Starting phenix.real_space_refine on Wed Mar 4 19:08:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jr7_22443/03_2026/7jr7_22443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jr7_22443/03_2026/7jr7_22443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jr7_22443/03_2026/7jr7_22443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jr7_22443/03_2026/7jr7_22443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jr7_22443/03_2026/7jr7_22443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jr7_22443/03_2026/7jr7_22443.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10115 2.51 5 N 2657 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15799 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4626 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 2 Chain: "B" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4609 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 24, 'TRANS': 554} Chain breaks: 3 Chain: "C" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1638 Classifications: {'peptide': 210} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1627 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1663 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202} Time building chain proxies: 3.75, per 1000 atoms: 0.24 Number of scatterers: 15799 At special positions: 0 Unit cell: (158.82, 158.82, 130.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2940 8.00 N 2657 7.00 C 10115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 204 " distance=2.05 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 757.1 milliseconds 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3772 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 25 sheets defined 40.0% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.604A pdb=" N GLN A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.565A pdb=" N GLN A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.623A pdb=" N GLY A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.807A pdb=" N GLN A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 331 removed outlier: 3.588A pdb=" N LYS A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.678A pdb=" N LYS A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 404 removed outlier: 5.443A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 455 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.768A pdb=" N MET A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.705A pdb=" N VAL A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 522 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 546 removed outlier: 3.515A pdb=" N VAL A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 4.014A pdb=" N MET A 555 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 566 through 581 removed outlier: 4.218A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.630A pdb=" N PHE A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 Processing helix chain 'A' and resid 619 through 628 Processing helix chain 'A' and resid 629 through 646 removed outlier: 3.573A pdb=" N ALA A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 228 removed outlier: 4.226A pdb=" N GLN B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 261 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 326 Processing helix chain 'B' and resid 331 through 353 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.583A pdb=" N PHE B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 360' Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 removed outlier: 3.514A pdb=" N LEU B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.814A pdb=" N VAL B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 488 through 499 removed outlier: 3.626A pdb=" N TYR B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 519 removed outlier: 4.048A pdb=" N ALA B 506 " --> pdb=" O PRO B 502 " (cutoff:3.500A) Proline residue: B 514 - end of helix Processing helix chain 'B' and resid 524 through 551 removed outlier: 3.586A pdb=" N PHE B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.719A pdb=" N VAL B 593 " --> pdb=" O TRP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 Processing helix chain 'B' and resid 625 through 633 Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.582A pdb=" N THR C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.795A pdb=" N ALA D 84 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.520A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 6.660A pdb=" N GLU A 112 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.123A pdb=" N TYR A 45 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.197A pdb=" N MET A 82 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 96 removed outlier: 3.647A pdb=" N ASN B 90 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU B 52 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 92 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B 50 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 94 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU B 48 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG B 96 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 46 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 52 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER B 129 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR B 54 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 127 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.479A pdb=" N LEU B 101 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 283 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 294 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 285 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.531A pdb=" N SER C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.644A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.973A pdb=" N CYS C 96 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP C 109 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG C 98 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 105 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.027A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER C 184 " --> pdb=" O PRO C 173 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 186 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N THR C 171 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.372A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N SER D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N SER D 68 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ALA D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.853A pdb=" N SER D 66 " --> pdb=" O ALA D 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.682A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'D' and resid 115 through 119 removed outlier: 4.840A pdb=" N SER D 132 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D 182 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL D 134 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA D 180 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE D 136 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER D 178 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN D 138 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET D 176 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.489A pdb=" N ILE E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 133 removed outlier: 4.346A pdb=" N GLY E 148 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR E 184 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER E 187 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER E 189 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 174 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR E 191 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 172 " --> pdb=" O THR E 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.417A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.928A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 118 removed outlier: 4.730A pdb=" N SER F 131 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU F 181 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL F 133 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU F 179 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE F 135 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER F 177 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN F 137 " --> pdb=" O MET F 175 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET F 175 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 153 through 154 830 hydrogen bonds defined for protein. 2271 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: 3.10 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4790 1.34 - 1.47: 4216 1.47 - 1.59: 7029 1.59 - 1.72: 0 1.72 - 1.84: 136 Bond restraints: 16171 Sorted by residual: bond pdb=" CG LEU E 37 " pdb=" CD1 LEU E 37 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.82e+00 bond pdb=" CG1 ILE B 403 " pdb=" CD1 ILE B 403 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.93e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.333 1.373 -0.039 1.44e-02 4.82e+03 7.48e+00 bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.44e-02 4.82e+03 6.63e+00 bond pdb=" CG LEU B 486 " pdb=" CD2 LEU B 486 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.12e+00 ... (remaining 16166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 21229 3.23 - 6.46: 630 6.46 - 9.69: 73 9.69 - 12.92: 17 12.92 - 16.16: 10 Bond angle restraints: 21959 Sorted by residual: angle pdb=" N GLY E 104 " pdb=" CA GLY E 104 " pdb=" C GLY E 104 " ideal model delta sigma weight residual 112.34 128.50 -16.16 2.04e+00 2.40e-01 6.27e+01 angle pdb=" C ARG F 211 " pdb=" N ALA F 212 " pdb=" CA ALA F 212 " ideal model delta sigma weight residual 121.70 135.22 -13.52 1.80e+00 3.09e-01 5.64e+01 angle pdb=" C ARG C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta sigma weight residual 122.74 133.50 -10.76 1.44e+00 4.82e-01 5.58e+01 angle pdb=" C THR B 287 " pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 120.81 132.74 -11.93 1.63e+00 3.76e-01 5.36e+01 angle pdb=" CA CYS F 134 " pdb=" CB CYS F 134 " pdb=" SG CYS F 134 " ideal model delta sigma weight residual 114.40 129.93 -15.53 2.30e+00 1.89e-01 4.56e+01 ... (remaining 21954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9075 17.64 - 35.28: 411 35.28 - 52.92: 104 52.92 - 70.55: 28 70.55 - 88.19: 12 Dihedral angle restraints: 9630 sinusoidal: 3763 harmonic: 5867 Sorted by residual: dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 170.39 -77.39 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS F 134 " pdb=" SG CYS F 134 " pdb=" SG CYS F 194 " pdb=" CB CYS F 194 " ideal model delta sinusoidal sigma weight residual 93.00 159.01 -66.01 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" C ILE B 459 " pdb=" N ILE B 459 " pdb=" CA ILE B 459 " pdb=" CB ILE B 459 " ideal model delta harmonic sigma weight residual -122.00 -133.10 11.10 0 2.50e+00 1.60e-01 1.97e+01 ... (remaining 9627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2208 0.112 - 0.225: 264 0.225 - 0.337: 30 0.337 - 0.450: 0 0.450 - 0.562: 1 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CG LEU D 34 " pdb=" CB LEU D 34 " pdb=" CD1 LEU D 34 " pdb=" CD2 LEU D 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CB ILE A 81 " pdb=" CA ILE A 81 " pdb=" CG1 ILE A 81 " pdb=" CG2 ILE A 81 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE B 235 " pdb=" CA ILE B 235 " pdb=" CG1 ILE B 235 " pdb=" CG2 ILE B 235 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2500 not shown) Planarity restraints: 2763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 189 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL C 189 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL C 189 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO C 190 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 617 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C THR A 617 " -0.058 2.00e-02 2.50e+03 pdb=" O THR A 617 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 618 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 49 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C SER F 49 " 0.057 2.00e-02 2.50e+03 pdb=" O SER F 49 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA F 50 " -0.020 2.00e-02 2.50e+03 ... (remaining 2760 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3170 2.78 - 3.31: 14434 3.31 - 3.84: 26231 3.84 - 4.37: 29867 4.37 - 4.90: 53606 Nonbonded interactions: 127308 Sorted by model distance: nonbonded pdb=" OG SER D 122 " pdb=" OE1 GLU D 124 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 287 " pdb=" O THR B 325 " model vdw 2.258 3.040 nonbonded pdb=" NZ LYS B 605 " pdb=" O TYR B 638 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG B 164 " pdb=" OE2 GLU B 189 " model vdw 2.267 3.120 nonbonded pdb=" O GLY C 163 " pdb=" OG SER C 166 " model vdw 2.268 3.040 ... (remaining 127303 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: 4.900 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.480 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.010 0.110 16180 Z= 0.403 Angle : 1.343 16.156 21977 Z= 0.750 Chirality : 0.076 0.562 2503 Planarity : 0.008 0.041 2763 Dihedral : 11.829 88.193 5831 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.56 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 4.99 % Favored : 94.44 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 1994 helix: 0.78 (0.18), residues: 727 sheet: 0.76 (0.23), residues: 475 loop : -0.00 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 62 TYR 0.049 0.005 TYR B 472 PHE 0.054 0.005 PHE C 83 TRP 0.036 0.004 TRP B 229 HIS 0.012 0.003 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00959 (16171) covalent geometry : angle 1.33822 (21959) SS BOND : bond 0.00846 ( 9) SS BOND : angle 4.11564 ( 18) hydrogen bonds : bond 0.14134 ( 808) hydrogen bonds : angle 6.40262 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 327 time to evaluate : 0.622 Fit side-chains REVERT: A 413 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7282 (tppt) REVERT: A 480 MET cc_start: 0.7756 (mmm) cc_final: 0.7366 (mmt) REVERT: B 89 GLN cc_start: 0.6824 (mt0) cc_final: 0.6533 (mt0) REVERT: B 413 ASP cc_start: 0.7893 (t0) cc_final: 0.7625 (t70) REVERT: E 183 LEU cc_start: 0.8402 (mp) cc_final: 0.8014 (mm) REVERT: F 15 LEU cc_start: 0.8097 (tt) cc_final: 0.7531 (mp) outliers start: 10 outliers final: 5 residues processed: 336 average time/residue: 0.1511 time to fit residues: 72.7646 Evaluate side-chains 201 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 196 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain F residue 181 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 551 ASN A 578 ASN B 55 GLN B 89 GLN B 343 GLN C 78 GLN D 54 ASN E 43 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 166 GLN F 210 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125822 restraints weight = 21224.789| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.17 r_work: 0.3337 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16180 Z= 0.148 Angle : 0.666 10.060 21977 Z= 0.356 Chirality : 0.045 0.220 2503 Planarity : 0.005 0.092 2763 Dihedral : 4.883 33.757 2198 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.26 % Favored : 97.59 % Rotamer: Outliers : 2.27 % Allowed : 9.02 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 1994 helix: 1.56 (0.19), residues: 730 sheet: 0.83 (0.23), residues: 498 loop : -0.07 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 118 TYR 0.031 0.002 TYR B 472 PHE 0.025 0.002 PHE A 608 TRP 0.015 0.001 TRP B 229 HIS 0.005 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00322 (16171) covalent geometry : angle 0.66534 (21959) SS BOND : bond 0.00528 ( 9) SS BOND : angle 1.18293 ( 18) hydrogen bonds : bond 0.04777 ( 808) hydrogen bonds : angle 5.11363 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 227 THR cc_start: 0.8602 (m) cc_final: 0.8353 (m) REVERT: A 322 VAL cc_start: 0.8727 (t) cc_final: 0.8500 (m) REVERT: A 452 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 480 MET cc_start: 0.8244 (mmm) cc_final: 0.7460 (mmt) REVERT: B 89 GLN cc_start: 0.7452 (mt0) cc_final: 0.7156 (mt0) REVERT: B 615 MET cc_start: 0.5926 (tmm) cc_final: 0.5177 (ttp) REVERT: B 668 LYS cc_start: 0.8779 (mttm) cc_final: 0.8503 (mtmm) REVERT: C 89 GLU cc_start: 0.8453 (tp30) cc_final: 0.8127 (mp0) REVERT: F 15 LEU cc_start: 0.8386 (tt) cc_final: 0.7618 (mp) REVERT: F 105 GLU cc_start: 0.7614 (pt0) cc_final: 0.7400 (pt0) outliers start: 40 outliers final: 21 residues processed: 248 average time/residue: 0.1243 time to fit residues: 47.3807 Evaluate side-chains 207 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 56 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 chunk 122 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN B 299 HIS B 504 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS F 89 GLN F 138 ASN F 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126167 restraints weight = 21562.366| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.12 r_work: 0.3360 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16180 Z= 0.126 Angle : 0.606 9.112 21977 Z= 0.318 Chirality : 0.043 0.187 2503 Planarity : 0.004 0.051 2763 Dihedral : 4.466 34.724 2192 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 1.99 % Allowed : 11.00 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1994 helix: 1.66 (0.19), residues: 740 sheet: 0.89 (0.23), residues: 499 loop : -0.14 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.025 0.002 TYR B 472 PHE 0.022 0.002 PHE A 608 TRP 0.013 0.001 TRP C 109 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00271 (16171) covalent geometry : angle 0.60537 (21959) SS BOND : bond 0.00378 ( 9) SS BOND : angle 1.03035 ( 18) hydrogen bonds : bond 0.04193 ( 808) hydrogen bonds : angle 4.67033 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 227 THR cc_start: 0.8563 (m) cc_final: 0.8295 (m) REVERT: A 322 VAL cc_start: 0.8739 (t) cc_final: 0.8535 (m) REVERT: A 413 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7131 (tppt) REVERT: A 452 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 470 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.8541 (p90) REVERT: A 480 MET cc_start: 0.8321 (mmm) cc_final: 0.7784 (mmt) REVERT: B 121 ARG cc_start: 0.8325 (ptp-170) cc_final: 0.8060 (mtt180) REVERT: B 668 LYS cc_start: 0.8837 (mttm) cc_final: 0.8584 (mtmm) REVERT: C 45 LYS cc_start: 0.8027 (tptp) cc_final: 0.7775 (tptp) REVERT: C 82 GLN cc_start: 0.7603 (mp10) cc_final: 0.7259 (tp-100) REVERT: C 89 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: E 180 GLN cc_start: 0.7637 (pm20) cc_final: 0.7298 (pm20) REVERT: F 15 LEU cc_start: 0.8385 (tt) cc_final: 0.7599 (mp) outliers start: 35 outliers final: 24 residues processed: 229 average time/residue: 0.1204 time to fit residues: 42.5191 Evaluate side-chains 217 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 198 optimal weight: 0.3980 chunk 183 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN B 153 GLN C 5 GLN F 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123773 restraints weight = 21600.971| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.12 r_work: 0.3309 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16180 Z= 0.149 Angle : 0.597 9.129 21977 Z= 0.311 Chirality : 0.043 0.182 2503 Planarity : 0.005 0.042 2763 Dihedral : 4.462 37.399 2192 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % Rotamer: Outliers : 2.50 % Allowed : 11.80 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1994 helix: 1.63 (0.19), residues: 741 sheet: 0.86 (0.23), residues: 501 loop : -0.17 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.023 0.002 TYR B 472 PHE 0.019 0.002 PHE B 493 TRP 0.011 0.001 TRP C 109 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00346 (16171) covalent geometry : angle 0.59671 (21959) SS BOND : bond 0.00365 ( 9) SS BOND : angle 0.89129 ( 18) hydrogen bonds : bond 0.04195 ( 808) hydrogen bonds : angle 4.53315 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8162 (mt-10) REVERT: A 470 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.8680 (p90) REVERT: A 480 MET cc_start: 0.8339 (mmm) cc_final: 0.7753 (mmt) REVERT: B 121 ARG cc_start: 0.8255 (ptp-170) cc_final: 0.8049 (mtt90) REVERT: B 615 MET cc_start: 0.6079 (tmm) cc_final: 0.5280 (ttp) REVERT: B 668 LYS cc_start: 0.8947 (mttm) cc_final: 0.8659 (mtmt) REVERT: C 45 LYS cc_start: 0.8039 (tptp) cc_final: 0.7805 (tptp) REVERT: C 89 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: E 179 LEU cc_start: 0.7921 (mt) cc_final: 0.7683 (tp) REVERT: E 180 GLN cc_start: 0.7620 (pm20) cc_final: 0.7194 (pm20) REVERT: E 183 LEU cc_start: 0.8314 (mp) cc_final: 0.7852 (mm) REVERT: E 185 THR cc_start: 0.8341 (p) cc_final: 0.8116 (p) REVERT: F 167 ASP cc_start: 0.8457 (t70) cc_final: 0.8012 (t70) REVERT: F 170 ASP cc_start: 0.8464 (t0) cc_final: 0.7855 (t0) REVERT: F 195 GLU cc_start: 0.6311 (pm20) cc_final: 0.6031 (pm20) outliers start: 44 outliers final: 32 residues processed: 230 average time/residue: 0.1223 time to fit residues: 43.4335 Evaluate side-chains 225 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 172 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN B 526 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122009 restraints weight = 21442.944| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.14 r_work: 0.3297 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16180 Z= 0.158 Angle : 0.600 8.709 21977 Z= 0.313 Chirality : 0.044 0.195 2503 Planarity : 0.005 0.039 2763 Dihedral : 4.510 39.404 2192 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 3.06 % Allowed : 12.20 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1994 helix: 1.59 (0.19), residues: 743 sheet: 0.88 (0.23), residues: 499 loop : -0.31 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.024 0.002 TYR C 181 PHE 0.018 0.002 PHE B 493 TRP 0.013 0.001 TRP C 109 HIS 0.006 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00371 (16171) covalent geometry : angle 0.59957 (21959) SS BOND : bond 0.00348 ( 9) SS BOND : angle 0.87051 ( 18) hydrogen bonds : bond 0.04200 ( 808) hydrogen bonds : angle 4.48346 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.4673 (mmm) cc_final: 0.4465 (mmt) REVERT: A 452 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8155 (mt-10) REVERT: A 480 MET cc_start: 0.8329 (mmm) cc_final: 0.7727 (mmt) REVERT: B 668 LYS cc_start: 0.9038 (mttm) cc_final: 0.8659 (mtmt) REVERT: C 89 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: C 160 TRP cc_start: 0.3570 (m100) cc_final: 0.3354 (m100) REVERT: E 179 LEU cc_start: 0.7943 (mt) cc_final: 0.7675 (tp) REVERT: E 180 GLN cc_start: 0.7603 (pm20) cc_final: 0.7134 (pm20) REVERT: E 183 LEU cc_start: 0.8302 (mp) cc_final: 0.7850 (mm) REVERT: E 185 THR cc_start: 0.8377 (p) cc_final: 0.8123 (p) REVERT: F 167 ASP cc_start: 0.8487 (t70) cc_final: 0.7984 (t70) REVERT: F 170 ASP cc_start: 0.8519 (t0) cc_final: 0.7827 (t0) REVERT: F 195 GLU cc_start: 0.6427 (pm20) cc_final: 0.6116 (pm20) outliers start: 54 outliers final: 38 residues processed: 234 average time/residue: 0.1195 time to fit residues: 43.2543 Evaluate side-chains 225 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN B 526 GLN F 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124307 restraints weight = 21280.382| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.04 r_work: 0.3328 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16180 Z= 0.112 Angle : 0.559 7.362 21977 Z= 0.291 Chirality : 0.041 0.181 2503 Planarity : 0.004 0.038 2763 Dihedral : 4.331 38.228 2192 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 2.27 % Allowed : 13.50 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1994 helix: 1.80 (0.19), residues: 743 sheet: 0.95 (0.23), residues: 499 loop : -0.33 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 18 TYR 0.019 0.001 TYR B 571 PHE 0.015 0.001 PHE A 608 TRP 0.012 0.001 TRP B 584 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00241 (16171) covalent geometry : angle 0.55755 (21959) SS BOND : bond 0.00302 ( 9) SS BOND : angle 1.31702 ( 18) hydrogen bonds : bond 0.03726 ( 808) hydrogen bonds : angle 4.32038 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8114 (mt-10) REVERT: A 480 MET cc_start: 0.8332 (mmm) cc_final: 0.7692 (mmt) REVERT: B 668 LYS cc_start: 0.9027 (mttm) cc_final: 0.8640 (mtmt) REVERT: C 82 GLN cc_start: 0.7680 (mp10) cc_final: 0.7259 (tp-100) REVERT: C 89 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: E 179 LEU cc_start: 0.7989 (mt) cc_final: 0.7698 (tp) REVERT: E 180 GLN cc_start: 0.7420 (pm20) cc_final: 0.6938 (pm20) REVERT: E 183 LEU cc_start: 0.8305 (mt) cc_final: 0.7875 (mm) REVERT: E 185 THR cc_start: 0.8393 (p) cc_final: 0.8116 (p) REVERT: E 200 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5829 (mm-30) REVERT: F 167 ASP cc_start: 0.8481 (t70) cc_final: 0.8003 (t70) REVERT: F 170 ASP cc_start: 0.8477 (t0) cc_final: 0.7818 (t0) REVERT: F 195 GLU cc_start: 0.6384 (pm20) cc_final: 0.6018 (pm20) outliers start: 40 outliers final: 28 residues processed: 228 average time/residue: 0.1180 time to fit residues: 41.8642 Evaluate side-chains 218 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 39 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 182 optimal weight: 0.0070 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN B 526 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123502 restraints weight = 21221.159| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.07 r_work: 0.3319 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16180 Z= 0.127 Angle : 0.572 10.480 21977 Z= 0.296 Chirality : 0.042 0.182 2503 Planarity : 0.004 0.038 2763 Dihedral : 4.303 38.524 2192 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 2.33 % Allowed : 14.07 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1994 helix: 1.82 (0.19), residues: 741 sheet: 1.03 (0.24), residues: 492 loop : -0.34 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 419 TYR 0.020 0.001 TYR E 154 PHE 0.015 0.001 PHE B 493 TRP 0.018 0.001 TRP C 160 HIS 0.003 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00287 (16171) covalent geometry : angle 0.57084 (21959) SS BOND : bond 0.00584 ( 9) SS BOND : angle 1.39102 ( 18) hydrogen bonds : bond 0.03782 ( 808) hydrogen bonds : angle 4.30155 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.4565 (mmm) cc_final: 0.4293 (mmt) REVERT: A 452 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 480 MET cc_start: 0.8295 (mmm) cc_final: 0.7695 (mmt) REVERT: B 615 MET cc_start: 0.5682 (tmm) cc_final: 0.4872 (ttp) REVERT: B 668 LYS cc_start: 0.9039 (mttm) cc_final: 0.8644 (mtmt) REVERT: C 89 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: D 148 LYS cc_start: 0.6176 (ptmt) cc_final: 0.5749 (tttm) REVERT: E 200 GLU cc_start: 0.6183 (mt-10) cc_final: 0.5847 (mm-30) REVERT: F 167 ASP cc_start: 0.8481 (t70) cc_final: 0.7941 (t70) REVERT: F 170 ASP cc_start: 0.8509 (t0) cc_final: 0.7832 (t0) outliers start: 41 outliers final: 34 residues processed: 222 average time/residue: 0.1125 time to fit residues: 38.9712 Evaluate side-chains 221 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 146 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.152405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119438 restraints weight = 21685.884| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.13 r_work: 0.3247 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16180 Z= 0.225 Angle : 0.647 9.284 21977 Z= 0.336 Chirality : 0.045 0.182 2503 Planarity : 0.005 0.042 2763 Dihedral : 4.616 42.910 2192 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.86 % Favored : 96.04 % Rotamer: Outliers : 2.67 % Allowed : 13.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1994 helix: 1.49 (0.19), residues: 743 sheet: 0.98 (0.24), residues: 493 loop : -0.46 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 550 TYR 0.026 0.002 TYR B 472 PHE 0.022 0.002 PHE B 493 TRP 0.023 0.002 TRP C 160 HIS 0.007 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00543 (16171) covalent geometry : angle 0.64563 (21959) SS BOND : bond 0.00536 ( 9) SS BOND : angle 1.53579 ( 18) hydrogen bonds : bond 0.04636 ( 808) hydrogen bonds : angle 4.48631 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.4890 (mmm) cc_final: 0.4639 (mmt) REVERT: A 452 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8174 (mt-10) REVERT: A 480 MET cc_start: 0.8292 (mmm) cc_final: 0.7690 (mmt) REVERT: B 615 MET cc_start: 0.5819 (tmm) cc_final: 0.5009 (ttp) REVERT: B 668 LYS cc_start: 0.9074 (mttm) cc_final: 0.8688 (mtmt) REVERT: C 45 LYS cc_start: 0.8000 (tptp) cc_final: 0.7777 (tptt) REVERT: C 89 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: D 79 MET cc_start: 0.7816 (ttm) cc_final: 0.7158 (mtt) REVERT: E 200 GLU cc_start: 0.6329 (mt-10) cc_final: 0.5864 (mm-30) REVERT: F 167 ASP cc_start: 0.8481 (t70) cc_final: 0.7953 (t70) REVERT: F 170 ASP cc_start: 0.8574 (t0) cc_final: 0.7852 (t0) REVERT: F 195 GLU cc_start: 0.6581 (pm20) cc_final: 0.6379 (pm20) outliers start: 47 outliers final: 37 residues processed: 225 average time/residue: 0.1178 time to fit residues: 41.0688 Evaluate side-chains 221 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 148 optimal weight: 0.0070 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122498 restraints weight = 21478.683| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.05 r_work: 0.3304 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16180 Z= 0.120 Angle : 0.571 8.725 21977 Z= 0.296 Chirality : 0.042 0.180 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.416 40.759 2192 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Rotamer: Outliers : 2.10 % Allowed : 14.18 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 1994 helix: 1.77 (0.19), residues: 741 sheet: 0.97 (0.24), residues: 486 loop : -0.44 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.023 0.001 TYR E 131 PHE 0.017 0.001 PHE C 152 TRP 0.018 0.001 TRP C 160 HIS 0.003 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00266 (16171) covalent geometry : angle 0.57093 (21959) SS BOND : bond 0.00484 ( 9) SS BOND : angle 1.00110 ( 18) hydrogen bonds : bond 0.03837 ( 808) hydrogen bonds : angle 4.30582 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 480 MET cc_start: 0.8282 (mmm) cc_final: 0.7680 (mmt) REVERT: B 615 MET cc_start: 0.5819 (tmm) cc_final: 0.4958 (ttp) REVERT: B 668 LYS cc_start: 0.9048 (mttm) cc_final: 0.8658 (mtmt) REVERT: C 89 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: D 148 LYS cc_start: 0.5737 (tttm) cc_final: 0.5395 (ttpp) REVERT: E 200 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5867 (mm-30) REVERT: F 167 ASP cc_start: 0.8474 (t70) cc_final: 0.7928 (t70) REVERT: F 170 ASP cc_start: 0.8516 (t0) cc_final: 0.7783 (t0) outliers start: 37 outliers final: 33 residues processed: 218 average time/residue: 0.1172 time to fit residues: 39.8073 Evaluate side-chains 219 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 76 optimal weight: 0.0050 chunk 151 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122457 restraints weight = 21468.086| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.06 r_work: 0.3305 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16180 Z= 0.135 Angle : 0.587 12.564 21977 Z= 0.303 Chirality : 0.042 0.181 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.381 40.389 2192 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 1.99 % Allowed : 14.63 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 1994 helix: 1.81 (0.19), residues: 741 sheet: 1.00 (0.24), residues: 484 loop : -0.43 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 240 TYR 0.021 0.001 TYR B 571 PHE 0.015 0.001 PHE B 493 TRP 0.016 0.001 TRP C 160 HIS 0.003 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00312 (16171) covalent geometry : angle 0.58679 (21959) SS BOND : bond 0.00425 ( 9) SS BOND : angle 1.14188 ( 18) hydrogen bonds : bond 0.03886 ( 808) hydrogen bonds : angle 4.28716 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8087 (mt-10) REVERT: A 480 MET cc_start: 0.8295 (mmm) cc_final: 0.7683 (mmt) REVERT: B 615 MET cc_start: 0.5800 (tmm) cc_final: 0.4957 (ttp) REVERT: B 668 LYS cc_start: 0.9044 (mttm) cc_final: 0.8655 (mtmt) REVERT: C 89 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: D 148 LYS cc_start: 0.5616 (tttm) cc_final: 0.5132 (ttpp) REVERT: D 196 GLU cc_start: 0.7144 (mp0) cc_final: 0.6838 (pp20) REVERT: E 200 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5833 (mm-30) REVERT: F 167 ASP cc_start: 0.8465 (t70) cc_final: 0.7918 (t70) REVERT: F 170 ASP cc_start: 0.8500 (t0) cc_final: 0.7731 (t0) outliers start: 35 outliers final: 33 residues processed: 210 average time/residue: 0.1184 time to fit residues: 38.8358 Evaluate side-chains 217 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 139 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122436 restraints weight = 21418.548| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.05 r_work: 0.3303 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16180 Z= 0.137 Angle : 0.585 12.217 21977 Z= 0.302 Chirality : 0.042 0.181 2503 Planarity : 0.004 0.044 2763 Dihedral : 4.373 40.353 2192 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 2.04 % Allowed : 14.63 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 1994 helix: 1.82 (0.19), residues: 741 sheet: 1.00 (0.24), residues: 490 loop : -0.44 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.021 0.002 TYR B 571 PHE 0.015 0.001 PHE B 493 TRP 0.014 0.001 TRP C 160 HIS 0.004 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00316 (16171) covalent geometry : angle 0.58442 (21959) SS BOND : bond 0.00435 ( 9) SS BOND : angle 1.17708 ( 18) hydrogen bonds : bond 0.03870 ( 808) hydrogen bonds : angle 4.26932 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4826.46 seconds wall clock time: 83 minutes 11.32 seconds (4991.32 seconds total)