Starting phenix.real_space_refine on Sun May 3 06:26:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5t_33624/05_2026/7y5t_33624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5t_33624/05_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_33624/05_2026/7y5t_33624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5t_33624/05_2026/7y5t_33624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5t_33624/05_2026/7y5t_33624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5t_33624/05_2026/7y5t_33624.map" } 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-2.1rc2-6044/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 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: 2.72, per 1000 atoms: 0.25 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: 0.89 Conformation dependent library (CDL) restraints added in 510.8 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: 0.32 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: 1.74 Time building geometry restraints manager: 1.19 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 - 22.94: 6684 22.94 - 45.87: 195 45.87 - 68.80: 37 68.80 - 91.74: 20 91.74 - 114.67: 22 Dihedral angle restraints: 6958 sinusoidal: 3122 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 6955 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 13.826 114.675 4474 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 covalent geometry : bond 0.00710 (11124) covalent geometry : angle 0.99472 (15181) SS BOND : bond 0.00983 ( 4) SS BOND : angle 2.82302 ( 8) hydrogen bonds : bond 0.17401 ( 552) hydrogen bonds : angle 6.70895 ( 1605) link_BETA1-3 : bond 0.00114 ( 1) link_BETA1-3 : angle 1.41040 ( 3) link_BETA1-4 : bond 0.00631 ( 7) link_BETA1-4 : angle 2.53615 ( 21) link_BETA1-6 : bond 0.00424 ( 1) link_BETA1-6 : angle 1.37967 ( 3) link_NAG-ASN : bond 0.26414 ( 12) link_NAG-ASN : angle 12.67081 ( 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 : 0.356 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: 0.6102 time to fit residues: 134.4186 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 : 0.418 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3312 r_free = 0.3312 target = 0.098622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.077771 restraints weight = 19181.039| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.25 r_work: 0.2853 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11149 Z= 0.162 Angle : 0.693 10.226 15252 Z= 0.340 Chirality : 0.045 0.238 1812 Planarity : 0.005 0.041 1829 Dihedral : 12.783 118.159 2166 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.64 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: -1.07 (0.22), residues: 1304 helix: 0.45 (0.19), residues: 699 sheet: -0.95 (0.49), residues: 116 loop : -2.38 (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 covalent geometry : bond 0.00374 (11124) covalent geometry : angle 0.67401 (15181) SS BOND : bond 0.00565 ( 4) SS BOND : angle 1.40122 ( 8) hydrogen bonds : bond 0.04965 ( 552) hydrogen bonds : angle 4.37701 ( 1605) link_BETA1-3 : bond 0.00786 ( 1) link_BETA1-3 : angle 1.85992 ( 3) link_BETA1-4 : bond 0.00588 ( 7) link_BETA1-4 : angle 1.73058 ( 21) link_BETA1-6 : bond 0.01160 ( 1) link_BETA1-6 : angle 2.05448 ( 3) link_NAG-ASN : bond 0.00316 ( 12) link_NAG-ASN : angle 2.96429 ( 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 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9252 (mmm) cc_final: 0.8990 (tpp) REVERT: A 617 LEU cc_start: 0.8292 (mt) cc_final: 0.8047 (tp) REVERT: B 112 GLN cc_start: 0.7999 (tt0) cc_final: 0.7796 (tt0) REVERT: B 184 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8504 (mm-30) REVERT: B 270 MET cc_start: 0.7314 (mmm) cc_final: 0.7090 (mmm) REVERT: C 28 ASP cc_start: 0.8379 (t0) cc_final: 0.8094 (t0) REVERT: C 99 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7134 (tm-30) REVERT: C 104 LEU cc_start: 0.7327 (mt) cc_final: 0.7112 (mm) REVERT: C 186 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7155 (mtp180) REVERT: C 211 GLU cc_start: 0.8136 (mp0) cc_final: 0.7847 (mp0) REVERT: D 17 LYS cc_start: 0.8331 (mttm) cc_final: 0.7968 (ttmm) REVERT: D 40 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: D 91 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.7568 (m-80) outliers start: 22 outliers final: 10 residues processed: 135 average time/residue: 0.5214 time to fit residues: 76.5503 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 : 0.270 ------------------------------------------------------------------------------- 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: 0.0670 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.078205 restraints weight = 19294.594| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.30 r_work: 0.2841 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11149 Z= 0.142 Angle : 0.642 9.990 15252 Z= 0.311 Chirality : 0.044 0.266 1812 Planarity : 0.004 0.033 1829 Dihedral : 11.079 117.016 2164 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.48 % Allowed : 10.29 % Favored : 87.22 % 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: -0.16 (0.24), residues: 1304 helix: 1.34 (0.20), residues: 700 sheet: -0.81 (0.48), residues: 123 loop : -2.16 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 62 TYR 0.014 0.001 TYR A 569 PHE 0.031 0.002 PHE A 302 TRP 0.013 0.001 TRP C 209 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00334 (11124) covalent geometry : angle 0.62613 (15181) SS BOND : bond 0.00493 ( 4) SS BOND : angle 1.24255 ( 8) hydrogen bonds : bond 0.04336 ( 552) hydrogen bonds : angle 4.03676 ( 1605) link_BETA1-3 : bond 0.00821 ( 1) link_BETA1-3 : angle 1.65364 ( 3) link_BETA1-4 : bond 0.00470 ( 7) link_BETA1-4 : angle 1.66664 ( 21) link_BETA1-6 : bond 0.01541 ( 1) link_BETA1-6 : angle 1.52742 ( 3) link_NAG-ASN : bond 0.00307 ( 12) link_NAG-ASN : angle 2.67736 ( 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 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8138 (mtt) REVERT: A 543 ARG cc_start: 0.8497 (ptt-90) cc_final: 0.8251 (ptt-90) REVERT: A 624 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9045 (m) REVERT: B 112 GLN cc_start: 0.7980 (tt0) cc_final: 0.7692 (tt0) REVERT: B 184 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 257 ASP cc_start: 0.8256 (t70) cc_final: 0.7256 (t0) REVERT: B 454 GLN cc_start: 0.8677 (tp40) cc_final: 0.8440 (tp-100) REVERT: C 28 ASP cc_start: 0.8384 (t0) cc_final: 0.8062 (t0) REVERT: C 104 LEU cc_start: 0.7335 (mt) cc_final: 0.6704 (tp) REVERT: C 186 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7101 (mtp180) REVERT: C 211 GLU cc_start: 0.8272 (mp0) cc_final: 0.7863 (mp0) REVERT: D 17 LYS cc_start: 0.8327 (mttm) cc_final: 0.8044 (ttmm) REVERT: D 40 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7465 (tm-30) REVERT: D 49 GLU cc_start: 0.7705 (mp0) cc_final: 0.7498 (mp0) outliers start: 28 outliers final: 11 residues processed: 124 average time/residue: 0.4668 time to fit residues: 63.2054 Evaluate side-chains 109 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET 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 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: 0.9990 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.098736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077634 restraints weight = 19298.553| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.31 r_work: 0.2849 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11149 Z= 0.127 Angle : 0.601 9.883 15252 Z= 0.292 Chirality : 0.043 0.294 1812 Planarity : 0.004 0.033 1829 Dihedral : 10.314 116.736 2164 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.57 % Allowed : 10.83 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1304 helix: 1.81 (0.20), residues: 698 sheet: -0.51 (0.49), residues: 121 loop : -1.99 (0.27), residues: 485 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 0.030 0.002 PHE A 302 TRP 0.011 0.001 TRP C 209 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00296 (11124) covalent geometry : angle 0.58718 (15181) SS BOND : bond 0.00387 ( 4) SS BOND : angle 1.15690 ( 8) hydrogen bonds : bond 0.03952 ( 552) hydrogen bonds : angle 3.85734 ( 1605) link_BETA1-3 : bond 0.00778 ( 1) link_BETA1-3 : angle 1.50184 ( 3) link_BETA1-4 : bond 0.00441 ( 7) link_BETA1-4 : angle 1.54430 ( 21) link_BETA1-6 : bond 0.01749 ( 1) link_BETA1-6 : angle 1.57241 ( 3) link_NAG-ASN : bond 0.00285 ( 12) link_NAG-ASN : angle 2.35504 ( 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 134 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8226 (mtt) REVERT: A 543 ARG cc_start: 0.8485 (ptt-90) cc_final: 0.8227 (ptt-90) REVERT: A 624 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9069 (m) REVERT: B 112 GLN cc_start: 0.8019 (tt0) cc_final: 0.7740 (tt0) REVERT: B 127 GLN cc_start: 0.6229 (pt0) cc_final: 0.5850 (pp30) REVERT: B 135 ASN cc_start: 0.7448 (m-40) cc_final: 0.7220 (m110) REVERT: B 184 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8538 (mm-30) REVERT: B 257 ASP cc_start: 0.8473 (t70) cc_final: 0.7801 (t0) REVERT: B 454 GLN cc_start: 0.8693 (tp40) cc_final: 0.8402 (tp-100) REVERT: C 28 ASP cc_start: 0.8412 (t0) cc_final: 0.8115 (t0) REVERT: C 47 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8646 (tt) REVERT: C 186 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7062 (mtp180) REVERT: C 211 GLU cc_start: 0.8334 (mp0) cc_final: 0.7888 (mp0) REVERT: D 17 LYS cc_start: 0.8317 (mttm) cc_final: 0.8116 (ttmm) REVERT: D 40 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7614 (tm-30) REVERT: D 49 GLU cc_start: 0.7717 (mp0) cc_final: 0.7465 (mp0) outliers start: 29 outliers final: 12 residues processed: 128 average time/residue: 0.4528 time to fit residues: 63.6391 Evaluate side-chains 112 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET 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 140 ILE Chi-restraints excluded: chain B residue 422 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 58 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.075535 restraints weight = 19138.234| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.27 r_work: 0.2813 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11149 Z= 0.181 Angle : 0.650 9.956 15252 Z= 0.316 Chirality : 0.045 0.311 1812 Planarity : 0.004 0.036 1829 Dihedral : 10.379 117.013 2164 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.19 % Allowed : 10.83 % Favored : 85.98 % 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: 1.92 (0.20), residues: 694 sheet: -0.59 (0.50), residues: 124 loop : -1.91 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 543 TYR 0.014 0.002 TYR A 569 PHE 0.030 0.002 PHE A 302 TRP 0.010 0.001 TRP C 209 HIS 0.005 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00438 (11124) covalent geometry : angle 0.63511 (15181) SS BOND : bond 0.00595 ( 4) SS BOND : angle 1.35039 ( 8) hydrogen bonds : bond 0.04453 ( 552) hydrogen bonds : angle 3.89989 ( 1605) link_BETA1-3 : bond 0.00626 ( 1) link_BETA1-3 : angle 1.92181 ( 3) link_BETA1-4 : bond 0.00360 ( 7) link_BETA1-4 : angle 1.52629 ( 21) link_BETA1-6 : bond 0.01760 ( 1) link_BETA1-6 : angle 1.64881 ( 3) link_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 2.58904 ( 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 133 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: A 624 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9087 (m) REVERT: B 112 GLN cc_start: 0.8112 (tt0) cc_final: 0.7815 (tt0) REVERT: B 127 GLN cc_start: 0.6015 (pt0) cc_final: 0.5713 (pp30) REVERT: B 135 ASN cc_start: 0.7473 (m-40) cc_final: 0.7264 (m110) REVERT: B 184 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8542 (mm-30) REVERT: B 257 ASP cc_start: 0.8577 (t70) cc_final: 0.7942 (t70) REVERT: B 270 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6811 (mtp) REVERT: C 28 ASP cc_start: 0.8412 (t0) cc_final: 0.8116 (t0) REVERT: C 47 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8665 (tt) REVERT: C 104 LEU cc_start: 0.7481 (mm) cc_final: 0.6915 (tp) REVERT: C 186 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7078 (mtp180) REVERT: C 211 GLU cc_start: 0.8372 (mp0) cc_final: 0.7842 (mp0) REVERT: D 40 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: D 49 GLU cc_start: 0.7806 (mp0) cc_final: 0.7530 (mp0) outliers start: 36 outliers final: 14 residues processed: 123 average time/residue: 0.4959 time to fit residues: 66.4870 Evaluate side-chains 116 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET 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 270 MET Chi-restraints excluded: chain B residue 422 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 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: 4.9990 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.076513 restraints weight = 19172.477| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.24 r_work: 0.2829 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11149 Z= 0.143 Angle : 0.607 9.827 15252 Z= 0.295 Chirality : 0.043 0.293 1812 Planarity : 0.004 0.036 1829 Dihedral : 10.144 114.481 2164 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.93 % Allowed : 10.83 % Favored : 86.25 % 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: 0.64 (0.24), residues: 1304 helix: 2.06 (0.20), residues: 696 sheet: -0.55 (0.49), residues: 124 loop : -1.85 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 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 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00338 (11124) covalent geometry : angle 0.59413 (15181) SS BOND : bond 0.00485 ( 4) SS BOND : angle 1.20516 ( 8) hydrogen bonds : bond 0.04073 ( 552) hydrogen bonds : angle 3.81923 ( 1605) link_BETA1-3 : bond 0.00799 ( 1) link_BETA1-3 : angle 1.53727 ( 3) link_BETA1-4 : bond 0.00382 ( 7) link_BETA1-4 : angle 1.50049 ( 21) link_BETA1-6 : bond 0.01714 ( 1) link_BETA1-6 : angle 1.64554 ( 3) link_NAG-ASN : bond 0.00280 ( 12) link_NAG-ASN : angle 2.29147 ( 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 139 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8315 (mtt) REVERT: A 242 ILE cc_start: 0.8060 (tp) cc_final: 0.7823 (tp) REVERT: A 253 ASP cc_start: 0.8761 (t0) cc_final: 0.8482 (t70) REVERT: A 624 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9094 (m) REVERT: A 683 SER cc_start: 0.9038 (m) cc_final: 0.8767 (p) REVERT: B 112 GLN cc_start: 0.8112 (tt0) cc_final: 0.7823 (tt0) REVERT: B 127 GLN cc_start: 0.6003 (pt0) cc_final: 0.5664 (pp30) REVERT: B 135 ASN cc_start: 0.7448 (m-40) cc_final: 0.7241 (m110) REVERT: B 184 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8515 (mm-30) REVERT: B 254 SER cc_start: 0.8551 (m) cc_final: 0.8246 (p) REVERT: B 257 ASP cc_start: 0.8649 (t70) cc_final: 0.8096 (t70) REVERT: B 270 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6891 (mtp) REVERT: C 28 ASP cc_start: 0.8361 (t0) cc_final: 0.8038 (t0) REVERT: C 47 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8694 (tt) REVERT: C 104 LEU cc_start: 0.7374 (mm) cc_final: 0.6862 (tp) REVERT: C 186 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7061 (mtp180) REVERT: C 211 GLU cc_start: 0.8431 (mp0) cc_final: 0.7904 (mp0) REVERT: C 241 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7001 (mtm180) REVERT: D 40 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: D 49 GLU cc_start: 0.7924 (mp0) cc_final: 0.7623 (mp0) outliers start: 33 outliers final: 14 residues processed: 129 average time/residue: 0.4895 time to fit residues: 68.9312 Evaluate side-chains 121 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET 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 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 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 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: 1.9990 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 606 GLN B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.074224 restraints weight = 19255.725| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.27 r_work: 0.2788 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11149 Z= 0.223 Angle : 0.692 10.125 15252 Z= 0.336 Chirality : 0.047 0.298 1812 Planarity : 0.004 0.039 1829 Dihedral : 10.441 115.162 2164 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.19 % Allowed : 11.00 % 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: 1.94 (0.20), residues: 698 sheet: -0.58 (0.49), residues: 124 loop : -1.88 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 629 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 0.006 0.002 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00542 (11124) covalent geometry : angle 0.67668 (15181) SS BOND : bond 0.00654 ( 4) SS BOND : angle 1.52288 ( 8) hydrogen bonds : bond 0.04808 ( 552) hydrogen bonds : angle 3.96745 ( 1605) link_BETA1-3 : bond 0.00606 ( 1) link_BETA1-3 : angle 1.96976 ( 3) link_BETA1-4 : bond 0.00398 ( 7) link_BETA1-4 : angle 1.66702 ( 21) link_BETA1-6 : bond 0.01776 ( 1) link_BETA1-6 : angle 1.71984 ( 3) link_NAG-ASN : bond 0.00363 ( 12) link_NAG-ASN : angle 2.67908 ( 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 132 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: A 624 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.9098 (m) REVERT: B 112 GLN cc_start: 0.8230 (tt0) cc_final: 0.7940 (tt0) REVERT: B 127 GLN cc_start: 0.5971 (pt0) cc_final: 0.5721 (pt0) REVERT: B 135 ASN cc_start: 0.7525 (m-40) cc_final: 0.7323 (m110) REVERT: B 184 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8549 (mm-30) REVERT: B 254 SER cc_start: 0.8675 (m) cc_final: 0.8379 (p) REVERT: B 257 ASP cc_start: 0.8451 (t70) cc_final: 0.7960 (t70) REVERT: B 270 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6920 (mtp) REVERT: C 28 ASP cc_start: 0.8421 (t0) cc_final: 0.8167 (t0) REVERT: C 104 LEU cc_start: 0.7508 (mm) cc_final: 0.6967 (tp) REVERT: C 186 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7042 (mtp180) REVERT: C 211 GLU cc_start: 0.8507 (mp0) cc_final: 0.8008 (mp0) REVERT: D 40 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: D 49 GLU cc_start: 0.8081 (mp0) cc_final: 0.7763 (mp0) outliers start: 36 outliers final: 16 residues processed: 121 average time/residue: 0.4991 time to fit residues: 65.9775 Evaluate side-chains 114 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 601 GLU 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 422 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 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: 2.9990 chunk 75 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.097904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.077135 restraints weight = 19124.975| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.28 r_work: 0.2831 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11149 Z= 0.130 Angle : 0.601 9.772 15252 Z= 0.292 Chirality : 0.043 0.285 1812 Planarity : 0.003 0.036 1829 Dihedral : 10.039 114.338 2164 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.13 % Allowed : 12.24 % 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: 0.74 (0.24), residues: 1304 helix: 2.14 (0.20), residues: 701 sheet: -0.59 (0.48), residues: 126 loop : -1.82 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 543 TYR 0.014 0.001 TYR A 569 PHE 0.029 0.001 PHE A 302 TRP 0.009 0.001 TRP B 203 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00304 (11124) covalent geometry : angle 0.58847 (15181) SS BOND : bond 0.00534 ( 4) SS BOND : angle 1.18688 ( 8) hydrogen bonds : bond 0.04026 ( 552) hydrogen bonds : angle 3.81284 ( 1605) link_BETA1-3 : bond 0.00796 ( 1) link_BETA1-3 : angle 1.43021 ( 3) link_BETA1-4 : bond 0.00391 ( 7) link_BETA1-4 : angle 1.46393 ( 21) link_BETA1-6 : bond 0.01816 ( 1) link_BETA1-6 : angle 1.74203 ( 3) link_NAG-ASN : bond 0.00291 ( 12) link_NAG-ASN : angle 2.21775 ( 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 122 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 624 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9111 (m) REVERT: A 683 SER cc_start: 0.9049 (m) cc_final: 0.8794 (p) REVERT: B 112 GLN cc_start: 0.8151 (tt0) cc_final: 0.7892 (tt0) REVERT: B 127 GLN cc_start: 0.5953 (pt0) cc_final: 0.5691 (pt0) REVERT: B 184 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8499 (mm-30) REVERT: B 254 SER cc_start: 0.8544 (m) cc_final: 0.8263 (p) REVERT: B 257 ASP cc_start: 0.8447 (t70) cc_final: 0.7976 (t70) REVERT: B 270 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6801 (mtp) REVERT: C 47 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8729 (tt) REVERT: C 104 LEU cc_start: 0.7426 (mm) cc_final: 0.6925 (tp) REVERT: C 186 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6997 (mtp180) REVERT: D 40 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: D 49 GLU cc_start: 0.8186 (mp0) cc_final: 0.7937 (mp0) outliers start: 24 outliers final: 11 residues processed: 115 average time/residue: 0.4937 time to fit residues: 62.1777 Evaluate side-chains 111 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain C residue 186 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.097762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.077162 restraints weight = 19009.838| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.25 r_work: 0.2837 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11149 Z= 0.122 Angle : 0.590 9.743 15252 Z= 0.288 Chirality : 0.043 0.273 1812 Planarity : 0.003 0.037 1829 Dihedral : 9.762 113.459 2164 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 12.33 % 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: 0.88 (0.24), residues: 1304 helix: 2.23 (0.20), residues: 701 sheet: -0.51 (0.48), residues: 126 loop : -1.73 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.014 0.001 TYR A 569 PHE 0.029 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 covalent geometry : bond 0.00280 (11124) covalent geometry : angle 0.57783 (15181) SS BOND : bond 0.00444 ( 4) SS BOND : angle 1.14644 ( 8) hydrogen bonds : bond 0.03812 ( 552) hydrogen bonds : angle 3.75208 ( 1605) link_BETA1-3 : bond 0.00798 ( 1) link_BETA1-3 : angle 1.49349 ( 3) link_BETA1-4 : bond 0.00347 ( 7) link_BETA1-4 : angle 1.37560 ( 21) link_BETA1-6 : bond 0.01746 ( 1) link_BETA1-6 : angle 1.93431 ( 3) link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.16637 ( 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 119 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ARG cc_start: 0.8524 (ptt-90) cc_final: 0.8307 (ptt-90) REVERT: A 624 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9149 (m) REVERT: B 112 GLN cc_start: 0.8143 (tt0) cc_final: 0.7901 (tt0) REVERT: B 127 GLN cc_start: 0.5966 (pt0) cc_final: 0.5696 (pt0) REVERT: B 184 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8469 (mm-30) REVERT: B 254 SER cc_start: 0.8387 (m) cc_final: 0.8088 (t) REVERT: B 257 ASP cc_start: 0.8471 (t70) cc_final: 0.8089 (t70) REVERT: B 270 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6768 (mtp) REVERT: C 47 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8738 (tt) REVERT: C 186 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6993 (mtp180) REVERT: D 40 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: D 49 GLU cc_start: 0.8166 (mp0) cc_final: 0.7912 (mp0) outliers start: 23 outliers final: 11 residues processed: 111 average time/residue: 0.4770 time to fit residues: 57.9974 Evaluate side-chains 107 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 149 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 C residue 186 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.076514 restraints weight = 19103.949| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.26 r_work: 0.2827 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11149 Z= 0.143 Angle : 0.610 9.812 15252 Z= 0.297 Chirality : 0.044 0.268 1812 Planarity : 0.004 0.038 1829 Dihedral : 9.702 113.513 2164 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.86 % Allowed : 12.69 % 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: 0.86 (0.24), residues: 1304 helix: 2.21 (0.20), residues: 701 sheet: -0.60 (0.47), residues: 129 loop : -1.72 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 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 covalent geometry : bond 0.00340 (11124) covalent geometry : angle 0.59786 (15181) SS BOND : bond 0.00509 ( 4) SS BOND : angle 1.20822 ( 8) hydrogen bonds : bond 0.03999 ( 552) hydrogen bonds : angle 3.77535 ( 1605) link_BETA1-3 : bond 0.00790 ( 1) link_BETA1-3 : angle 1.51878 ( 3) link_BETA1-4 : bond 0.00348 ( 7) link_BETA1-4 : angle 1.40453 ( 21) link_BETA1-6 : bond 0.01823 ( 1) link_BETA1-6 : angle 2.06881 ( 3) link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 2.24995 ( 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 113 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 112 GLN cc_start: 0.8142 (tt0) cc_final: 0.7925 (tt0) REVERT: B 127 GLN cc_start: 0.5964 (pt0) cc_final: 0.5685 (pt0) REVERT: B 184 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 254 SER cc_start: 0.8376 (m) cc_final: 0.8100 (t) REVERT: B 257 ASP cc_start: 0.8407 (t70) cc_final: 0.8061 (t70) REVERT: B 270 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6729 (mtp) REVERT: C 47 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8737 (tt) REVERT: D 40 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: D 49 GLU cc_start: 0.8193 (mp0) cc_final: 0.7942 (mp0) outliers start: 21 outliers final: 12 residues processed: 108 average time/residue: 0.5115 time to fit residues: 60.0168 Evaluate side-chains 107 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 601 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 149 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: 4.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.076076 restraints weight = 19264.535| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.30 r_work: 0.2822 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 0.052 11149 Z= 0.151 Angle : 0.624 9.867 15252 Z= 0.304 Chirality : 0.044 0.264 1812 Planarity : 0.004 0.039 1829 Dihedral : 9.655 113.316 2164 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.86 % Allowed : 12.69 % 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: 0.86 (0.24), residues: 1304 helix: 2.19 (0.20), residues: 701 sheet: -0.62 (0.47), residues: 129 loop : -1.67 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 237 TYR 0.015 0.001 TYR B 77 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 covalent geometry : bond 0.00359 (11124) covalent geometry : angle 0.61160 (15181) SS BOND : bond 0.00538 ( 4) SS BOND : angle 1.22783 ( 8) hydrogen bonds : bond 0.04063 ( 552) hydrogen bonds : angle 3.79176 ( 1605) link_BETA1-3 : bond 0.00791 ( 1) link_BETA1-3 : angle 1.53961 ( 3) link_BETA1-4 : bond 0.00367 ( 7) link_BETA1-4 : angle 1.42116 ( 21) link_BETA1-6 : bond 0.01799 ( 1) link_BETA1-6 : angle 2.14902 ( 3) link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.25825 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3259.79 seconds wall clock time: 56 minutes 20.72 seconds (3380.72 seconds total)