Starting phenix.real_space_refine on Sat Jul 20 16:46:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/07_2024/8k8e_36948.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/07_2024/8k8e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/07_2024/8k8e_36948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/07_2024/8k8e_36948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/07_2024/8k8e_36948.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8e_36948/07_2024/8k8e_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 Residue "A GLU 475": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.79, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 4.69 Conformation dependent library (CDL) restraints added in 2.0 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: 1.29 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: 3.08 Time building geometry restraints manager: 4.93 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: 99.68 - 106.55: 319 106.55 - 113.42: 6130 113.42 - 120.29: 4005 120.29 - 127.16: 4415 127.16 - 134.04: 132 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 2.440 nonbonded pdb=" O GLN B 464 " pdb=" ND2 ASN C 207 " model vdw 2.222 2.520 nonbonded pdb=" N GLU D 9 " pdb=" OE1 GLU D 9 " model vdw 2.243 2.520 nonbonded pdb=" O SER A 235 " pdb=" OG SER A 238 " model vdw 2.245 2.440 nonbonded pdb=" O ILE C 34 " pdb=" OH TYR C 90 " model vdw 2.257 2.440 ... (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 ========== 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: 1.780 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.280 Find NCS groups from input model: 0.100 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- 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 10994 Z= 0.298 Angle : 0.683 8.053 15001 Z= 0.348 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.195 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: 1.2802 time to fit residues: 153.2629 Evaluate side-chains 90 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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: 0.7980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** B 223 GLN D 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10994 Z= 0.197 Angle : 0.576 7.465 15001 Z= 0.297 Chirality : 0.042 0.392 1766 Planarity : 0.004 0.053 1824 Dihedral : 11.545 98.285 1915 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.99 % Allowed : 13.64 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1299 helix: 2.05 (0.20), residues: 694 sheet: -0.85 (0.47), residues: 124 loop : -1.53 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.014 0.001 TYR D 91 ARG 0.007 0.001 ARG B 108 *********************** 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 fitting. rotamer outliers: 45 poor density : 92 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8901 (tp) REVERT: A 237 GLN cc_start: 0.8979 (tp40) cc_final: 0.7831 (tm-30) REVERT: A 626 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8777 (mtt-85) REVERT: B 112 GLN cc_start: 0.8635 (mt0) cc_final: 0.8431 (pt0) REVERT: B 159 TYR cc_start: 0.3862 (t80) cc_final: 0.3560 (t80) REVERT: C 96 LYS cc_start: 0.7372 (mttt) cc_final: 0.6968 (tppt) REVERT: C 192 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8870 (tt) outliers start: 45 outliers final: 15 residues processed: 128 average time/residue: 0.9738 time to fit residues: 137.5709 Evaluate side-chains 94 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 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 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 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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** B 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10994 Z= 0.229 Angle : 0.576 7.903 15001 Z= 0.295 Chirality : 0.043 0.401 1766 Planarity : 0.004 0.054 1824 Dihedral : 10.179 91.550 1908 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.90 % Allowed : 15.32 % Favored : 80.78 % 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: 0.86 (0.25), residues: 1299 helix: 2.18 (0.20), residues: 693 sheet: -0.85 (0.45), residues: 130 loop : -1.51 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 449 PHE 0.027 0.001 PHE A 302 TYR 0.014 0.001 TYR B 466 ARG 0.007 0.001 ARG A 114 *********************** 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 125 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 81 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8877 (tp40) cc_final: 0.7845 (tm-30) REVERT: A 414 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7942 (mtm110) REVERT: B 93 MET cc_start: 0.9483 (mtm) cc_final: 0.9213 (mtm) REVERT: B 159 TYR cc_start: 0.3881 (t80) cc_final: 0.3588 (t80) REVERT: C 96 LYS cc_start: 0.7376 (mttt) cc_final: 0.6946 (tppt) REVERT: C 192 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8855 (tt) outliers start: 44 outliers final: 19 residues processed: 116 average time/residue: 0.9299 time to fit residues: 120.1755 Evaluate side-chains 98 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 414 ARG Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 390 SER 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 214 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 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 ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10994 Z= 0.241 Angle : 0.576 7.952 15001 Z= 0.293 Chirality : 0.043 0.396 1766 Planarity : 0.004 0.053 1824 Dihedral : 9.570 85.488 1904 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.45 % Allowed : 16.03 % Favored : 80.51 % 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: 0.96 (0.25), residues: 1299 helix: 2.25 (0.20), residues: 694 sheet: -0.88 (0.46), residues: 124 loop : -1.44 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.006 0.001 HIS A 449 PHE 0.027 0.001 PHE A 302 TYR 0.014 0.001 TYR B 466 ARG 0.006 0.000 ARG B 108 *********************** 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 124 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8895 (tp40) cc_final: 0.7856 (tm-30) REVERT: A 414 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7970 (mtm110) REVERT: B 93 MET cc_start: 0.9478 (mtm) cc_final: 0.9230 (mtm) REVERT: B 159 TYR cc_start: 0.3818 (t80) cc_final: 0.3468 (t80) REVERT: B 278 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.3548 (mpt180) REVERT: C 96 LYS cc_start: 0.7374 (mttt) cc_final: 0.6934 (tppt) REVERT: C 192 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8914 (tt) REVERT: C 236 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9211 (tt) outliers start: 39 outliers final: 17 residues processed: 116 average time/residue: 0.9749 time to fit residues: 124.6235 Evaluate side-chains 99 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 414 ARG Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 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 104 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 222 HIS A 358 ASN A 387 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10994 Z= 0.381 Angle : 0.645 9.127 15001 Z= 0.331 Chirality : 0.047 0.436 1766 Planarity : 0.004 0.053 1824 Dihedral : 9.231 78.582 1904 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.52 % Allowed : 15.41 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.24), residues: 1299 helix: 2.13 (0.20), residues: 696 sheet: -0.91 (0.46), residues: 123 loop : -1.41 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.007 0.001 HIS A 449 PHE 0.027 0.002 PHE A 302 TYR 0.024 0.002 TYR B 466 ARG 0.005 0.001 ARG B 108 *********************** 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 136 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 85 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8864 (tp40) cc_final: 0.7817 (tm-30) REVERT: B 93 MET cc_start: 0.9479 (mtm) cc_final: 0.9216 (mtm) REVERT: B 159 TYR cc_start: 0.3895 (t80) cc_final: 0.3515 (t80) REVERT: B 278 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.3362 (mpt180) REVERT: C 96 LYS cc_start: 0.7146 (mttt) cc_final: 0.6765 (tppt) REVERT: D 11 LYS cc_start: 0.8422 (mttp) cc_final: 0.8176 (mttp) outliers start: 51 outliers final: 20 residues processed: 127 average time/residue: 0.9873 time to fit residues: 138.1150 Evaluate side-chains 99 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 390 SER 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 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 42 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10994 Z= 0.176 Angle : 0.564 7.371 15001 Z= 0.288 Chirality : 0.042 0.387 1766 Planarity : 0.004 0.051 1824 Dihedral : 8.611 69.445 1904 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.01 % Allowed : 17.27 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1299 helix: 2.28 (0.20), residues: 695 sheet: -1.02 (0.47), residues: 121 loop : -1.32 (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 0.027 0.001 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.009 0.000 ARG B 108 *********************** 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 115 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8813 (tp40) cc_final: 0.7704 (tm130) REVERT: B 93 MET cc_start: 0.9456 (mtm) cc_final: 0.9218 (mtm) REVERT: C 96 LYS cc_start: 0.7072 (mttt) cc_final: 0.6700 (tppt) REVERT: C 192 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8944 (tt) outliers start: 34 outliers final: 18 residues processed: 107 average time/residue: 0.9966 time to fit residues: 117.6036 Evaluate side-chains 99 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10994 Z= 0.360 Angle : 0.639 9.004 15001 Z= 0.327 Chirality : 0.046 0.426 1766 Planarity : 0.004 0.054 1824 Dihedral : 8.508 67.783 1904 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.99 % Allowed : 17.09 % Favored : 78.92 % 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: 2.23 (0.20), residues: 692 sheet: -1.06 (0.46), residues: 121 loop : -1.28 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.006 0.001 HIS A 449 PHE 0.026 0.002 PHE A 302 TYR 0.021 0.002 TYR B 466 ARG 0.010 0.001 ARG B 108 *********************** 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 126 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 81 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8841 (tp40) cc_final: 0.7720 (tm130) REVERT: B 93 MET cc_start: 0.9468 (mtm) cc_final: 0.9230 (mtm) REVERT: B 278 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5531 (mpt180) REVERT: C 96 LYS cc_start: 0.7120 (mttt) cc_final: 0.6710 (tppt) REVERT: D 11 LYS cc_start: 0.8410 (mttp) cc_final: 0.8166 (mttp) outliers start: 45 outliers final: 24 residues processed: 115 average time/residue: 0.9965 time to fit residues: 126.5506 Evaluate side-chains 103 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain A residue 247 VAL 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 A residue 663 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 390 SER 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 243 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0270 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS B 112 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10994 Z= 0.164 Angle : 0.560 8.250 15001 Z= 0.287 Chirality : 0.042 0.370 1766 Planarity : 0.004 0.051 1824 Dihedral : 7.775 64.122 1904 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.39 % Allowed : 18.87 % 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: 1.13 (0.25), residues: 1299 helix: 2.41 (0.20), residues: 690 sheet: -0.91 (0.45), residues: 125 loop : -1.32 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.011 0.001 TYR B 225 ARG 0.010 0.000 ARG B 108 *********************** 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 117 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8792 (tp40) cc_final: 0.7757 (tm-30) REVERT: B 93 MET cc_start: 0.9435 (mtm) cc_final: 0.9190 (mtm) REVERT: B 277 GLU cc_start: 0.6716 (pt0) cc_final: 0.6444 (pt0) REVERT: C 96 LYS cc_start: 0.7121 (mttt) cc_final: 0.6737 (tppt) REVERT: C 106 GLU cc_start: 0.5515 (tm-30) cc_final: 0.5297 (pp20) REVERT: C 183 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8449 (mm-30) REVERT: C 192 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8949 (tt) outliers start: 27 outliers final: 13 residues processed: 111 average time/residue: 0.9969 time to fit residues: 122.0003 Evaluate side-chains 96 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain 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 390 SER 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 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 109 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 0.0570 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10994 Z= 0.347 Angle : 0.639 8.857 15001 Z= 0.326 Chirality : 0.045 0.415 1766 Planarity : 0.004 0.056 1824 Dihedral : 7.895 62.619 1904 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.13 % Allowed : 19.49 % Favored : 78.39 % 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: 2.29 (0.20), residues: 692 sheet: -1.03 (0.46), residues: 121 loop : -1.27 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.006 0.001 HIS A 449 PHE 0.026 0.001 PHE A 302 TYR 0.018 0.002 TYR B 466 ARG 0.012 0.001 ARG B 108 *********************** 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 105 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8827 (tp40) cc_final: 0.7789 (tm-30) REVERT: B 93 MET cc_start: 0.9461 (mtm) cc_final: 0.9235 (mtm) REVERT: B 157 ARG cc_start: 0.5210 (mmm160) cc_final: 0.4993 (mmm160) REVERT: C 96 LYS cc_start: 0.7075 (mttt) cc_final: 0.6661 (tppt) REVERT: C 183 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8495 (mm-30) REVERT: D 11 LYS cc_start: 0.8471 (mttp) cc_final: 0.8165 (mttp) outliers start: 24 outliers final: 18 residues processed: 99 average time/residue: 1.0458 time to fit residues: 113.7012 Evaluate side-chains 98 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 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 390 SER 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 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 75 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10994 Z= 0.191 Angle : 0.584 8.952 15001 Z= 0.296 Chirality : 0.042 0.384 1766 Planarity : 0.004 0.049 1824 Dihedral : 7.487 61.076 1904 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.77 % Allowed : 19.93 % Favored : 78.30 % 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: 1.14 (0.25), residues: 1299 helix: 2.39 (0.20), residues: 692 sheet: -0.86 (0.46), residues: 125 loop : -1.31 (0.30), residues: 482 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 0.012 0.001 TYR B 225 ARG 0.014 0.001 ARG B 108 ********************** 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 99 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8794 (tp40) cc_final: 0.7781 (tm-30) REVERT: B 93 MET cc_start: 0.9441 (mtm) cc_final: 0.9208 (mtm) REVERT: B 157 ARG cc_start: 0.5085 (mmm160) cc_final: 0.4861 (mmm160) REVERT: C 96 LYS cc_start: 0.7108 (mttt) cc_final: 0.6736 (tppt) REVERT: C 183 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8438 (mm-30) REVERT: C 192 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8957 (tt) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 1.0600 time to fit residues: 109.4972 Evaluate side-chains 94 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 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 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 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 31 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** 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 = 0.3315 r_free = 0.3315 target = 0.075892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056859 restraints weight = 27780.046| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.52 r_work: 0.2764 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10994 Z= 0.224 Angle : 0.601 8.938 15001 Z= 0.306 Chirality : 0.043 0.383 1766 Planarity : 0.004 0.054 1824 Dihedral : 7.343 60.722 1904 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.68 % Allowed : 20.19 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1299 helix: 2.39 (0.20), residues: 691 sheet: -0.93 (0.45), residues: 127 loop : -1.30 (0.30), residues: 481 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 0.013 0.001 TYR B 225 ARG 0.013 0.001 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.52 seconds wall clock time: 59 minutes 32.00 seconds (3572.00 seconds total)