Starting phenix.real_space_refine on Mon Jul 28 14:52:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kah_22770/07_2025/7kah_22770.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kah_22770/07_2025/7kah_22770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kah_22770/07_2025/7kah_22770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kah_22770/07_2025/7kah_22770.map" model { file = "/net/cci-nas-00/data/ceres_data/7kah_22770/07_2025/7kah_22770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kah_22770/07_2025/7kah_22770.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.034 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 42 5.16 5 C 6849 2.51 5 N 1762 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10495 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3362 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3869 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 28, 'TRANS': 464} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 86 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 6.09, per 1000 atoms: 0.58 Number of scatterers: 10495 At special positions: 0 Unit cell: (109.48, 127.33, 135.66, 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 42 16.00 O 1842 8.00 N 1762 7.00 C 6849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 66.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.525A pdb=" N TRP A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.671A pdb=" N LYS A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.725A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.562A pdb=" N ARG A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.126A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.852A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 4.542A pdb=" N ILE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.541A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.501A pdb=" N ALA A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.594A pdb=" N THR A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.588A pdb=" N TYR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 4.065A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 removed outlier: 3.766A pdb=" N GLY B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.817A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 65 removed outlier: 4.224A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.647A pdb=" N PHE D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.927A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.713A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.688A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.612A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 294' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.861A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.779A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.843A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 removed outlier: 3.522A pdb=" N LEU D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.939A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.348A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.505A pdb=" N LYS D 493 " --> pdb=" O MET D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.869A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 124 removed outlier: 3.756A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 4.044A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 4.022A pdb=" N VAL E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.155A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.548A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.764A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 4.070A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.704A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix removed outlier: 3.932A pdb=" N SER F 111 " --> pdb=" O PHE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.728A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 174 through 192 removed outlier: 4.080A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436 removed outlier: 3.777A pdb=" N LYS D 432 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D 434 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 637 hydrogen bonds defined for protein. 1872 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: 2.87 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3297 1.34 - 1.46: 2048 1.46 - 1.58: 5293 1.58 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 10705 Sorted by residual: bond pdb=" CA VAL D 610 " pdb=" CB VAL D 610 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.26e-01 bond pdb=" CG LEU F 129 " pdb=" CD2 LEU F 129 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.22e-01 bond pdb=" CB LYS E 86 " pdb=" CG LYS E 86 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.76e-01 bond pdb=" CB VAL C 61 " pdb=" CG1 VAL C 61 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.17e-01 bond pdb=" CA GLN A 102 " pdb=" CB GLN A 102 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.70e-02 3.46e+03 4.96e-01 ... (remaining 10700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 14206 1.46 - 2.92: 244 2.92 - 4.38: 43 4.38 - 5.83: 15 5.83 - 7.29: 5 Bond angle restraints: 14513 Sorted by residual: angle pdb=" N SER A 289 " pdb=" CA SER A 289 " pdb=" C SER A 289 " ideal model delta sigma weight residual 111.37 115.17 -3.80 1.64e+00 3.72e-01 5.36e+00 angle pdb=" CA LYS E 86 " pdb=" CB LYS E 86 " pdb=" CG LYS E 86 " ideal model delta sigma weight residual 114.10 118.13 -4.03 2.00e+00 2.50e-01 4.06e+00 angle pdb=" N TRP D 14 " pdb=" CA TRP D 14 " pdb=" C TRP D 14 " ideal model delta sigma weight residual 109.81 114.09 -4.28 2.21e+00 2.05e-01 3.75e+00 angle pdb=" CA LEU F 129 " pdb=" CB LEU F 129 " pdb=" CG LEU F 129 " ideal model delta sigma weight residual 116.30 123.00 -6.70 3.50e+00 8.16e-02 3.67e+00 angle pdb=" CA LEU F 4 " pdb=" CB LEU F 4 " pdb=" CG LEU F 4 " ideal model delta sigma weight residual 116.30 122.74 -6.44 3.50e+00 8.16e-02 3.39e+00 ... (remaining 14508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 5821 16.11 - 32.22: 486 32.22 - 48.33: 117 48.33 - 64.43: 10 64.43 - 80.54: 13 Dihedral angle restraints: 6447 sinusoidal: 2528 harmonic: 3919 Sorted by residual: dihedral pdb=" CA ARG D 509 " pdb=" C ARG D 509 " pdb=" N ARG D 510 " pdb=" CA ARG D 510 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLN F 155 " pdb=" C GLN F 155 " pdb=" N TRP F 156 " pdb=" CA TRP F 156 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.34e+00 dihedral pdb=" CA LEU F 153 " pdb=" C LEU F 153 " pdb=" N ARG F 154 " pdb=" CA ARG F 154 " ideal model delta harmonic sigma weight residual 180.00 164.91 15.09 0 5.00e+00 4.00e-02 9.11e+00 ... (remaining 6444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1171 0.035 - 0.069: 398 0.069 - 0.104: 121 0.104 - 0.138: 29 0.138 - 0.173: 2 Chirality restraints: 1721 Sorted by residual: chirality pdb=" CG LEU F 129 " pdb=" CB LEU F 129 " pdb=" CD1 LEU F 129 " pdb=" CD2 LEU F 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA THR A 291 " pdb=" N THR A 291 " pdb=" C THR A 291 " pdb=" CB THR A 291 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 1718 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO F 48 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 366 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO D 367 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 14 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO D 15 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 15 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 15 " -0.019 5.00e-02 4.00e+02 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2392 2.79 - 3.31: 9871 3.31 - 3.84: 16199 3.84 - 4.37: 18004 4.37 - 4.90: 32727 Nonbonded interactions: 79193 Sorted by model distance: nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 82 " model vdw 2.257 3.040 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.259 3.120 nonbonded pdb=" OE2 GLU E 102 " pdb=" NH2 ARG E 105 " model vdw 2.287 3.120 nonbonded pdb=" O THR D 444 " pdb=" OG SER D 447 " model vdw 2.305 3.040 nonbonded pdb=" OD1 ASN D 427 " pdb=" OG1 THR D 599 " model vdw 2.314 3.040 ... (remaining 79188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 23.800 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 0.003 0.029 10705 Z= 0.137 Angle : 0.533 7.293 14513 Z= 0.281 Chirality : 0.039 0.173 1721 Planarity : 0.004 0.042 1805 Dihedral : 12.901 80.542 3903 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1325 helix: 0.10 (0.17), residues: 815 sheet: -2.50 (0.46), residues: 90 loop : -2.32 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 14 HIS 0.006 0.001 HIS D 330 PHE 0.015 0.001 PHE D 547 TYR 0.011 0.001 TYR F 190 ARG 0.003 0.000 ARG E 178 Details of bonding type rmsd hydrogen bonds : bond 0.12427 ( 637) hydrogen bonds : angle 4.57408 ( 1872) covalent geometry : bond 0.00318 (10705) covalent geometry : angle 0.53329 (14513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8258 (t70) cc_final: 0.8025 (t0) REVERT: C 52 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8265 (ttmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2447 time to fit residues: 29.5076 Evaluate side-chains 62 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN D 390 HIS E 88 HIS F 68 ASN F 71 GLN F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046114 restraints weight = 37666.396| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.05 r_work: 0.2682 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10705 Z= 0.231 Angle : 0.592 10.678 14513 Z= 0.296 Chirality : 0.042 0.167 1721 Planarity : 0.004 0.051 1805 Dihedral : 3.741 19.212 1429 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.25 % Allowed : 11.06 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1325 helix: 1.32 (0.19), residues: 814 sheet: -2.01 (0.48), residues: 90 loop : -1.79 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 14 HIS 0.008 0.001 HIS D 330 PHE 0.013 0.001 PHE D 547 TYR 0.014 0.001 TYR F 190 ARG 0.008 0.001 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 637) hydrogen bonds : angle 3.71767 ( 1872) covalent geometry : bond 0.00560 (10705) covalent geometry : angle 0.59168 (14513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 295 LEU cc_start: 0.9258 (mp) cc_final: 0.9036 (mp) REVERT: C 40 LYS cc_start: 0.9031 (tttp) cc_final: 0.8611 (ttpp) REVERT: C 46 GLU cc_start: 0.9000 (tt0) cc_final: 0.8778 (pt0) REVERT: C 52 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8109 (ttmm) outliers start: 14 outliers final: 7 residues processed: 73 average time/residue: 0.2077 time to fit residues: 23.0898 Evaluate side-chains 65 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 150 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 118 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.047184 restraints weight = 38090.204| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.11 r_work: 0.2713 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10705 Z= 0.132 Angle : 0.514 9.539 14513 Z= 0.255 Chirality : 0.039 0.146 1721 Planarity : 0.004 0.048 1805 Dihedral : 3.519 17.617 1429 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.69 % Allowed : 12.67 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1325 helix: 1.91 (0.19), residues: 816 sheet: -1.73 (0.47), residues: 92 loop : -1.44 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 156 HIS 0.005 0.001 HIS D 330 PHE 0.009 0.001 PHE D 481 TYR 0.010 0.001 TYR F 190 ARG 0.006 0.000 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 637) hydrogen bonds : angle 3.42857 ( 1872) covalent geometry : bond 0.00310 (10705) covalent geometry : angle 0.51399 (14513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 295 LEU cc_start: 0.9266 (mp) cc_final: 0.9057 (mp) REVERT: C 40 LYS cc_start: 0.9034 (tttp) cc_final: 0.8708 (ttpp) REVERT: C 44 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7696 (tt) REVERT: C 52 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8068 (ttmm) REVERT: D 553 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7876 (mmm) REVERT: F 70 GLN cc_start: 0.8975 (mp10) cc_final: 0.8760 (pm20) outliers start: 19 outliers final: 10 residues processed: 74 average time/residue: 0.2140 time to fit residues: 24.1434 Evaluate side-chains 68 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.064835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046397 restraints weight = 38323.939| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.14 r_work: 0.2687 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10705 Z= 0.165 Angle : 0.530 9.227 14513 Z= 0.263 Chirality : 0.039 0.146 1721 Planarity : 0.004 0.048 1805 Dihedral : 3.525 16.955 1429 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.41 % Allowed : 13.38 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1325 helix: 2.13 (0.19), residues: 815 sheet: -1.51 (0.49), residues: 92 loop : -1.30 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 156 HIS 0.006 0.001 HIS D 330 PHE 0.015 0.001 PHE B 66 TYR 0.012 0.001 TYR F 190 ARG 0.005 0.000 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 637) hydrogen bonds : angle 3.45259 ( 1872) covalent geometry : bond 0.00396 (10705) covalent geometry : angle 0.52975 (14513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.9102 (t70) cc_final: 0.8878 (t0) REVERT: C 40 LYS cc_start: 0.9007 (tttp) cc_final: 0.8615 (ttpp) REVERT: C 43 ASP cc_start: 0.8480 (p0) cc_final: 0.6989 (p0) REVERT: C 52 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8088 (ttmm) REVERT: D 57 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7832 (mp0) outliers start: 27 outliers final: 15 residues processed: 83 average time/residue: 0.2039 time to fit residues: 26.0980 Evaluate side-chains 75 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 21 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.063135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.044959 restraints weight = 38150.303| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.07 r_work: 0.2651 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10705 Z= 0.254 Angle : 0.602 9.354 14513 Z= 0.304 Chirality : 0.042 0.168 1721 Planarity : 0.004 0.064 1805 Dihedral : 3.782 18.975 1429 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.50 % Allowed : 14.99 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1325 helix: 2.07 (0.19), residues: 815 sheet: -1.39 (0.50), residues: 92 loop : -1.27 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 156 HIS 0.009 0.001 HIS D 330 PHE 0.013 0.001 PHE D 481 TYR 0.014 0.001 TYR F 190 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 637) hydrogen bonds : angle 3.69854 ( 1872) covalent geometry : bond 0.00615 (10705) covalent geometry : angle 0.60162 (14513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8100 (mmp) cc_final: 0.7879 (mmp) REVERT: A 350 MET cc_start: 0.8312 (ptt) cc_final: 0.8110 (mmm) REVERT: C 40 LYS cc_start: 0.9028 (tttp) cc_final: 0.8639 (ttpp) REVERT: C 52 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8067 (ttmm) REVERT: D 57 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7824 (mp0) outliers start: 28 outliers final: 16 residues processed: 83 average time/residue: 0.2022 time to fit residues: 25.5887 Evaluate side-chains 73 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 82 optimal weight: 0.0980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.047948 restraints weight = 38692.415| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.17 r_work: 0.2735 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10705 Z= 0.098 Angle : 0.501 8.605 14513 Z= 0.248 Chirality : 0.038 0.161 1721 Planarity : 0.004 0.067 1805 Dihedral : 3.383 15.192 1429 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 15.88 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1325 helix: 2.39 (0.19), residues: 820 sheet: -1.14 (0.50), residues: 92 loop : -1.05 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.019 0.001 PHE B 66 TYR 0.011 0.001 TYR A 287 ARG 0.006 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 637) hydrogen bonds : angle 3.32572 ( 1872) covalent geometry : bond 0.00212 (10705) covalent geometry : angle 0.50110 (14513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.215 Fit side-chains REVERT: A 135 MET cc_start: 0.7932 (mmp) cc_final: 0.7703 (mmp) REVERT: C 40 LYS cc_start: 0.8860 (tttp) cc_final: 0.8413 (ttpp) REVERT: C 52 LYS cc_start: 0.8272 (ttmt) cc_final: 0.8023 (ttmm) REVERT: D 57 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: F 70 GLN cc_start: 0.9011 (mp10) cc_final: 0.8810 (pm20) outliers start: 21 outliers final: 10 residues processed: 81 average time/residue: 0.2203 time to fit residues: 26.4657 Evaluate side-chains 68 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain F residue 13 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 93 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.046097 restraints weight = 38663.291| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.12 r_work: 0.2684 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10705 Z= 0.172 Angle : 0.542 8.722 14513 Z= 0.271 Chirality : 0.040 0.163 1721 Planarity : 0.004 0.070 1805 Dihedral : 3.485 17.164 1429 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.78 % Allowed : 16.77 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1325 helix: 2.40 (0.19), residues: 822 sheet: -1.12 (0.50), residues: 92 loop : -1.05 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.017 0.001 PHE B 66 TYR 0.012 0.001 TYR F 190 ARG 0.006 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 637) hydrogen bonds : angle 3.44119 ( 1872) covalent geometry : bond 0.00416 (10705) covalent geometry : angle 0.54214 (14513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8008 (mmp) cc_final: 0.7783 (mmp) REVERT: C 40 LYS cc_start: 0.8916 (tttp) cc_final: 0.8496 (ttpp) REVERT: C 52 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8071 (ttmm) REVERT: D 57 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7750 (mp0) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.2064 time to fit residues: 24.5040 Evaluate side-chains 73 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 13 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.048026 restraints weight = 37871.713| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.07 r_work: 0.2741 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10705 Z= 0.098 Angle : 0.504 8.299 14513 Z= 0.250 Chirality : 0.038 0.178 1721 Planarity : 0.004 0.069 1805 Dihedral : 3.306 14.828 1429 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 17.22 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.24), residues: 1325 helix: 2.54 (0.19), residues: 822 sheet: -0.91 (0.50), residues: 92 loop : -0.91 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 14 HIS 0.005 0.001 HIS D 309 PHE 0.021 0.001 PHE B 66 TYR 0.009 0.001 TYR A 287 ARG 0.007 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 637) hydrogen bonds : angle 3.27373 ( 1872) covalent geometry : bond 0.00219 (10705) covalent geometry : angle 0.50383 (14513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 1.334 Fit side-chains REVERT: A 92 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8184 (m-10) REVERT: C 40 LYS cc_start: 0.8822 (tttp) cc_final: 0.8414 (ttpp) REVERT: D 57 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: F 139 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8517 (mm110) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.2009 time to fit residues: 25.1433 Evaluate side-chains 75 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 13 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 29 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.046329 restraints weight = 38688.648| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.16 r_work: 0.2691 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10705 Z= 0.163 Angle : 0.555 8.959 14513 Z= 0.275 Chirality : 0.040 0.173 1721 Planarity : 0.004 0.071 1805 Dihedral : 3.431 16.824 1429 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.78 % Allowed : 17.31 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.24), residues: 1325 helix: 2.52 (0.19), residues: 822 sheet: -0.95 (0.50), residues: 92 loop : -0.92 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.019 0.001 PHE B 66 TYR 0.011 0.001 TYR E 121 ARG 0.008 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 637) hydrogen bonds : angle 3.40034 ( 1872) covalent geometry : bond 0.00393 (10705) covalent geometry : angle 0.55535 (14513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: C 40 LYS cc_start: 0.8877 (tttp) cc_final: 0.8417 (ttpp) REVERT: D 57 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7700 (mp0) outliers start: 20 outliers final: 15 residues processed: 74 average time/residue: 0.1927 time to fit residues: 21.9657 Evaluate side-chains 74 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 13 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 61 optimal weight: 0.0770 chunk 87 optimal weight: 7.9990 chunk 90 optimal weight: 0.1980 chunk 11 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 0.0170 chunk 83 optimal weight: 0.9980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049129 restraints weight = 37713.413| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.05 r_work: 0.2776 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10705 Z= 0.095 Angle : 0.515 9.219 14513 Z= 0.252 Chirality : 0.038 0.176 1721 Planarity : 0.004 0.069 1805 Dihedral : 3.195 14.105 1429 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.52 % Allowed : 17.75 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1325 helix: 2.65 (0.19), residues: 823 sheet: -0.75 (0.50), residues: 92 loop : -0.82 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 14 HIS 0.005 0.001 HIS D 309 PHE 0.009 0.001 PHE F 107 TYR 0.008 0.001 TYR A 287 ARG 0.008 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 637) hydrogen bonds : angle 3.20169 ( 1872) covalent geometry : bond 0.00208 (10705) covalent geometry : angle 0.51496 (14513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 1.700 Fit side-chains REVERT: C 40 LYS cc_start: 0.8782 (tttp) cc_final: 0.8539 (ttpp) REVERT: C 41 LYS cc_start: 0.9260 (mptt) cc_final: 0.9010 (mmtm) REVERT: D 57 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: F 139 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8525 (mm-40) outliers start: 17 outliers final: 11 residues processed: 75 average time/residue: 0.3978 time to fit residues: 43.0273 Evaluate side-chains 70 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 547 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 105 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.047858 restraints weight = 37937.785| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.05 r_work: 0.2739 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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 0.039 10705 Z= 0.115 Angle : 0.535 8.852 14513 Z= 0.262 Chirality : 0.038 0.166 1721 Planarity : 0.004 0.071 1805 Dihedral : 3.217 15.298 1429 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.43 % Allowed : 17.93 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1325 helix: 2.68 (0.19), residues: 823 sheet: -0.73 (0.50), residues: 92 loop : -0.79 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 131 HIS 0.004 0.001 HIS D 330 PHE 0.022 0.001 PHE B 66 TYR 0.018 0.001 TYR E 121 ARG 0.008 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 637) hydrogen bonds : angle 3.23892 ( 1872) covalent geometry : bond 0.00270 (10705) covalent geometry : angle 0.53518 (14513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5543.82 seconds wall clock time: 98 minutes 4.86 seconds (5884.86 seconds total)