Starting phenix.real_space_refine on Fri Jul 3 01:21:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y5t_33624/07_2026/7y5t_33624.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 42 5.16 5 Cl 1 4.86 5 C 7109 2.51 5 N 1707 2.21 5 O 1978 1.98 5 F 5 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10844 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: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2444 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 1 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 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 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 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 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 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 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 chiralities: 6 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'IGD': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 1.79, per 1000 atoms: 0.17 Number of scatterers: 10844 At special positions: 0 Unit cell: (110.415, 95.26, 133.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 42 16.00 P 2 15.00 F 5 9.00 O 1978 8.00 N 1707 7.00 C 7109 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=2.02 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.01 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 0.79 Conformation dependent library (CDL) restraints added in 415.7 milliseconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 57.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.567A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.806A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.667A pdb=" N TYR A 173 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 174' Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.662A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.715A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 407 removed outlier: 4.039A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.936A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.795A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.779A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.838A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.702A 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 637 removed outlier: 3.727A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.525A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.668A pdb=" N PHE A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.945A pdb=" N TYR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 removed outlier: 3.851A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 removed outlier: 3.720A pdb=" N TYR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.795A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 removed outlier: 3.742A pdb=" N GLU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 274 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 404 through 429 removed outlier: 3.613A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.642A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.968A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 24 removed outlier: 3.504A pdb=" N PHE C 18 " --> pdb=" O PHE C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 60 removed outlier: 3.872A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 102 removed outlier: 3.664A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 139 removed outlier: 3.697A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.571A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.857A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (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 210 through 233 removed outlier: 3.747A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 21 removed outlier: 3.588A pdb=" N GLY D 21 " --> pdb=" O LYS D 17 " (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 36 removed outlier: 3.610A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 81 removed outlier: 3.793A pdb=" N ILE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.558A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR A 94 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.512A 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: 4.425A pdb=" N SER A 437 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 605 removed outlier: 3.503A pdb=" N SER A 623 " --> pdb=" O GLU A 601 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.667A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 288 552 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1935 1.33 - 1.45: 3079 1.45 - 1.58: 6039 1.58 - 1.71: 6 1.71 - 1.83: 65 Bond restraints: 11124 Sorted by residual: bond pdb=" N13 IGD B 502 " pdb=" S03 IGD B 502 " ideal model delta sigma weight residual 1.604 1.702 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C1 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.410 1.472 -0.062 2.00e-02 2.50e+03 9.60e+00 bond pdb=" C32 IGD B 502 " pdb="CL1 IGD B 502 " ideal model delta sigma weight residual 1.725 1.785 -0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" C5 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.417 1.474 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" C1 BMA F 5 " pdb=" C2 BMA F 5 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.69e+00 ... (remaining 11119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 15066 4.16 - 8.31: 106 8.31 - 12.47: 7 12.47 - 16.62: 0 16.62 - 20.78: 2 Bond angle restraints: 15181 Sorted by residual: angle pdb=" O11 IGD B 502 " pdb=" S03 IGD B 502 " pdb=" O12 IGD B 502 " ideal model delta sigma weight residual 121.96 101.18 20.78 3.00e+00 1.11e-01 4.80e+01 angle pdb=" O09 IGD B 502 " pdb=" S02 IGD B 502 " pdb=" O10 IGD B 502 " ideal model delta sigma weight residual 118.25 99.22 19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 113.53 108.93 4.60 9.80e-01 1.04e+00 2.20e+01 angle pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 121.97 130.18 -8.21 1.80e+00 3.09e-01 2.08e+01 angle pdb=" C PHE B 86 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " ideal model delta sigma weight residual 120.33 123.88 -3.55 8.00e-01 1.56e+00 1.97e+01 ... (remaining 15176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6061 17.71 - 35.43: 229 35.43 - 53.14: 33 53.14 - 70.85: 6 70.85 - 88.56: 8 Dihedral angle restraints: 6337 sinusoidal: 2501 harmonic: 3836 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 93.00 -178.44 -88.56 1 1.00e+01 1.00e-02 9.36e+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 93.00 179.32 -86.32 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -147.26 -32.74 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 6334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1612 0.091 - 0.181: 182 0.181 - 0.272: 10 0.272 - 0.362: 4 0.362 - 0.453: 4 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 464 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.13e+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 -2.01 -0.39 2.00e-01 2.50e+01 3.71e+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 -0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 1809 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 464 " -0.007 2.00e-02 2.50e+03 2.44e-01 7.47e+02 pdb=" CG ASN A 464 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 464 " 0.261 2.00e-02 2.50e+03 pdb=" ND2 ASN A 464 " -0.424 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.029 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP C 227 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO A 560 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.041 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2663 2.79 - 3.32: 9718 3.32 - 3.85: 17636 3.85 - 4.37: 20738 4.37 - 4.90: 35987 Nonbonded interactions: 86742 Sorted by model distance: nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.265 3.040 nonbonded pdb=" O LYS B 216 " pdb=" OH TYR D 18 " model vdw 2.288 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR A 148 " pdb=" OD1 ASP A 381 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU A 595 " pdb=" OH TYR A 602 " model vdw 2.309 3.040 ... (remaining 86737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:5.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.011 0.915 11149 Z= 0.533 Angle : 1.174 61.262 15252 Z= 0.548 Chirality : 0.060 0.453 1812 Planarity : 0.007 0.073 1829 Dihedral : 10.475 80.342 3853 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.18 % Allowed : 1.86 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.18), residues: 1304 helix: -1.82 (0.15), residues: 689 sheet: -1.40 (0.47), residues: 121 loop : -2.91 (0.22), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 434 TYR 0.040 0.003 TYR A 565 PHE 0.047 0.004 PHE C 132 TRP 0.056 0.004 TRP C 227 HIS 0.017 0.003 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.31 (11124) covalent geometry : angle 0.99472 / 0.51 (15181) SS BOND : bond 0.00983 / 0.49 ( 4) SS BOND : angle 2.82302 / 1.86 ( 8) hydrogen bonds : bond 0.17401 / 11.09 ( 552) hydrogen bonds : angle 6.70895 / 4.64 ( 1605) link_BETA1-3 : bond 0.00114 / 0.06 ( 1) link_BETA1-3 : angle 1.41040 / 0.88 ( 3) link_BETA1-4 : bond 0.00631 / 0.32 ( 7) link_BETA1-4 : angle 2.53615 / 2.02 ( 21) link_BETA1-6 : bond 0.00424 / 0.22 ( 1) link_BETA1-6 : angle 1.37967 / 1.14 ( 3) link_NAG-ASN : bond 0.26414 / 13.90 ( 12) link_NAG-ASN : angle 12.67081 / 5.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.9140 (mmm) cc_final: 0.8883 (tpp) REVERT: A 242 ILE cc_start: 0.7871 (tt) cc_final: 0.7612 (tp) REVERT: A 617 LEU cc_start: 0.8196 (mt) cc_final: 0.7923 (tp) REVERT: B 112 GLN cc_start: 0.7891 (tt0) cc_final: 0.7686 (tt0) REVERT: B 184 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 270 MET cc_start: 0.6764 (mmm) cc_final: 0.6561 (mmm) REVERT: C 28 ASP cc_start: 0.8295 (t0) cc_final: 0.8041 (t0) REVERT: C 99 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6968 (pp20) REVERT: C 104 LEU cc_start: 0.7085 (mt) cc_final: 0.6842 (mm) REVERT: C 159 THR cc_start: 0.8889 (m) cc_final: 0.8595 (p) REVERT: C 180 ASP cc_start: 0.8546 (t0) cc_final: 0.8282 (t70) REVERT: D 17 LYS cc_start: 0.8184 (mttm) cc_final: 0.7817 (ttmm) REVERT: D 54 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7303 (tttp) outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 0.5649 time to fit residues: 125.0489 Evaluate side-chains 111 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 436 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS A 163 GLN A 355 GLN A 358 ASN A 385 GLN A 531 ASN A 552 GLN A 606 GLN B 204 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.098626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.077767 restraints weight = 19177.121| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.25 r_work: 0.2854 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11149 Z= 0.161 Angle : 0.678 10.149 15252 Z= 0.336 Chirality : 0.044 0.246 1812 Planarity : 0.005 0.042 1829 Dihedral : 6.271 58.783 1545 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.95 % Allowed : 8.70 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.22), residues: 1304 helix: 0.46 (0.19), residues: 699 sheet: -0.95 (0.49), residues: 116 loop : -2.36 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 543 TYR 0.015 0.002 TYR A 569 PHE 0.032 0.002 PHE A 302 TRP 0.021 0.002 TRP C 227 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (11124) covalent geometry : angle 0.66049 / 0.33 (15181) SS BOND : bond 0.00579 / 0.29 ( 4) SS BOND : angle 1.37626 / 0.88 ( 8) hydrogen bonds : bond 0.04976 / 3.26 ( 552) hydrogen bonds : angle 4.36939 / 3.01 ( 1605) link_BETA1-3 : bond 0.00233 / 0.12 ( 1) link_BETA1-3 : angle 1.84281 / 1.50 ( 3) link_BETA1-4 : bond 0.00503 / 0.24 ( 7) link_BETA1-4 : angle 1.61454 / 1.37 ( 21) link_BETA1-6 : bond 0.01212 / 0.64 ( 1) link_BETA1-6 : angle 1.51913 / 1.10 ( 3) link_NAG-ASN : bond 0.00296 / 0.18 ( 12) link_NAG-ASN : angle 2.84604 / 1.60 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9251 (mmm) cc_final: 0.8987 (tpp) REVERT: A 617 LEU cc_start: 0.8289 (mt) cc_final: 0.8041 (tp) REVERT: B 112 GLN cc_start: 0.7999 (tt0) cc_final: 0.7794 (tt0) REVERT: B 184 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8486 (mm-30) REVERT: B 270 MET cc_start: 0.7345 (mmm) cc_final: 0.7120 (mmm) REVERT: C 28 ASP cc_start: 0.8377 (t0) cc_final: 0.8091 (t0) REVERT: C 99 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7130 (tm-30) REVERT: C 104 LEU cc_start: 0.7349 (mt) cc_final: 0.7128 (mm) REVERT: C 186 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: C 211 GLU cc_start: 0.8133 (mp0) cc_final: 0.7836 (mp0) REVERT: D 17 LYS cc_start: 0.8349 (mttm) cc_final: 0.7987 (ttmm) REVERT: D 40 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: D 42 PHE cc_start: 0.7464 (m-10) cc_final: 0.7256 (m-80) REVERT: D 91 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7566 (m-80) outliers start: 22 outliers final: 10 residues processed: 133 average time/residue: 0.5314 time to fit residues: 76.8425 Evaluate side-chains 107 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.076871 restraints weight = 19291.598| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.28 r_work: 0.2833 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11149 Z= 0.153 Angle : 0.638 9.950 15252 Z= 0.313 Chirality : 0.043 0.243 1812 Planarity : 0.004 0.033 1829 Dihedral : 6.000 57.192 1543 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.66 % Allowed : 10.03 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1304 helix: 1.45 (0.20), residues: 694 sheet: -0.81 (0.48), residues: 123 loop : -2.08 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 543 TYR 0.015 0.001 TYR B 256 PHE 0.031 0.002 PHE A 302 TRP 0.015 0.001 TRP C 209 HIS 0.005 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (11124) covalent geometry : angle 0.62236 / 0.31 (15181) SS BOND : bond 0.00538 / 0.27 ( 4) SS BOND : angle 1.33087 / 0.82 ( 8) hydrogen bonds : bond 0.04401 / 2.86 ( 552) hydrogen bonds : angle 3.99788 / 2.74 ( 1605) link_BETA1-3 : bond 0.00295 / 0.16 ( 1) link_BETA1-3 : angle 1.57928 / 1.09 ( 3) link_BETA1-4 : bond 0.00378 / 0.19 ( 7) link_BETA1-4 : angle 1.57421 / 1.30 ( 21) link_BETA1-6 : bond 0.00902 / 0.47 ( 1) link_BETA1-6 : angle 1.30533 / 0.97 ( 3) link_NAG-ASN : bond 0.00298 / 0.17 ( 12) link_NAG-ASN : angle 2.59306 / 1.48 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ARG cc_start: 0.8474 (ptt-90) cc_final: 0.8231 (ptt-90) REVERT: A 624 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9047 (m) REVERT: B 112 GLN cc_start: 0.7973 (tt0) cc_final: 0.7698 (tt0) REVERT: B 184 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8555 (mm-30) REVERT: B 257 ASP cc_start: 0.8313 (t70) cc_final: 0.7381 (t0) REVERT: C 28 ASP cc_start: 0.8384 (t0) cc_final: 0.8053 (t0) REVERT: C 104 LEU cc_start: 0.7359 (mt) cc_final: 0.6721 (tp) REVERT: C 186 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7119 (mtp180) REVERT: C 211 GLU cc_start: 0.8291 (mp0) cc_final: 0.7879 (mp0) REVERT: D 17 LYS cc_start: 0.8335 (mttm) cc_final: 0.8058 (ttmm) REVERT: D 40 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7534 (tm-30) REVERT: D 42 PHE cc_start: 0.7275 (m-10) cc_final: 0.6855 (m-80) outliers start: 30 outliers final: 12 residues processed: 125 average time/residue: 0.4951 time to fit residues: 68.0199 Evaluate side-chains 108 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.077072 restraints weight = 19311.861| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.28 r_work: 0.2823 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11149 Z= 0.157 Angle : 0.622 9.903 15252 Z= 0.306 Chirality : 0.043 0.245 1812 Planarity : 0.004 0.034 1829 Dihedral : 5.949 54.844 1543 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.93 % Allowed : 11.00 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1304 helix: 1.79 (0.20), residues: 694 sheet: -0.69 (0.49), residues: 124 loop : -1.97 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 543 TYR 0.014 0.001 TYR A 569 PHE 0.030 0.002 PHE A 302 TRP 0.011 0.001 TRP C 209 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (11124) covalent geometry : angle 0.60843 / 0.30 (15181) SS BOND : bond 0.00489 / 0.24 ( 4) SS BOND : angle 1.33396 / 0.79 ( 8) hydrogen bonds : bond 0.04321 / 2.81 ( 552) hydrogen bonds : angle 3.88345 / 2.66 ( 1605) link_BETA1-3 : bond 0.00227 / 0.12 ( 1) link_BETA1-3 : angle 1.54437 / 1.09 ( 3) link_BETA1-4 : bond 0.00361 / 0.18 ( 7) link_BETA1-4 : angle 1.52559 / 1.27 ( 21) link_BETA1-6 : bond 0.00912 / 0.48 ( 1) link_BETA1-6 : angle 1.39300 / 1.04 ( 3) link_NAG-ASN : bond 0.00273 / 0.16 ( 12) link_NAG-ASN : angle 2.39290 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ARG cc_start: 0.8496 (ptt-90) cc_final: 0.8241 (ptt-90) REVERT: A 624 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9072 (m) REVERT: B 112 GLN cc_start: 0.8095 (tt0) cc_final: 0.7825 (tt0) REVERT: B 127 GLN cc_start: 0.6237 (pt0) cc_final: 0.5858 (pp30) REVERT: B 135 ASN cc_start: 0.7494 (m-40) cc_final: 0.7280 (m110) REVERT: B 184 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8560 (mm-30) REVERT: B 257 ASP cc_start: 0.8496 (t70) cc_final: 0.7806 (t0) REVERT: C 28 ASP cc_start: 0.8431 (t0) cc_final: 0.8128 (t0) REVERT: C 47 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8671 (tt) REVERT: C 186 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7075 (mtp180) REVERT: C 211 GLU cc_start: 0.8332 (mp0) cc_final: 0.7761 (mp0) REVERT: D 40 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7567 (tm-30) outliers start: 33 outliers final: 10 residues processed: 121 average time/residue: 0.5102 time to fit residues: 67.7910 Evaluate side-chains 110 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 80 optimal weight: 0.0020 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.076672 restraints weight = 19104.459| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.27 r_work: 0.2817 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11149 Z= 0.156 Angle : 0.615 9.891 15252 Z= 0.302 Chirality : 0.043 0.242 1812 Planarity : 0.004 0.036 1829 Dihedral : 5.960 54.040 1543 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.02 % Allowed : 11.18 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1304 helix: 1.97 (0.20), residues: 694 sheet: -0.60 (0.49), residues: 124 loop : -1.90 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 543 TYR 0.014 0.001 TYR A 569 PHE 0.029 0.002 PHE A 302 TRP 0.009 0.001 TRP B 203 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (11124) covalent geometry : angle 0.60177 / 0.30 (15181) SS BOND : bond 0.00527 / 0.26 ( 4) SS BOND : angle 1.24355 / 0.69 ( 8) hydrogen bonds : bond 0.04249 / 2.76 ( 552) hydrogen bonds : angle 3.84800 / 2.63 ( 1605) link_BETA1-3 : bond 0.00350 / 0.18 ( 1) link_BETA1-3 : angle 1.44509 / 1.00 ( 3) link_BETA1-4 : bond 0.00338 / 0.17 ( 7) link_BETA1-4 : angle 1.50617 / 1.25 ( 21) link_BETA1-6 : bond 0.00827 / 0.44 ( 1) link_BETA1-6 : angle 1.36327 / 1.02 ( 3) link_NAG-ASN : bond 0.00274 / 0.16 ( 12) link_NAG-ASN : angle 2.32252 / 1.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: A 624 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9085 (m) REVERT: B 112 GLN cc_start: 0.8143 (tt0) cc_final: 0.7862 (tt0) REVERT: B 127 GLN cc_start: 0.5987 (pt0) cc_final: 0.5670 (pp30) REVERT: B 135 ASN cc_start: 0.7458 (m-40) cc_final: 0.7245 (m110) REVERT: B 184 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 254 SER cc_start: 0.8599 (m) cc_final: 0.8309 (p) REVERT: B 257 ASP cc_start: 0.8584 (t70) cc_final: 0.7946 (t70) REVERT: B 270 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6832 (mtp) REVERT: C 28 ASP cc_start: 0.8372 (t0) cc_final: 0.8053 (t0) REVERT: C 47 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8701 (tt) REVERT: C 104 LEU cc_start: 0.7367 (mm) cc_final: 0.6850 (tp) REVERT: C 186 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7053 (mtp180) REVERT: C 211 GLU cc_start: 0.8397 (mp0) cc_final: 0.7854 (mp0) REVERT: C 241 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7201 (tpp80) REVERT: D 19 TYR cc_start: 0.8664 (t80) cc_final: 0.8444 (t80) REVERT: D 40 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7366 (tp30) outliers start: 34 outliers final: 13 residues processed: 127 average time/residue: 0.4918 time to fit residues: 68.8629 Evaluate side-chains 116 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN A 606 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.074312 restraints weight = 19267.289| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.26 r_work: 0.2793 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11149 Z= 0.201 Angle : 0.666 10.062 15252 Z= 0.326 Chirality : 0.045 0.242 1812 Planarity : 0.004 0.038 1829 Dihedral : 6.219 54.758 1543 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.11 % Allowed : 11.09 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1304 helix: 1.91 (0.20), residues: 700 sheet: -0.57 (0.48), residues: 124 loop : -1.89 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 432 TYR 0.015 0.002 TYR A 569 PHE 0.029 0.002 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.005 0.002 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (11124) covalent geometry : angle 0.65267 / 0.32 (15181) SS BOND : bond 0.00649 / 0.32 ( 4) SS BOND : angle 1.48461 / 0.85 ( 8) hydrogen bonds : bond 0.04638 / 3.01 ( 552) hydrogen bonds : angle 3.92905 / 2.70 ( 1605) link_BETA1-3 : bond 0.00057 / 0.03 ( 1) link_BETA1-3 : angle 1.37113 / 0.91 ( 3) link_BETA1-4 : bond 0.00369 / 0.18 ( 7) link_BETA1-4 : angle 1.59755 / 1.33 ( 21) link_BETA1-6 : bond 0.00813 / 0.43 ( 1) link_BETA1-6 : angle 1.33946 / 1.00 ( 3) link_NAG-ASN : bond 0.00307 / 0.17 ( 12) link_NAG-ASN : angle 2.50295 / 1.47 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.9097 (m) REVERT: B 112 GLN cc_start: 0.8223 (tt0) cc_final: 0.7919 (tt0) REVERT: B 127 GLN cc_start: 0.5962 (pt0) cc_final: 0.5726 (pt0) REVERT: B 135 ASN cc_start: 0.7466 (m-40) cc_final: 0.7265 (m110) REVERT: B 184 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8555 (mm-30) REVERT: B 254 SER cc_start: 0.8674 (m) cc_final: 0.8376 (p) REVERT: B 257 ASP cc_start: 0.8634 (t70) cc_final: 0.8091 (t70) REVERT: B 270 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6825 (mtp) REVERT: C 28 ASP cc_start: 0.8400 (t0) cc_final: 0.8152 (t0) REVERT: C 47 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8686 (tt) REVERT: C 104 LEU cc_start: 0.7383 (mm) cc_final: 0.6857 (tp) REVERT: C 186 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7042 (mtp180) REVERT: C 211 GLU cc_start: 0.8466 (mp0) cc_final: 0.8037 (mp0) REVERT: C 241 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6988 (mtm110) REVERT: D 40 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7428 (tp30) outliers start: 35 outliers final: 15 residues processed: 123 average time/residue: 0.5035 time to fit residues: 68.0245 Evaluate side-chains 118 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.074053 restraints weight = 19204.233| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.28 r_work: 0.2784 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11149 Z= 0.221 Angle : 0.690 10.144 15252 Z= 0.335 Chirality : 0.046 0.245 1812 Planarity : 0.004 0.038 1829 Dihedral : 6.434 55.077 1543 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.84 % Allowed : 11.36 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1304 helix: 1.89 (0.20), residues: 698 sheet: -0.61 (0.48), residues: 124 loop : -1.87 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 432 TYR 0.015 0.002 TYR A 569 PHE 0.030 0.002 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.005 0.002 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (11124) covalent geometry : angle 0.67518 / 0.33 (15181) SS BOND : bond 0.00652 / 0.32 ( 4) SS BOND : angle 1.52309 / 0.88 ( 8) hydrogen bonds : bond 0.04820 / 3.13 ( 552) hydrogen bonds : angle 3.96295 / 2.72 ( 1605) link_BETA1-3 : bond 0.00147 / 0.08 ( 1) link_BETA1-3 : angle 1.35345 / 0.89 ( 3) link_BETA1-4 : bond 0.00337 / 0.17 ( 7) link_BETA1-4 : angle 1.64999 / 1.37 ( 21) link_BETA1-6 : bond 0.00841 / 0.44 ( 1) link_BETA1-6 : angle 1.30875 / 0.96 ( 3) link_NAG-ASN : bond 0.00344 / 0.19 ( 12) link_NAG-ASN : angle 2.63036 / 1.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9119 (m) REVERT: B 112 GLN cc_start: 0.8179 (tt0) cc_final: 0.7945 (tt0) REVERT: B 127 GLN cc_start: 0.5997 (pt0) cc_final: 0.5735 (pt0) REVERT: B 184 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8538 (mm-30) REVERT: B 254 SER cc_start: 0.8687 (m) cc_final: 0.8399 (p) REVERT: B 257 ASP cc_start: 0.8471 (t70) cc_final: 0.7970 (t70) REVERT: B 270 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6899 (mtp) REVERT: B 458 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: C 28 ASP cc_start: 0.8405 (t0) cc_final: 0.8138 (t0) REVERT: C 47 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8756 (tt) REVERT: C 104 LEU cc_start: 0.7510 (mm) cc_final: 0.6975 (tp) REVERT: D 40 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7225 (tp30) outliers start: 32 outliers final: 16 residues processed: 116 average time/residue: 0.5011 time to fit residues: 63.8958 Evaluate side-chains 113 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.075939 restraints weight = 19081.203| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.25 r_work: 0.2816 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11149 Z= 0.136 Angle : 0.609 9.842 15252 Z= 0.298 Chirality : 0.042 0.250 1812 Planarity : 0.003 0.036 1829 Dihedral : 6.137 52.947 1543 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.40 % Allowed : 12.16 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1304 helix: 2.10 (0.20), residues: 700 sheet: -0.61 (0.47), residues: 126 loop : -1.83 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 241 TYR 0.015 0.001 TYR A 569 PHE 0.029 0.002 PHE A 302 TRP 0.009 0.001 TRP B 203 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11124) covalent geometry : angle 0.59747 / 0.30 (15181) SS BOND : bond 0.00482 / 0.24 ( 4) SS BOND : angle 1.25659 / 0.65 ( 8) hydrogen bonds : bond 0.04115 / 2.67 ( 552) hydrogen bonds : angle 3.81564 / 2.61 ( 1605) link_BETA1-3 : bond 0.00254 / 0.13 ( 1) link_BETA1-3 : angle 1.14463 / 0.81 ( 3) link_BETA1-4 : bond 0.00382 / 0.19 ( 7) link_BETA1-4 : angle 1.43560 / 1.19 ( 21) link_BETA1-6 : bond 0.00824 / 0.43 ( 1) link_BETA1-6 : angle 1.36064 / 1.00 ( 3) link_NAG-ASN : bond 0.00281 / 0.16 ( 12) link_NAG-ASN : angle 2.15744 / 1.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.8775 (t0) cc_final: 0.8530 (t70) REVERT: A 624 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9137 (m) REVERT: A 683 SER cc_start: 0.9037 (m) cc_final: 0.8763 (p) REVERT: B 127 GLN cc_start: 0.5961 (pt0) cc_final: 0.5683 (pt0) REVERT: B 184 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8517 (mm-30) REVERT: B 254 SER cc_start: 0.8560 (m) cc_final: 0.8277 (p) REVERT: B 257 ASP cc_start: 0.8439 (t70) cc_final: 0.7971 (t70) REVERT: B 270 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6793 (mtp) REVERT: B 458 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: C 47 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8729 (tt) REVERT: C 104 LEU cc_start: 0.7427 (mm) cc_final: 0.6929 (tp) REVERT: D 40 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7216 (tp30) outliers start: 27 outliers final: 14 residues processed: 115 average time/residue: 0.5046 time to fit residues: 63.7520 Evaluate side-chains 110 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077678 restraints weight = 18985.309| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.25 r_work: 0.2858 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11149 Z= 0.113 Angle : 0.573 9.698 15252 Z= 0.283 Chirality : 0.041 0.250 1812 Planarity : 0.003 0.036 1829 Dihedral : 5.866 51.248 1543 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.77 % Allowed : 12.60 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1304 helix: 2.15 (0.20), residues: 713 sheet: -0.40 (0.47), residues: 124 loop : -1.76 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.015 0.001 TYR B 77 PHE 0.030 0.001 PHE A 302 TRP 0.008 0.001 TRP B 203 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11124) covalent geometry : angle 0.56236 / 0.28 (15181) SS BOND : bond 0.00418 / 0.21 ( 4) SS BOND : angle 1.12016 / 0.55 ( 8) hydrogen bonds : bond 0.03673 / 2.39 ( 552) hydrogen bonds : angle 3.71459 / 2.53 ( 1605) link_BETA1-3 : bond 0.00326 / 0.17 ( 1) link_BETA1-3 : angle 1.22392 / 0.89 ( 3) link_BETA1-4 : bond 0.00351 / 0.17 ( 7) link_BETA1-4 : angle 1.27345 / 1.02 ( 21) link_BETA1-6 : bond 0.00833 / 0.44 ( 1) link_BETA1-6 : angle 1.43932 / 1.08 ( 3) link_NAG-ASN : bond 0.00292 / 0.17 ( 12) link_NAG-ASN : angle 2.02083 / 1.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.8701 (t0) cc_final: 0.8500 (t70) REVERT: A 543 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.8322 (ptt-90) REVERT: A 624 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9181 (m) REVERT: B 127 GLN cc_start: 0.5943 (pt0) cc_final: 0.5656 (pt0) REVERT: B 184 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8556 (mm-30) REVERT: B 254 SER cc_start: 0.8400 (m) cc_final: 0.8108 (t) REVERT: B 257 ASP cc_start: 0.8468 (t70) cc_final: 0.8092 (t70) REVERT: B 270 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6782 (mtp) REVERT: C 47 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8737 (tt) REVERT: D 40 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7198 (tp30) outliers start: 20 outliers final: 10 residues processed: 111 average time/residue: 0.4753 time to fit residues: 58.2017 Evaluate side-chains 100 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 127 optimal weight: 0.0040 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.077280 restraints weight = 19048.557| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.25 r_work: 0.2842 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11149 Z= 0.125 Angle : 0.591 9.760 15252 Z= 0.291 Chirality : 0.042 0.246 1812 Planarity : 0.003 0.037 1829 Dihedral : 5.853 51.609 1543 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 13.40 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1304 helix: 2.20 (0.20), residues: 710 sheet: -0.46 (0.48), residues: 126 loop : -1.70 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 543 TYR 0.014 0.001 TYR A 569 PHE 0.029 0.001 PHE A 302 TRP 0.008 0.001 TRP D 67 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11124) covalent geometry : angle 0.58117 / 0.29 (15181) SS BOND : bond 0.00460 / 0.23 ( 4) SS BOND : angle 1.14469 / 0.59 ( 8) hydrogen bonds : bond 0.03791 / 2.47 ( 552) hydrogen bonds : angle 3.73152 / 2.54 ( 1605) link_BETA1-3 : bond 0.00349 / 0.18 ( 1) link_BETA1-3 : angle 1.26358 / 0.89 ( 3) link_BETA1-4 : bond 0.00343 / 0.17 ( 7) link_BETA1-4 : angle 1.28026 / 1.02 ( 21) link_BETA1-6 : bond 0.00773 / 0.41 ( 1) link_BETA1-6 : angle 1.40971 / 1.06 ( 3) link_NAG-ASN : bond 0.00265 / 0.16 ( 12) link_NAG-ASN : angle 1.99623 / 1.22 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9201 (m) REVERT: B 112 GLN cc_start: 0.8127 (tt0) cc_final: 0.7867 (tt0) REVERT: B 127 GLN cc_start: 0.5952 (pt0) cc_final: 0.5654 (pt0) REVERT: B 184 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8560 (mm-30) REVERT: B 254 SER cc_start: 0.8392 (m) cc_final: 0.8114 (t) REVERT: B 257 ASP cc_start: 0.8385 (t70) cc_final: 0.7937 (t70) REVERT: B 270 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6761 (mtp) REVERT: C 47 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8753 (tt) REVERT: D 40 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7188 (tp30) outliers start: 17 outliers final: 11 residues processed: 103 average time/residue: 0.4989 time to fit residues: 56.4495 Evaluate side-chains 104 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN B 214 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.075353 restraints weight = 19244.575| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.26 r_work: 0.2812 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11149 Z= 0.171 Angle : 0.642 11.207 15252 Z= 0.313 Chirality : 0.044 0.244 1812 Planarity : 0.004 0.038 1829 Dihedral : 6.100 55.739 1543 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.77 % Allowed : 13.40 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1304 helix: 2.12 (0.20), residues: 704 sheet: -0.37 (0.48), residues: 124 loop : -1.67 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 241 TYR 0.015 0.002 TYR A 569 PHE 0.029 0.002 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (11124) covalent geometry : angle 0.63073 / 0.31 (15181) SS BOND : bond 0.00596 / 0.30 ( 4) SS BOND : angle 1.30879 / 0.72 ( 8) hydrogen bonds : bond 0.04253 / 2.77 ( 552) hydrogen bonds : angle 3.81796 / 2.61 ( 1605) link_BETA1-3 : bond 0.00216 / 0.11 ( 1) link_BETA1-3 : angle 1.29982 / 0.86 ( 3) link_BETA1-4 : bond 0.00329 / 0.16 ( 7) link_BETA1-4 : angle 1.38201 / 1.11 ( 21) link_BETA1-6 : bond 0.00860 / 0.45 ( 1) link_BETA1-6 : angle 1.41227 / 1.06 ( 3) link_NAG-ASN : bond 0.00284 / 0.17 ( 12) link_NAG-ASN : angle 2.25179 / 1.36 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.65 seconds wall clock time: 60 minutes 43.62 seconds (3643.62 seconds total)