Starting phenix.real_space_refine on Wed May 14 06:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8e_36948/05_2025/8k8e_36948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8e_36948/05_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_36948/05_2025/8k8e_36948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8e_36948/05_2025/8k8e_36948.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8e_36948/05_2025/8k8e_36948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8e_36948/05_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-5687/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: 6.83, per 1000 atoms: 0.64 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: 3.36 Conformation dependent library (CDL) restraints added in 1.4 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: 1.01 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: 3.02 Time building geometry restraints manager: 3.66 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.740 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- 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 : 1.106 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: 1.2848 time to fit residues: 153.8636 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 : 1.251 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056461 restraints weight = 28082.840| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.51 r_work: 0.2762 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 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 98.933 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 3.19145 ( 21) link_BETA1-4 : bond 0.00040 ( 1) link_BETA1-4 : angle 1.48945 ( 3) hydrogen bonds : bond 0.04964 ( 591) hydrogen bonds : angle 4.32834 ( 1704) link_BETA1-6 : bond 0.01341 ( 1) link_BETA1-6 : angle 2.17269 ( 3) SS BOND : bond 0.00463 ( 5) SS BOND : angle 1.04633 ( 10) link_BETA1-3 : bond 0.01072 ( 1) link_BETA1-3 : angle 1.82740 ( 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 : 1.209 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.9087 (tp40) cc_final: 0.7935 (tm-30) REVERT: A 626 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.8778 (mtt-85) REVERT: B 112 GLN cc_start: 0.8636 (mt0) cc_final: 0.8427 (pt0) REVERT: B 159 TYR cc_start: 0.3848 (t80) cc_final: 0.3553 (t80) REVERT: C 96 LYS cc_start: 0.7460 (mttt) cc_final: 0.6938 (tppt) REVERT: C 192 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8830 (tt) REVERT: C 218 TYR cc_start: 0.9326 (m-80) cc_final: 0.9105 (m-80) outliers start: 47 outliers final: 20 residues processed: 125 average time/residue: 0.9560 time to fit residues: 131.8868 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 : 1.088 ------------------------------------------------------------------------------- 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: 0.7980 chunk 83 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** 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 = 0.3295 r_free = 0.3295 target = 0.074728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.055619 restraints weight = 28451.201| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.52 r_work: 0.2740 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11011 Z= 0.186 Angle : 0.627 11.251 15041 Z= 0.318 Chirality : 0.045 0.432 1766 Planarity : 0.004 0.054 1824 Dihedral : 10.447 92.431 1908 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.43 % Allowed : 14.70 % 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: 0.78 (0.24), residues: 1299 helix: 2.03 (0.20), residues: 698 sheet: -0.82 (0.46), residues: 123 loop : -1.45 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.007 0.001 HIS A 449 PHE 0.027 0.001 PHE A 302 TYR 0.018 0.001 TYR B 466 ARG 0.008 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 7) link_NAG-ASN : angle 3.47198 ( 21) link_BETA1-4 : bond 0.00411 ( 1) link_BETA1-4 : angle 1.91803 ( 3) hydrogen bonds : bond 0.04859 ( 591) hydrogen bonds : angle 4.15753 ( 1704) link_BETA1-6 : bond 0.01175 ( 1) link_BETA1-6 : angle 2.66849 ( 3) SS BOND : bond 0.00638 ( 5) SS BOND : angle 0.96886 ( 10) link_BETA1-3 : bond 0.00989 ( 1) link_BETA1-3 : angle 1.68342 ( 3) covalent geometry : bond 0.00442 (10994) covalent geometry : angle 0.61185 (15001) Misc. bond : bond 0.00013 ( 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: 50 poor density : 80 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8641 (pm20) cc_final: 0.8332 (pm20) REVERT: A 237 GLN cc_start: 0.8975 (tp40) cc_final: 0.7925 (tm-30) REVERT: A 626 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8990 (mtt-85) REVERT: B 159 TYR cc_start: 0.3872 (t80) cc_final: 0.3594 (t80) REVERT: C 96 LYS cc_start: 0.7466 (mttt) cc_final: 0.6909 (tppt) REVERT: C 218 TYR cc_start: 0.9367 (m-80) cc_final: 0.9153 (m-80) outliers start: 50 outliers final: 19 residues processed: 122 average time/residue: 1.0019 time to fit residues: 134.8968 Evaluate side-chains 97 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 214 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 358 ASN 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 = 0.3307 r_free = 0.3307 target = 0.075245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056197 restraints weight = 27935.954| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.52 r_work: 0.2754 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11011 Z= 0.155 Angle : 0.606 10.834 15041 Z= 0.307 Chirality : 0.044 0.417 1766 Planarity : 0.004 0.057 1824 Dihedral : 9.829 86.801 1908 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.81 % Allowed : 15.85 % 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: 2.16 (0.20), residues: 693 sheet: -0.92 (0.46), residues: 123 loop : -1.40 (0.29), 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 0.027 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.008 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 7) link_NAG-ASN : angle 3.35700 ( 21) link_BETA1-4 : bond 0.00143 ( 1) link_BETA1-4 : angle 1.65622 ( 3) hydrogen bonds : bond 0.04463 ( 591) hydrogen bonds : angle 4.07128 ( 1704) link_BETA1-6 : bond 0.01171 ( 1) link_BETA1-6 : angle 2.97853 ( 3) SS BOND : bond 0.00504 ( 5) SS BOND : angle 1.06818 ( 10) link_BETA1-3 : bond 0.00898 ( 1) link_BETA1-3 : angle 1.88747 ( 3) covalent geometry : bond 0.00365 (10994) covalent geometry : angle 0.59060 (15001) Misc. bond : bond 0.00015 ( 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: 43 poor density : 87 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8653 (pm20) cc_final: 0.8240 (pm20) REVERT: A 237 GLN cc_start: 0.8939 (tp40) cc_final: 0.7882 (tm-30) REVERT: A 626 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.9036 (mtt90) REVERT: B 159 TYR cc_start: 0.3876 (t80) cc_final: 0.3498 (t80) REVERT: B 278 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.3199 (mpt180) REVERT: C 96 LYS cc_start: 0.7459 (mttt) cc_final: 0.6888 (tppt) outliers start: 43 outliers final: 18 residues processed: 122 average time/residue: 0.9801 time to fit residues: 131.9666 Evaluate side-chains 96 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 129 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3253 r_free = 0.3253 target = 0.072629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053418 restraints weight = 28297.659| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.50 r_work: 0.2682 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 11011 Z= 0.311 Angle : 0.732 11.930 15041 Z= 0.369 Chirality : 0.050 0.470 1766 Planarity : 0.005 0.053 1824 Dihedral : 9.571 81.556 1908 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.05 % Allowed : 15.15 % Favored : 79.81 % 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: 0.72 (0.24), residues: 1299 helix: 1.96 (0.20), residues: 693 sheet: -0.87 (0.45), residues: 123 loop : -1.40 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.010 0.001 HIS A 449 PHE 0.028 0.002 PHE A 210 TYR 0.028 0.002 TYR B 466 ARG 0.009 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 7) link_NAG-ASN : angle 4.10001 ( 21) link_BETA1-4 : bond 0.01095 ( 1) link_BETA1-4 : angle 2.41624 ( 3) hydrogen bonds : bond 0.05403 ( 591) hydrogen bonds : angle 4.26621 ( 1704) link_BETA1-6 : bond 0.01003 ( 1) link_BETA1-6 : angle 3.41593 ( 3) SS BOND : bond 0.01087 ( 5) SS BOND : angle 1.66828 ( 10) link_BETA1-3 : bond 0.00914 ( 1) link_BETA1-3 : angle 2.72883 ( 3) covalent geometry : bond 0.00738 (10994) covalent geometry : angle 0.71246 (15001) Misc. bond : bond 0.00025 ( 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 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 82 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8653 (pm20) cc_final: 0.8437 (pm20) REVERT: A 237 GLN cc_start: 0.8973 (tp40) cc_final: 0.7837 (tm-30) REVERT: A 454 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8708 (pt0) REVERT: B 159 TYR cc_start: 0.3983 (t80) cc_final: 0.3564 (t80) REVERT: B 278 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.3298 (mpt180) REVERT: D 11 LYS cc_start: 0.8479 (mttp) cc_final: 0.8261 (mttp) outliers start: 57 outliers final: 22 residues processed: 129 average time/residue: 0.8888 time to fit residues: 127.3194 Evaluate side-chains 101 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 609 LEU 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 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: 0.9980 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.075273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056196 restraints weight = 28041.072| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.51 r_work: 0.2753 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11011 Z= 0.139 Angle : 0.605 10.934 15041 Z= 0.306 Chirality : 0.043 0.406 1766 Planarity : 0.004 0.055 1824 Dihedral : 8.678 70.114 1904 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 17.18 % Favored : 79.54 % 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: 0.98 (0.25), residues: 1299 helix: 2.20 (0.20), residues: 689 sheet: -0.89 (0.46), residues: 123 loop : -1.28 (0.29), residues: 487 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 0.028 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 0.00594 ( 7) link_NAG-ASN : angle 3.36335 ( 21) link_BETA1-4 : bond 0.00110 ( 1) link_BETA1-4 : angle 1.40407 ( 3) hydrogen bonds : bond 0.04278 ( 591) hydrogen bonds : angle 4.05207 ( 1704) link_BETA1-6 : bond 0.00969 ( 1) link_BETA1-6 : angle 3.61028 ( 3) SS BOND : bond 0.00794 ( 5) SS BOND : angle 1.36392 ( 10) link_BETA1-3 : bond 0.00893 ( 1) link_BETA1-3 : angle 2.00603 ( 3) covalent geometry : bond 0.00322 (10994) covalent geometry : angle 0.58881 (15001) Misc. bond : bond 0.00012 ( 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 119 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8919 (tp40) cc_final: 0.7824 (tm-30) REVERT: B 112 GLN cc_start: 0.8639 (mt0) cc_final: 0.8204 (pt0) REVERT: C 96 LYS cc_start: 0.7116 (mttt) cc_final: 0.6586 (tppt) outliers start: 37 outliers final: 18 residues processed: 109 average time/residue: 1.1326 time to fit residues: 134.9795 Evaluate side-chains 96 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 118 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 124 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.074904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.055791 restraints weight = 28604.597| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.53 r_work: 0.2741 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1751 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= 0.157 Angle : 0.621 10.962 15041 Z= 0.314 Chirality : 0.044 0.416 1766 Planarity : 0.004 0.058 1824 Dihedral : 8.237 68.413 1904 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.81 % Allowed : 17.45 % Favored : 78.74 % 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: 1.02 (0.25), residues: 1299 helix: 2.22 (0.20), residues: 694 sheet: -0.92 (0.46), residues: 123 loop : -1.23 (0.29), residues: 482 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 0.027 0.001 PHE A 302 TYR 0.015 0.001 TYR B 466 ARG 0.011 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 7) link_NAG-ASN : angle 3.45310 ( 21) link_BETA1-4 : bond 0.00263 ( 1) link_BETA1-4 : angle 1.60484 ( 3) hydrogen bonds : bond 0.04338 ( 591) hydrogen bonds : angle 4.01372 ( 1704) link_BETA1-6 : bond 0.00843 ( 1) link_BETA1-6 : angle 3.44219 ( 3) SS BOND : bond 0.00643 ( 5) SS BOND : angle 1.38623 ( 10) link_BETA1-3 : bond 0.00804 ( 1) link_BETA1-3 : angle 2.05718 ( 3) covalent geometry : bond 0.00370 (10994) covalent geometry : angle 0.60410 (15001) Misc. bond : bond 0.00006 ( 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: 43 poor density : 86 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8926 (tp40) cc_final: 0.7780 (tm-30) REVERT: B 112 GLN cc_start: 0.8645 (mt0) cc_final: 0.8237 (pt0) REVERT: C 96 LYS cc_start: 0.7218 (mttt) cc_final: 0.6677 (tppt) outliers start: 43 outliers final: 20 residues processed: 118 average time/residue: 0.9843 time to fit residues: 129.0896 Evaluate side-chains 100 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 118 ILE 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 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 215 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: 4.9990 chunk 115 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.075433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.056371 restraints weight = 28016.002| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.51 r_work: 0.2755 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11011 Z= 0.145 Angle : 0.629 10.876 15041 Z= 0.315 Chirality : 0.044 0.411 1766 Planarity : 0.004 0.058 1824 Dihedral : 7.855 69.894 1904 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.83 % Allowed : 19.13 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1299 helix: 2.30 (0.20), residues: 689 sheet: -0.81 (0.45), residues: 127 loop : -1.34 (0.29), 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 0.027 0.001 PHE A 302 TYR 0.015 0.001 TYR B 225 ARG 0.012 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 7) link_NAG-ASN : angle 3.33956 ( 21) link_BETA1-4 : bond 0.00055 ( 1) link_BETA1-4 : angle 1.40735 ( 3) hydrogen bonds : bond 0.04171 ( 591) hydrogen bonds : angle 3.99569 ( 1704) link_BETA1-6 : bond 0.00891 ( 1) link_BETA1-6 : angle 2.77840 ( 3) SS BOND : bond 0.00591 ( 5) SS BOND : angle 1.25628 ( 10) link_BETA1-3 : bond 0.00746 ( 1) link_BETA1-3 : angle 1.91158 ( 3) covalent geometry : bond 0.00341 (10994) covalent geometry : angle 0.61398 (15001) Misc. bond : bond 0.00015 ( 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 114 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8927 (tp40) cc_final: 0.7848 (tm-30) REVERT: B 112 GLN cc_start: 0.8651 (mt0) cc_final: 0.8255 (pt0) REVERT: B 277 GLU cc_start: 0.6248 (pt0) cc_final: 0.6011 (pt0) REVERT: B 385 ASP cc_start: 0.8892 (m-30) cc_final: 0.8659 (m-30) REVERT: C 96 LYS cc_start: 0.7233 (mttt) cc_final: 0.6693 (tppt) REVERT: C 192 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8939 (tt) outliers start: 32 outliers final: 22 residues processed: 108 average time/residue: 0.9576 time to fit residues: 114.5777 Evaluate side-chains 102 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 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 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 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 215 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.074294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055172 restraints weight = 28389.601| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.51 r_work: 0.2724 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1868 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= 0.194 Angle : 0.663 11.155 15041 Z= 0.333 Chirality : 0.045 0.428 1766 Planarity : 0.004 0.059 1824 Dihedral : 7.800 69.950 1904 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.30 % Allowed : 20.11 % Favored : 77.59 % 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: 0.98 (0.24), residues: 1299 helix: 2.19 (0.20), residues: 693 sheet: -0.93 (0.46), residues: 123 loop : -1.26 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.006 0.001 HIS A 553 PHE 0.026 0.001 PHE A 302 TYR 0.016 0.001 TYR B 466 ARG 0.013 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 7) link_NAG-ASN : angle 3.60442 ( 21) link_BETA1-4 : bond 0.00559 ( 1) link_BETA1-4 : angle 1.91288 ( 3) hydrogen bonds : bond 0.04542 ( 591) hydrogen bonds : angle 4.06775 ( 1704) link_BETA1-6 : bond 0.00574 ( 1) link_BETA1-6 : angle 2.67246 ( 3) SS BOND : bond 0.00732 ( 5) SS BOND : angle 1.70186 ( 10) link_BETA1-3 : bond 0.00656 ( 1) link_BETA1-3 : angle 1.93726 ( 3) covalent geometry : bond 0.00462 (10994) covalent geometry : angle 0.64664 (15001) Misc. bond : bond 0.00011 ( 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 107 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8942 (tp40) cc_final: 0.7885 (tm-30) REVERT: A 454 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: B 112 GLN cc_start: 0.8639 (mt0) cc_final: 0.8248 (pt0) REVERT: C 96 LYS cc_start: 0.7275 (mttt) cc_final: 0.6687 (tppt) outliers start: 26 outliers final: 22 residues processed: 100 average time/residue: 1.0099 time to fit residues: 111.1516 Evaluate side-chains 102 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 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 174 LEU 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 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 215 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.075622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056606 restraints weight = 28145.755| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.53 r_work: 0.2760 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1910 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= 0.139 Angle : 0.622 10.783 15041 Z= 0.313 Chirality : 0.043 0.408 1766 Planarity : 0.004 0.057 1824 Dihedral : 7.540 71.029 1904 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.21 % Allowed : 20.37 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1299 helix: 2.33 (0.20), residues: 688 sheet: -0.79 (0.45), residues: 127 loop : -1.32 (0.29), residues: 484 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 0.027 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 0.00618 ( 7) link_NAG-ASN : angle 3.30938 ( 21) link_BETA1-4 : bond 0.00013 ( 1) link_BETA1-4 : angle 1.45173 ( 3) hydrogen bonds : bond 0.04103 ( 591) hydrogen bonds : angle 4.01691 ( 1704) link_BETA1-6 : bond 0.00518 ( 1) link_BETA1-6 : angle 2.21415 ( 3) SS BOND : bond 0.00542 ( 5) SS BOND : angle 1.35702 ( 10) link_BETA1-3 : bond 0.00660 ( 1) link_BETA1-3 : angle 1.50516 ( 3) covalent geometry : bond 0.00327 (10994) covalent geometry : angle 0.60801 (15001) Misc. bond : bond 0.00006 ( 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 104 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8897 (tp40) cc_final: 0.7883 (tm-30) REVERT: B 112 GLN cc_start: 0.8629 (mt0) cc_final: 0.8231 (pt0) REVERT: C 96 LYS cc_start: 0.7222 (mttt) cc_final: 0.6672 (tppt) outliers start: 25 outliers final: 19 residues processed: 98 average time/residue: 1.0362 time to fit residues: 111.7547 Evaluate side-chains 96 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 111 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 = 0.075722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.056676 restraints weight = 28036.791| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.52 r_work: 0.2763 rms_B_bonded: 3.01 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: 0.8717 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11011 Z= 0.140 Angle : 0.620 10.636 15041 Z= 0.312 Chirality : 0.043 0.402 1766 Planarity : 0.004 0.059 1824 Dihedral : 7.375 71.805 1904 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.13 % Allowed : 20.46 % Favored : 77.41 % 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: 689 sheet: -0.77 (0.45), residues: 127 loop : -1.27 (0.29), 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 0.027 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 0.00619 ( 7) link_NAG-ASN : angle 3.27369 ( 21) link_BETA1-4 : bond 0.00080 ( 1) link_BETA1-4 : angle 1.52048 ( 3) hydrogen bonds : bond 0.04043 ( 591) hydrogen bonds : angle 4.00454 ( 1704) link_BETA1-6 : bond 0.00409 ( 1) link_BETA1-6 : angle 1.92697 ( 3) SS BOND : bond 0.00674 ( 5) SS BOND : angle 1.41638 ( 10) link_BETA1-3 : bond 0.00598 ( 1) link_BETA1-3 : angle 1.51137 ( 3) covalent geometry : bond 0.00328 (10994) covalent geometry : angle 0.60617 (15001) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7972.51 seconds wall clock time: 137 minutes 48.43 seconds (8268.43 seconds total)