Starting phenix.real_space_refine on Tue Jul 29 15:32:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8e_36948/07_2025/8k8e_36948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8e_36948/07_2025/8k8e_36948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8e_36948/07_2025/8k8e_36948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8e_36948/07_2025/8k8e_36948.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8e_36948/07_2025/8k8e_36948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8e_36948/07_2025/8k8e_36948.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 40 5.16 5 C 7044 2.51 5 N 1705 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10716 Number of models: 1 Model: "" Number of chains: 11 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: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2394 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 95 Unusual residues: {'BOC': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'LINK_CNp': 1, 'TRANS': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'AIB:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'JUU': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="JUU G 16 " pdbres="LEU G 17 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'JUU:plan-3': 1} Unresolved non-hydrogen planarities: 1 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.47, per 1000 atoms: 0.79 Number of scatterers: 10716 At special positions: 0 Unit cell: (112.58, 94.1775, 130.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 1 15.00 O 1926 8.00 N 1705 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.03 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 Atom "HETATM10322 O2 BOC G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-3 " BMA F 1 " - " BMA F 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " BMA F 1 " - " BMA F 3 " NAG-ASN " NAG A 801 " - " ASN A 45 " " NAG A 802 " - " ASN A 435 " " NAG A 803 " - " ASN A 573 " " NAG A 804 " - " ASN A 530 " " NAG A 805 " - " ASN A 506 " " NAG A 806 " - " ASN A 187 " " NAG E 1 " - " ASN A 55 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 2.1 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 61.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.964A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 4.011A 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 113 removed outlier: 3.781A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.551A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.604A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.683A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.061A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.981A pdb=" N ARG A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.590A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.680A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.504A pdb=" N ILE A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.071A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 removed outlier: 3.678A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.638A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.917A pdb=" N SER A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.550A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.726A pdb=" N ILE A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 104 removed outlier: 3.640A pdb=" N VAL B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.844A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 154 Processing helix chain 'B' and resid 160 through 189 removed outlier: 3.885A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.512A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.599A pdb=" N GLU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 403 through 429 Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.357A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.989A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.761A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 104 removed outlier: 3.513A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 6.002A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.632A pdb=" N GLU C 183 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 204 removed outlier: 3.745A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 209 through 232 removed outlier: 3.520A pdb=" N LEU C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 4.229A 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 244 Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 26 through 43 removed outlier: 3.601A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 85 removed outlier: 3.685A pdb=" N ILE D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.707A pdb=" N ASP D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.548A pdb=" N ILE G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 14 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.634A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 212 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.690A 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 221 through 222 removed outlier: 3.705A pdb=" N ARG A 652 " --> pdb=" O HIS A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 7.024A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.121A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.564A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 288 591 hydrogen bonds defined for protein. 1704 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: 4.46 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1632 1.31 - 1.44: 3135 1.44 - 1.57: 6163 1.57 - 1.70: 3 1.70 - 1.84: 61 Bond restraints: 10994 Sorted by residual: bond pdb=" C BOC G 1 " pdb=" O1 BOC G 1 " ideal model delta sigma weight residual 1.410 1.195 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C VLM G 18 " pdb=" NT VLM G 18 " ideal model delta sigma weight residual 1.338 1.451 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C BOC G 1 " pdb=" O2 BOC G 1 " ideal model delta sigma weight residual 1.250 1.336 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C72 JUU G 16 " pdb=" N16 JUU G 16 " ideal model delta sigma weight residual 1.440 1.526 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" N ASN A 243 " pdb=" CA ASN A 243 " ideal model delta sigma weight residual 1.458 1.488 -0.031 7.40e-03 1.83e+04 1.71e+01 ... (remaining 10989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 14524 1.61 - 3.22: 360 3.22 - 4.83: 73 4.83 - 6.44: 31 6.44 - 8.05: 13 Bond angle restraints: 15001 Sorted by residual: angle pdb=" CA ASN A 562 " pdb=" CB ASN A 562 " pdb=" CG ASN A 562 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA ASN A 562 " pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 120.90 117.07 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" N LEU B 286 " pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 114.75 110.35 4.40 1.26e+00 6.30e-01 1.22e+01 angle pdb=" CA GLU D 40 " pdb=" CB GLU D 40 " pdb=" CG GLU D 40 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 angle pdb=" CA GLU C 106 " pdb=" CB GLU C 106 " pdb=" CG GLU C 106 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.15e+01 ... (remaining 14996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 6202 22.74 - 45.48: 397 45.48 - 68.22: 61 68.22 - 90.95: 32 90.95 - 113.69: 12 Dihedral angle restraints: 6704 sinusoidal: 2855 harmonic: 3849 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -170.34 84.34 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -162.32 76.32 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 213 " pdb=" CB CYS A 213 " ideal model delta sinusoidal sigma weight residual 93.00 40.91 52.09 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 6701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1684 0.093 - 0.185: 72 0.185 - 0.278: 7 0.278 - 0.371: 1 0.371 - 0.463: 2 Chirality restraints: 1766 Sorted by residual: chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.95e+00 chirality pdb=" C1 NAG A 805 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A 805 " pdb=" O5 NAG A 805 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1763 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 211 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 40 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" CD GLU D 40 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU D 40 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU D 40 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 264 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ASN A 264 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN A 264 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 265 " 0.010 2.00e-02 2.50e+03 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1638 2.75 - 3.29: 10552 3.29 - 3.83: 18062 3.83 - 4.36: 21018 4.36 - 4.90: 36426 Nonbonded interactions: 87696 Sorted by model distance: nonbonded pdb=" OG SER C 113 " pdb=" OE1 GLN C 116 " model vdw 2.218 3.040 nonbonded pdb=" O GLN B 464 " pdb=" ND2 ASN C 207 " model vdw 2.222 3.120 nonbonded pdb=" N GLU D 9 " pdb=" OE1 GLU D 9 " model vdw 2.243 3.120 nonbonded pdb=" O SER A 235 " pdb=" OG SER A 238 " model vdw 2.245 3.040 nonbonded pdb=" O ILE C 34 " pdb=" OH TYR C 90 " model vdw 2.257 3.040 ... (remaining 87691 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 50.250 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:15.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 : 0.005 0.215 11011 Z= 0.248 Angle : 0.695 9.124 15041 Z= 0.350 Chirality : 0.047 0.463 1766 Planarity : 0.004 0.051 1824 Dihedral : 16.423 113.692 4211 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.33 % Allowed : 15.68 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1299 helix: 1.79 (0.20), residues: 682 sheet: -0.72 (0.49), residues: 108 loop : -1.61 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.024 0.001 PHE A 302 TYR 0.020 0.001 TYR D 47 ARG 0.014 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 7) link_NAG-ASN : angle 3.18872 ( 21) link_BETA1-4 : bond 0.02676 ( 1) link_BETA1-4 : angle 1.90184 ( 3) hydrogen bonds : bond 0.17039 ( 591) hydrogen bonds : angle 6.01632 ( 1704) link_BETA1-6 : bond 0.00660 ( 1) link_BETA1-6 : angle 0.87168 ( 3) SS BOND : bond 0.00460 ( 5) SS BOND : angle 1.47570 ( 10) link_BETA1-3 : bond 0.00292 ( 1) link_BETA1-3 : angle 1.22827 ( 3) covalent geometry : bond 0.00492 (10994) covalent geometry : angle 0.68339 (15001) Misc. bond : bond 0.00444 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8876 (tpp) cc_final: 0.8495 (mmt) REVERT: A 237 GLN cc_start: 0.9025 (tp40) cc_final: 0.8155 (tm-30) REVERT: B 112 GLN cc_start: 0.8641 (mt0) cc_final: 0.8433 (pt0) REVERT: B 159 TYR cc_start: 0.4058 (t80) cc_final: 0.3738 (t80) REVERT: C 96 LYS cc_start: 0.7423 (mttt) cc_final: 0.7003 (tppt) REVERT: C 115 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7160 (ttt180) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 1.6972 time to fit residues: 202.8082 Evaluate side-chains 90 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 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 222 HIS A 387 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056455 restraints weight = 28082.008| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.51 r_work: 0.2762 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11011 Z= 0.168 Angle : 0.623 10.261 15041 Z= 0.318 Chirality : 0.044 0.422 1766 Planarity : 0.004 0.057 1824 Dihedral : 11.689 98.934 1915 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.16 % Allowed : 13.73 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1299 helix: 2.00 (0.20), residues: 692 sheet: -0.81 (0.47), residues: 124 loop : -1.56 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.031 0.001 PHE A 302 TYR 0.015 0.001 TYR B 466 ARG 0.008 0.001 ARG C 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 7) link_NAG-ASN : angle 3.19146 ( 21) link_BETA1-4 : bond 0.00040 ( 1) link_BETA1-4 : angle 1.48936 ( 3) hydrogen bonds : bond 0.04964 ( 591) hydrogen bonds : angle 4.32835 ( 1704) link_BETA1-6 : bond 0.01341 ( 1) link_BETA1-6 : angle 2.17272 ( 3) SS BOND : bond 0.00463 ( 5) SS BOND : angle 1.04626 ( 10) link_BETA1-3 : bond 0.01072 ( 1) link_BETA1-3 : angle 1.82759 ( 3) covalent geometry : bond 0.00390 (10994) covalent geometry : angle 0.60996 (15001) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.9082 (tp40) cc_final: 0.7926 (tm-30) REVERT: A 626 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8779 (mtt-85) REVERT: B 112 GLN cc_start: 0.8634 (mt0) cc_final: 0.8424 (pt0) REVERT: B 159 TYR cc_start: 0.3844 (t80) cc_final: 0.3550 (t80) REVERT: C 96 LYS cc_start: 0.7463 (mttt) cc_final: 0.6935 (tppt) REVERT: C 192 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8829 (tt) REVERT: C 218 TYR cc_start: 0.9324 (m-80) cc_final: 0.9104 (m-80) outliers start: 47 outliers final: 20 residues processed: 125 average time/residue: 0.9877 time to fit residues: 136.2136 Evaluate side-chains 98 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 358 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.055178 restraints weight = 28477.821| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.52 r_work: 0.2728 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11011 Z= 0.205 Angle : 0.643 11.397 15041 Z= 0.326 Chirality : 0.045 0.437 1766 Planarity : 0.004 0.054 1824 Dihedral : 10.482 92.517 1908 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.52 % Allowed : 14.61 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1299 helix: 1.99 (0.20), residues: 698 sheet: -0.83 (0.46), residues: 123 loop : -1.44 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.008 0.001 HIS A 449 PHE 0.027 0.002 PHE A 302 TYR 0.019 0.001 TYR B 466 ARG 0.009 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 7) link_NAG-ASN : angle 3.57442 ( 21) link_BETA1-4 : bond 0.00724 ( 1) link_BETA1-4 : angle 1.98019 ( 3) hydrogen bonds : bond 0.04995 ( 591) hydrogen bonds : angle 4.17866 ( 1704) link_BETA1-6 : bond 0.01253 ( 1) link_BETA1-6 : angle 2.72255 ( 3) SS BOND : bond 0.00600 ( 5) SS BOND : angle 0.99022 ( 10) link_BETA1-3 : bond 0.00886 ( 1) link_BETA1-3 : angle 1.73652 ( 3) covalent geometry : bond 0.00491 (10994) covalent geometry : angle 0.62693 (15001) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 79 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8643 (pm20) cc_final: 0.8412 (pm20) REVERT: A 237 GLN cc_start: 0.8983 (tp40) cc_final: 0.7890 (tm-30) REVERT: A 626 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9027 (mtt-85) REVERT: B 159 TYR cc_start: 0.3888 (t80) cc_final: 0.3604 (t80) REVERT: C 96 LYS cc_start: 0.7488 (mttt) cc_final: 0.6923 (tppt) REVERT: C 192 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8871 (tt) outliers start: 51 outliers final: 17 residues processed: 121 average time/residue: 1.1755 time to fit residues: 156.3531 Evaluate side-chains 94 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 222 HIS A 387 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.055241 restraints weight = 28009.284| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.51 r_work: 0.2730 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11011 Z= 0.191 Angle : 0.631 11.029 15041 Z= 0.320 Chirality : 0.045 0.427 1766 Planarity : 0.004 0.056 1824 Dihedral : 9.763 86.600 1908 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.99 % Allowed : 15.68 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1299 helix: 2.13 (0.20), residues: 691 sheet: -0.90 (0.46), residues: 123 loop : -1.34 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.006 0.001 HIS A 553 PHE 0.027 0.001 PHE A 302 TYR 0.018 0.001 TYR B 466 ARG 0.007 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 7) link_NAG-ASN : angle 3.54348 ( 21) link_BETA1-4 : bond 0.00388 ( 1) link_BETA1-4 : angle 1.91145 ( 3) hydrogen bonds : bond 0.04723 ( 591) hydrogen bonds : angle 4.10576 ( 1704) link_BETA1-6 : bond 0.01180 ( 1) link_BETA1-6 : angle 2.98952 ( 3) SS BOND : bond 0.00805 ( 5) SS BOND : angle 1.27366 ( 10) link_BETA1-3 : bond 0.00921 ( 1) link_BETA1-3 : angle 2.06562 ( 3) covalent geometry : bond 0.00455 (10994) covalent geometry : angle 0.61397 (15001) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8659 (pm20) cc_final: 0.8430 (pm20) REVERT: A 237 GLN cc_start: 0.8942 (tp40) cc_final: 0.7753 (tm-30) REVERT: B 159 TYR cc_start: 0.3913 (t80) cc_final: 0.3523 (t80) REVERT: B 278 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.3134 (mpt180) REVERT: C 96 LYS cc_start: 0.7189 (mttt) cc_final: 0.6665 (tppt) REVERT: C 192 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 236 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9219 (tt) outliers start: 45 outliers final: 19 residues processed: 121 average time/residue: 0.9292 time to fit residues: 124.5965 Evaluate side-chains 99 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** B 204 ASN ** 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 = 0.3266 r_free = 0.3266 target = 0.073247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054021 restraints weight = 28211.052| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.51 r_work: 0.2699 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11011 Z= 0.256 Angle : 0.690 11.655 15041 Z= 0.348 Chirality : 0.048 0.453 1766 Planarity : 0.004 0.053 1824 Dihedral : 9.318 79.691 1904 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.78 % Allowed : 15.32 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1299 helix: 2.08 (0.20), residues: 691 sheet: -0.94 (0.46), residues: 123 loop : -1.39 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.009 0.001 HIS A 449 PHE 0.028 0.002 PHE A 302 TYR 0.023 0.002 TYR B 466 ARG 0.008 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 7) link_NAG-ASN : angle 3.90446 ( 21) link_BETA1-4 : bond 0.00726 ( 1) link_BETA1-4 : angle 2.27975 ( 3) hydrogen bonds : bond 0.05098 ( 591) hydrogen bonds : angle 4.18407 ( 1704) link_BETA1-6 : bond 0.00925 ( 1) link_BETA1-6 : angle 3.41309 ( 3) SS BOND : bond 0.00969 ( 5) SS BOND : angle 1.42078 ( 10) link_BETA1-3 : bond 0.00992 ( 1) link_BETA1-3 : angle 2.63881 ( 3) covalent geometry : bond 0.00611 (10994) covalent geometry : angle 0.67086 (15001) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 83 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8646 (pm20) cc_final: 0.8425 (pm20) REVERT: A 237 GLN cc_start: 0.8964 (tp40) cc_final: 0.7852 (tm-30) REVERT: A 454 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: B 159 TYR cc_start: 0.3942 (t80) cc_final: 0.3532 (t80) REVERT: C 96 LYS cc_start: 0.7234 (mttt) cc_final: 0.6705 (tppt) REVERT: C 236 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9214 (tt) outliers start: 54 outliers final: 24 residues processed: 127 average time/residue: 1.2398 time to fit residues: 175.2035 Evaluate side-chains 105 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** B 204 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.075933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056940 restraints weight = 28006.105| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.52 r_work: 0.2771 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11011 Z= 0.125 Angle : 0.590 10.679 15041 Z= 0.299 Chirality : 0.043 0.396 1766 Planarity : 0.004 0.055 1824 Dihedral : 8.442 69.106 1904 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.19 % Allowed : 17.45 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1299 helix: 2.27 (0.20), residues: 689 sheet: -0.82 (0.45), residues: 127 loop : -1.30 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.011 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 7) link_NAG-ASN : angle 3.23992 ( 21) link_BETA1-4 : bond 0.00302 ( 1) link_BETA1-4 : angle 1.19178 ( 3) hydrogen bonds : bond 0.04083 ( 591) hydrogen bonds : angle 4.00501 ( 1704) link_BETA1-6 : bond 0.00934 ( 1) link_BETA1-6 : angle 3.57898 ( 3) SS BOND : bond 0.00639 ( 5) SS BOND : angle 1.02348 ( 10) link_BETA1-3 : bond 0.01007 ( 1) link_BETA1-3 : angle 1.91412 ( 3) covalent geometry : bond 0.00281 (10994) covalent geometry : angle 0.57452 (15001) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8645 (pm20) cc_final: 0.8377 (pm20) REVERT: A 237 GLN cc_start: 0.8929 (tp40) cc_final: 0.7821 (tm-30) REVERT: A 500 GLU cc_start: 0.9161 (tp30) cc_final: 0.8893 (tp30) REVERT: B 112 GLN cc_start: 0.8641 (mt0) cc_final: 0.8228 (pt0) REVERT: B 130 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8429 (tm) REVERT: C 96 LYS cc_start: 0.7156 (mttt) cc_final: 0.6653 (tppt) REVERT: C 192 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8915 (tt) REVERT: C 236 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9210 (tt) outliers start: 36 outliers final: 15 residues processed: 116 average time/residue: 1.0803 time to fit residues: 137.1304 Evaluate side-chains 98 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 124 optimal weight: 0.0670 chunk 88 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 110 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057376 restraints weight = 28519.847| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.54 r_work: 0.2781 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11011 Z= 0.120 Angle : 0.588 10.636 15041 Z= 0.296 Chirality : 0.043 0.400 1766 Planarity : 0.004 0.056 1824 Dihedral : 7.861 69.549 1904 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.63 % Allowed : 17.80 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1299 helix: 2.33 (0.20), residues: 692 sheet: -0.81 (0.45), residues: 127 loop : -1.26 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 PHE 0.027 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.011 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 7) link_NAG-ASN : angle 3.17363 ( 21) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 1.21703 ( 3) hydrogen bonds : bond 0.03915 ( 591) hydrogen bonds : angle 3.94562 ( 1704) link_BETA1-6 : bond 0.00987 ( 1) link_BETA1-6 : angle 2.88968 ( 3) SS BOND : bond 0.00513 ( 5) SS BOND : angle 1.20447 ( 10) link_BETA1-3 : bond 0.00819 ( 1) link_BETA1-3 : angle 1.89145 ( 3) covalent geometry : bond 0.00272 (10994) covalent geometry : angle 0.57323 (15001) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 210 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6971 (t80) REVERT: A 237 GLN cc_start: 0.8920 (tp40) cc_final: 0.7801 (tm-30) REVERT: A 500 GLU cc_start: 0.9178 (tp30) cc_final: 0.8891 (tp30) REVERT: B 112 GLN cc_start: 0.8632 (mt0) cc_final: 0.8229 (pt0) REVERT: B 385 ASP cc_start: 0.8850 (m-30) cc_final: 0.8626 (m-30) REVERT: C 96 LYS cc_start: 0.7186 (mttt) cc_final: 0.6679 (tppt) REVERT: C 192 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8932 (tt) REVERT: C 236 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9218 (tt) outliers start: 41 outliers final: 15 residues processed: 118 average time/residue: 0.9650 time to fit residues: 126.4508 Evaluate side-chains 101 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057093 restraints weight = 28006.512| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.52 r_work: 0.2774 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11011 Z= 0.135 Angle : 0.608 10.700 15041 Z= 0.305 Chirality : 0.043 0.405 1766 Planarity : 0.004 0.059 1824 Dihedral : 7.646 71.331 1904 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.01 % Allowed : 18.87 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1299 helix: 2.31 (0.20), residues: 691 sheet: -0.89 (0.45), residues: 125 loop : -1.23 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.026 0.001 PHE A 302 TYR 0.014 0.001 TYR B 225 ARG 0.012 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 7) link_NAG-ASN : angle 3.22821 ( 21) link_BETA1-4 : bond 0.00078 ( 1) link_BETA1-4 : angle 1.30612 ( 3) hydrogen bonds : bond 0.03978 ( 591) hydrogen bonds : angle 3.96116 ( 1704) link_BETA1-6 : bond 0.00739 ( 1) link_BETA1-6 : angle 2.74989 ( 3) SS BOND : bond 0.00534 ( 5) SS BOND : angle 1.31220 ( 10) link_BETA1-3 : bond 0.00771 ( 1) link_BETA1-3 : angle 1.81455 ( 3) covalent geometry : bond 0.00315 (10994) covalent geometry : angle 0.59328 (15001) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 210 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 237 GLN cc_start: 0.8915 (tp40) cc_final: 0.7835 (tm-30) REVERT: A 454 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: A 500 GLU cc_start: 0.9188 (tp30) cc_final: 0.8893 (tp30) REVERT: B 112 GLN cc_start: 0.8623 (mt0) cc_final: 0.8218 (pt0) REVERT: B 385 ASP cc_start: 0.8859 (m-30) cc_final: 0.8629 (m-30) REVERT: C 96 LYS cc_start: 0.7172 (mttt) cc_final: 0.6656 (tppt) outliers start: 34 outliers final: 20 residues processed: 107 average time/residue: 0.9812 time to fit residues: 116.1544 Evaluate side-chains 102 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057432 restraints weight = 28279.797| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.55 r_work: 0.2781 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11011 Z= 0.127 Angle : 0.599 10.525 15041 Z= 0.301 Chirality : 0.043 0.399 1766 Planarity : 0.004 0.057 1824 Dihedral : 7.399 71.750 1904 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.48 % Allowed : 19.66 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1299 helix: 2.32 (0.20), residues: 691 sheet: -0.87 (0.45), residues: 125 loop : -1.21 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.026 0.001 PHE A 302 TYR 0.014 0.001 TYR B 225 ARG 0.013 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 7) link_NAG-ASN : angle 3.16030 ( 21) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.27008 ( 3) hydrogen bonds : bond 0.03876 ( 591) hydrogen bonds : angle 3.94441 ( 1704) link_BETA1-6 : bond 0.00574 ( 1) link_BETA1-6 : angle 2.30305 ( 3) SS BOND : bond 0.00540 ( 5) SS BOND : angle 1.26292 ( 10) link_BETA1-3 : bond 0.00724 ( 1) link_BETA1-3 : angle 1.57710 ( 3) covalent geometry : bond 0.00294 (10994) covalent geometry : angle 0.58564 (15001) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8912 (tp40) cc_final: 0.7825 (tm-30) REVERT: A 454 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: A 500 GLU cc_start: 0.9201 (tp30) cc_final: 0.8898 (tp30) REVERT: B 112 GLN cc_start: 0.8639 (mt0) cc_final: 0.8233 (pt0) REVERT: B 385 ASP cc_start: 0.8832 (m-30) cc_final: 0.8597 (m-30) REVERT: C 96 LYS cc_start: 0.7156 (mttt) cc_final: 0.6658 (tppt) outliers start: 28 outliers final: 17 residues processed: 102 average time/residue: 1.0190 time to fit residues: 114.7639 Evaluate side-chains 98 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 0.0030 chunk 74 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.056677 restraints weight = 28189.749| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.52 r_work: 0.2763 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11011 Z= 0.152 Angle : 0.623 10.673 15041 Z= 0.314 Chirality : 0.044 0.409 1766 Planarity : 0.004 0.058 1824 Dihedral : 7.407 71.389 1904 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.13 % Allowed : 20.02 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1299 helix: 2.34 (0.20), residues: 688 sheet: -0.87 (0.45), residues: 125 loop : -1.24 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.026 0.001 PHE A 302 TYR 0.014 0.001 TYR B 225 ARG 0.014 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 7) link_NAG-ASN : angle 3.29206 ( 21) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 1.59597 ( 3) hydrogen bonds : bond 0.04097 ( 591) hydrogen bonds : angle 4.04044 ( 1704) link_BETA1-6 : bond 0.00426 ( 1) link_BETA1-6 : angle 2.06114 ( 3) SS BOND : bond 0.00640 ( 5) SS BOND : angle 1.46444 ( 10) link_BETA1-3 : bond 0.00683 ( 1) link_BETA1-3 : angle 1.61751 ( 3) covalent geometry : bond 0.00360 (10994) covalent geometry : angle 0.60899 (15001) Misc. bond : bond 0.00005 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8925 (tp40) cc_final: 0.7896 (tm-30) REVERT: A 343 MET cc_start: 0.9461 (OUTLIER) cc_final: 0.9252 (tpt) REVERT: A 454 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: A 500 GLU cc_start: 0.9210 (tp30) cc_final: 0.8939 (tp30) REVERT: B 112 GLN cc_start: 0.8637 (mt0) cc_final: 0.8235 (pt0) REVERT: C 96 LYS cc_start: 0.7165 (mttt) cc_final: 0.6733 (tppt) outliers start: 24 outliers final: 17 residues processed: 99 average time/residue: 1.0419 time to fit residues: 114.0792 Evaluate side-chains 99 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057122 restraints weight = 28041.640| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.52 r_work: 0.2773 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11011 Z= 0.140 Angle : 0.619 10.554 15041 Z= 0.311 Chirality : 0.043 0.403 1766 Planarity : 0.004 0.058 1824 Dihedral : 7.276 71.623 1904 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.13 % Allowed : 20.11 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1299 helix: 2.35 (0.20), residues: 688 sheet: -0.82 (0.45), residues: 125 loop : -1.22 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 PHE 0.026 0.001 PHE A 302 TYR 0.015 0.001 TYR B 225 ARG 0.014 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 7) link_NAG-ASN : angle 3.22403 ( 21) link_BETA1-4 : bond 0.00058 ( 1) link_BETA1-4 : angle 1.49732 ( 3) hydrogen bonds : bond 0.04021 ( 591) hydrogen bonds : angle 4.07728 ( 1704) link_BETA1-6 : bond 0.00413 ( 1) link_BETA1-6 : angle 1.89960 ( 3) SS BOND : bond 0.00574 ( 5) SS BOND : angle 1.35760 ( 10) link_BETA1-3 : bond 0.00612 ( 1) link_BETA1-3 : angle 1.44023 ( 3) covalent geometry : bond 0.00327 (10994) covalent geometry : angle 0.60585 (15001) Misc. bond : bond 0.00008 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9191.01 seconds wall clock time: 161 minutes 17.26 seconds (9677.26 seconds total)