : bond 0.00236 (10223) covalent geometry : angle 0.60248 (13953) *********************** 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 190 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7766 (mmm-85) REVERT: A 476 ASP cc_start: 0.8960 (m-30) cc_final: 0.8717 (m-30) REVERT: A 669 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 171 TRP cc_start: 0.4689 (t60) cc_final: 0.4141 (t60) REVERT: B 174 MET cc_start: 0.7794 (tmt) cc_final: 0.7178 (tmm) REVERT: B 435 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8226 (ttp80) REVERT: B 439 ASP cc_start: 0.8580 (m-30) cc_final: 0.8351 (m-30) REVERT: C 83 GLN cc_start: 0.9144 (mt0) cc_final: 0.8933 (mt0) REVERT: C 84 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8240 (mm-30) REVERT: C 136 ASN cc_start: 0.8733 (m-40) cc_final: 0.8498 (m-40) REVERT: C 180 ASP cc_start: 0.8914 (t0) cc_final: 0.8559 (t0) REVERT: C 196 SER cc_start: 0.9263 (m) cc_final: 0.9044 (t) REVERT: C 221 THR cc_start: 0.8705 (m) cc_final: 0.8307 (m) REVERT: D 66 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: D 85 TRP cc_start: 0.8154 (m-10) cc_final: 0.7160 (m100) outliers start: 41 outliers final: 31 residues processed: 174 average time/residue: 0.1781 time to fit residues: 47.2618 Evaluate side-chains 174 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 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 184 THR 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 433 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 0.0570 overall best weight: 1.5904 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.099059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.077507 restraints weight = 23103.875| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.91 r_work: 0.2967 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10248 Z= 0.129 Angle : 0.640 11.014 14024 Z= 0.300 Chirality : 0.045 0.283 1670 Planarity : 0.004 0.041 1689 Dihedral : 9.355 103.671 1969 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.66 % Allowed : 14.84 % 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: -0.38 (0.26), residues: 1202 helix: 1.12 (0.22), residues: 647 sheet: -1.56 (0.45), residues: 135 loop : -2.00 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.018 0.001 TYR D 18 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 12) link_NAG-ASN : angle 2.68034 ( 36) link_BETA1-4 : bond 0.00211 ( 7) link_BETA1-4 : angle 1.41484 ( 21) hydrogen bonds : bond 0.03350 ( 474) hydrogen bonds : angle 3.97422 ( 1374) link_BETA1-6 : bond 0.01480 ( 1) link_BETA1-6 : angle 3.36723 ( 3) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.79184 ( 8) link_BETA1-3 : bond 0.01099 ( 1) link_BETA1-3 : angle 1.40323 ( 3) covalent geometry : bond 0.00292 (10223) covalent geometry : angle 0.62236 (13953) *********************** 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 179 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7769 (mmm-85) REVERT: A 476 ASP cc_start: 0.8963 (m-30) cc_final: 0.8725 (m-30) REVERT: A 669 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 171 TRP cc_start: 0.4738 (t60) cc_final: 0.4177 (t60) REVERT: B 174 MET cc_start: 0.7804 (tmt) cc_final: 0.7195 (tmm) REVERT: B 435 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8264 (ttp80) REVERT: B 439 ASP cc_start: 0.8620 (m-30) cc_final: 0.8415 (m-30) REVERT: C 83 GLN cc_start: 0.9159 (mt0) cc_final: 0.8912 (mt0) REVERT: C 84 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8256 (mm-30) REVERT: C 90 TYR cc_start: 0.9156 (t80) cc_final: 0.8624 (t80) REVERT: C 136 ASN cc_start: 0.8776 (m-40) cc_final: 0.8531 (m-40) REVERT: C 180 ASP cc_start: 0.8910 (t0) cc_final: 0.8565 (t0) REVERT: C 196 SER cc_start: 0.9221 (m) cc_final: 0.9004 (t) REVERT: C 221 THR cc_start: 0.8710 (m) cc_final: 0.8302 (m) REVERT: C 240 GLN cc_start: 0.7375 (mt0) cc_final: 0.6338 (tp40) REVERT: D 66 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: D 85 TRP cc_start: 0.8199 (m-10) cc_final: 0.7212 (m100) outliers start: 38 outliers final: 34 residues processed: 165 average time/residue: 0.1906 time to fit residues: 47.4533 Evaluate side-chains 171 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 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 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 433 LEU 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 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.072033 restraints weight = 23580.617| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.77 r_work: 0.2856 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 10248 Z= 0.405 Angle : 0.882 11.961 14024 Z= 0.421 Chirality : 0.055 0.291 1670 Planarity : 0.005 0.049 1689 Dihedral : 9.890 105.145 1969 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.43 % Allowed : 15.13 % Favored : 80.44 % 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: -0.89 (0.25), residues: 1202 helix: 0.66 (0.21), residues: 642 sheet: -1.63 (0.47), residues: 129 loop : -2.18 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 36 HIS 0.007 0.002 HIS A 553 PHE 0.031 0.003 PHE C 41 TYR 0.034 0.003 TYR D 18 ARG 0.005 0.001 ARG A 626 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 12) link_NAG-ASN : angle 3.44312 ( 36) link_BETA1-4 : bond 0.00496 ( 7) link_BETA1-4 : angle 1.90698 ( 21) hydrogen bonds : bond 0.04559 ( 474) hydrogen bonds : angle 4.47782 ( 1374) link_BETA1-6 : bond 0.01412 ( 1) link_BETA1-6 : angle 3.27881 ( 3) SS BOND : bond 0.00719 ( 4) SS BOND : angle 1.70802 ( 8) link_BETA1-3 : bond 0.01060 ( 1) link_BETA1-3 : angle 2.16092 ( 3) covalent geometry : bond 0.00938 (10223) covalent geometry : angle 0.86119 (13953) *********************** 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 174 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8067 (tpp80) cc_final: 0.7812 (mmm-85) REVERT: B 171 TRP cc_start: 0.5009 (t60) cc_final: 0.4303 (t60) REVERT: B 174 MET cc_start: 0.7928 (tmt) cc_final: 0.7301 (tmm) REVERT: B 262 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6900 (p90) REVERT: B 435 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8375 (ttp80) REVERT: C 90 TYR cc_start: 0.9187 (t80) cc_final: 0.8307 (t80) REVERT: C 136 ASN cc_start: 0.8881 (m-40) cc_final: 0.8649 (m-40) REVERT: C 180 ASP cc_start: 0.8936 (t0) cc_final: 0.8483 (t0) REVERT: C 224 MET cc_start: 0.8948 (tpp) cc_final: 0.8366 (mmp) REVERT: D 85 TRP cc_start: 0.8466 (m-10) cc_final: 0.7557 (m100) outliers start: 46 outliers final: 43 residues processed: 160 average time/residue: 0.1837 time to fit residues: 43.4869 Evaluate side-chains 167 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 VAL Chi-restraints excluded: chain A residue 282 LEU 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 A residue 685 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 184 THR 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 225 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain 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 182 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 VAL 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: 1.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.098040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076775 restraints weight = 22880.604| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.81 r_work: 0.2954 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10248 Z= 0.123 Angle : 0.664 12.365 14024 Z= 0.311 Chirality : 0.045 0.270 1670 Planarity : 0.004 0.043 1689 Dihedral : 9.250 105.068 1969 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.47 % Allowed : 16.76 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.26), residues: 1202 helix: 1.01 (0.21), residues: 651 sheet: -1.48 (0.45), residues: 133 loop : -1.92 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 67 HIS 0.006 0.001 HIS C 197 PHE 0.027 0.001 PHE A 302 TYR 0.022 0.002 TYR C 119 ARG 0.007 0.000 ARG D 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 2.64945 ( 36) link_BETA1-4 : bond 0.00412 ( 7) link_BETA1-4 : angle 1.35147 ( 21) hydrogen bonds : bond 0.03579 ( 474) hydrogen bonds : angle 4.04939 ( 1374) link_BETA1-6 : bond 0.01377 ( 1) link_BETA1-6 : angle 3.79747 ( 3) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.79675 ( 8) link_BETA1-3 : bond 0.01139 ( 1) link_BETA1-3 : angle 1.40126 ( 3) covalent geometry : bond 0.00274 (10223) covalent geometry : angle 0.64694 (13953) *********************** 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 175 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.8980 (m-30) cc_final: 0.8686 (m-30) REVERT: B 171 TRP cc_start: 0.4827 (t60) cc_final: 0.4179 (t60) REVERT: B 174 MET cc_start: 0.7922 (tmt) cc_final: 0.7322 (tmm) REVERT: B 435 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8270 (ttp80) REVERT: C 84 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8247 (mm-30) REVERT: C 136 ASN cc_start: 0.8675 (m-40) cc_final: 0.8444 (m-40) REVERT: C 180 ASP cc_start: 0.8877 (t0) cc_final: 0.8568 (t0) REVERT: C 221 THR cc_start: 0.8792 (m) cc_final: 0.8362 (m) REVERT: C 240 GLN cc_start: 0.6949 (mt0) cc_final: 0.5998 (tp40) REVERT: D 66 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: D 85 TRP cc_start: 0.8296 (m-10) cc_final: 0.7361 (m100) outliers start: 36 outliers final: 32 residues processed: 159 average time/residue: 0.2023 time to fit residues: 47.7787 Evaluate side-chains 162 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 VAL Chi-restraints excluded: chain A residue 282 LEU 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 253 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 262 TYR 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 146 VAL 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 32 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 66 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.097461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076220 restraints weight = 23001.836| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.80 r_work: 0.2948 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10248 Z= 0.148 Angle : 0.676 13.068 14024 Z= 0.316 Chirality : 0.046 0.312 1670 Planarity : 0.004 0.043 1689 Dihedral : 8.993 105.240 1969 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.37 % Allowed : 16.96 % 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: -0.36 (0.26), residues: 1202 helix: 1.08 (0.21), residues: 647 sheet: -1.42 (0.46), residues: 133 loop : -1.92 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.024 0.002 TYR D 18 ARG 0.008 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 12) link_NAG-ASN : angle 2.67893 ( 36) link_BETA1-4 : bond 0.00252 ( 7) link_BETA1-4 : angle 1.38350 ( 21) hydrogen bonds : bond 0.03518 ( 474) hydrogen bonds : angle 4.05003 ( 1374) link_BETA1-6 : bond 0.01185 ( 1) link_BETA1-6 : angle 3.95630 ( 3) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.88247 ( 8) link_BETA1-3 : bond 0.01142 ( 1) link_BETA1-3 : angle 1.56788 ( 3) covalent geometry : bond 0.00341 (10223) covalent geometry : angle 0.65804 (13953) ********************** 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 161 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.8987 (m-30) cc_final: 0.8692 (m-30) REVERT: B 171 TRP cc_start: 0.4885 (t60) cc_final: 0.4204 (t60) REVERT: B 174 MET cc_start: 0.7909 (tmt) cc_final: 0.7277 (tmm) REVERT: B 262 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6913 (p90) REVERT: B 435 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8246 (ttp80) REVERT: C 84 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8246 (mm-30) REVERT: C 136 ASN cc_start: 0.8719 (m-40) cc_final: 0.8473 (m-40) REVERT: C 180 ASP cc_start: 0.8913 (t0) cc_final: 0.8575 (t0) REVERT: C 240 GLN cc_start: 0.7023 (mt0) cc_final: 0.5992 (tp40) REVERT: D 66 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: D 85 TRP cc_start: 0.8367 (m-10) cc_final: 0.7425 (m100) outliers start: 35 outliers final: 30 residues processed: 148 average time/residue: 0.1801 time to fit residues: 39.7199 Evaluate side-chains 154 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 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 B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 262 TYR 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 146 VAL 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 32 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.094750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.073473 restraints weight = 23365.961| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.78 r_work: 0.2895 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10248 Z= 0.271 Angle : 0.771 13.603 14024 Z= 0.364 Chirality : 0.050 0.327 1670 Planarity : 0.004 0.046 1689 Dihedral : 9.047 105.690 1969 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.28 % Allowed : 17.34 % Favored : 79.38 % 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: 0.85 (0.21), residues: 649 sheet: -1.53 (0.46), residues: 133 loop : -1.99 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 36 HIS 0.006 0.001 HIS A 553 PHE 0.027 0.002 PHE A 302 TYR 0.034 0.002 TYR D 18 ARG 0.008 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 12) link_NAG-ASN : angle 2.99028 ( 36) link_BETA1-4 : bond 0.00271 ( 7) link_BETA1-4 : angle 1.63385 ( 21) hydrogen bonds : bond 0.04031 ( 474) hydrogen bonds : angle 4.25777 ( 1374) link_BETA1-6 : bond 0.00937 ( 1) link_BETA1-6 : angle 4.13498 ( 3) SS BOND : bond 0.00515 ( 4) SS BOND : angle 1.29703 ( 8) link_BETA1-3 : bond 0.01105 ( 1) link_BETA1-3 : angle 2.01144 ( 3) covalent geometry : bond 0.00630 (10223) covalent geometry : angle 0.75162 (13953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4318.83 seconds wall clock time: 75 minutes 14.04 seconds (4514.04 seconds total)