Starting phenix.real_space_refine on Fri Jul 3 03:03:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eao_47838/07_2026/9eao_47838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eao_47838/07_2026/9eao_47838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eao_47838/07_2026/9eao_47838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eao_47838/07_2026/9eao_47838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eao_47838/07_2026/9eao_47838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eao_47838/07_2026/9eao_47838.map" } resolution = 2.6 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= 0.003 sd= 0.475 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 48 5.16 5 C 7602 2.51 5 N 1941 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11798 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3949 Classifications: {'peptide': 514} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 467} Chain: "B" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3963 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 470} Chain breaks: 3 Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3883 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.71, per 1000 atoms: 0.23 Number of scatterers: 11798 At special positions: 0 Unit cell: (119.9, 116.6, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 48 16.00 O 2204 8.00 N 1941 7.00 C 7602 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: 0.87 Conformation dependent library (CDL) restraints added in 565.6 milliseconds 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 19 sheets defined 10.6% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.500A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.164A pdb=" N ASN A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.779A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.569A pdb=" N TRP A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 286 " --> pdb=" O GLY A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.854A pdb=" N ALA B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 54 through 58 removed outlier: 4.102A pdb=" N ASN B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.657A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.818A pdb=" N PHE B 144 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.615A pdb=" N TRP B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.543A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.784A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.775A pdb=" N THR C 142 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 144 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.782A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.617A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.907A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 205 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83 removed outlier: 6.766A pdb=" N CYS A 183 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A 81 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 181 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 182 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 127 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N MET A 184 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 125 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR A 186 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 123 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS A 121 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451 Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451 removed outlier: 5.372A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 485 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 479 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 487 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA A 472 " --> pdb=" O TRP A 520 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP A 520 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 474 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 297 removed outlier: 4.294A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER A 332 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE A 401 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU A 338 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N GLN A 340 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ALA A 393 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 389 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69 removed outlier: 12.790A pdb=" N GLN B 61 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N SER B 207 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY B 65 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.809A pdb=" N ILE B 78 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 185 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 80 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 121 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA B 119 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB1, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.772A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU B 252 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.772A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE B 497 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 477 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 488 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 475 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS B 490 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 473 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 474 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 298 removed outlier: 4.170A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER B 332 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE B 401 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU B 338 " --> pdb=" O PRO B 395 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N GLN B 340 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ALA B 393 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 11.866A pdb=" N GLU B 342 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N VAL B 391 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.605A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.828A pdb=" N ILE C 78 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 185 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB7, first strand: chain 'C' and resid 449 through 451 removed outlier: 3.547A pdb=" N GLY C 251 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU C 252 " --> pdb=" O PHE C 509 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 354 removed outlier: 3.639A pdb=" N THR C 353 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 339 " --> pdb=" O THR C 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 354 removed outlier: 3.639A pdb=" N THR C 353 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 339 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER C 332 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C 401 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 397 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU C 338 " --> pdb=" O PRO C 395 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N GLN C 340 " --> pdb=" O ALA C 393 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ALA C 393 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 11.781A pdb=" N GLU C 342 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 11.430A pdb=" N VAL C 391 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 427 through 429 removed outlier: 5.245A pdb=" N SER C 500 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLU C 488 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR C 477 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU C 488 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 475 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS C 490 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 473 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA C 472 " --> pdb=" O TRP C 520 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TRP C 520 " --> pdb=" O ALA C 472 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 474 " --> pdb=" O VAL C 518 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 786 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: 1.79 Time building geometry restraints manager: 1.20 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: 3828 1.34 - 1.46: 2085 1.46 - 1.57: 6133 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 12118 Sorted by residual: bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.33e+00 bond pdb=" CG PRO B 23 " pdb=" CD PRO B 23 " ideal model delta sigma weight residual 1.503 1.545 -0.042 3.40e-02 8.65e+02 1.53e+00 bond pdb=" CA ASP B 174 " pdb=" CB ASP B 174 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.15e-01 bond pdb=" CB ILE A 405 " pdb=" CG1 ILE A 405 " ideal model delta sigma weight residual 1.530 1.547 -0.017 2.00e-02 2.50e+03 7.03e-01 bond pdb=" C LEU C 159 " pdb=" N PRO C 160 " ideal model delta sigma weight residual 1.330 1.340 -0.010 1.23e-02 6.61e+03 6.93e-01 ... (remaining 12113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 16370 2.26 - 4.53: 220 4.53 - 6.79: 13 6.79 - 9.06: 6 9.06 - 11.32: 3 Bond angle restraints: 16612 Sorted by residual: angle pdb=" C THR C 363 " pdb=" CA THR C 363 " pdb=" CB THR C 363 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" C GLN C 469 " pdb=" N SER C 470 " pdb=" CA SER C 470 " ideal model delta sigma weight residual 121.90 115.00 6.90 1.26e+00 6.30e-01 3.00e+01 angle pdb=" CA PRO B 23 " pdb=" N PRO B 23 " pdb=" CD PRO B 23 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" CA THR C 363 " pdb=" C THR C 363 " pdb=" N ASN C 364 " ideal model delta sigma weight residual 119.52 116.53 2.99 7.90e-01 1.60e+00 1.43e+01 angle pdb=" N PHE A 423 " pdb=" CA PHE A 423 " pdb=" C PHE A 423 " ideal model delta sigma weight residual 110.35 115.58 -5.23 1.40e+00 5.10e-01 1.39e+01 ... (remaining 16607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 6197 17.39 - 34.78: 690 34.78 - 52.17: 222 52.17 - 69.56: 62 69.56 - 86.95: 18 Dihedral angle restraints: 7189 sinusoidal: 2762 harmonic: 4427 Sorted by residual: dihedral pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N ASP B 196 " pdb=" CA ASP B 196 " ideal model delta harmonic sigma weight residual 180.00 149.33 30.67 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA VAL B 22 " pdb=" C VAL B 22 " pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta harmonic sigma weight residual 180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLY A 421 " pdb=" C GLY A 421 " pdb=" N PRO A 422 " pdb=" CA PRO A 422 " ideal model delta harmonic sigma weight residual 0.00 -25.80 25.80 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 7186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1393 0.044 - 0.089: 333 0.089 - 0.133: 162 0.133 - 0.178: 3 0.178 - 0.222: 1 Chirality restraints: 1892 Sorted by residual: chirality pdb=" CA PRO B 23 " pdb=" N PRO B 23 " pdb=" C PRO B 23 " pdb=" CB PRO B 23 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU B 64 " pdb=" CB LEU B 64 " pdb=" CD1 LEU B 64 " pdb=" CD2 LEU B 64 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA PRO C 129 " pdb=" N PRO C 129 " pdb=" C PRO C 129 " pdb=" CB PRO C 129 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1889 not shown) Planarity restraints: 2174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 22 " -0.093 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO B 23 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 128 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO C 129 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 62 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO B 63 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.032 5.00e-02 4.00e+02 ... (remaining 2171 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 143 2.66 - 3.22: 9533 3.22 - 3.78: 16554 3.78 - 4.34: 23779 4.34 - 4.90: 40143 Nonbonded interactions: 90152 Sorted by model distance: nonbonded pdb=" OG SER C 383 " pdb=" OD1 ASP C 385 " model vdw 2.103 3.040 nonbonded pdb=" ND2 ASN C 261 " pdb=" O ILE C 420 " model vdw 2.266 3.120 nonbonded pdb=" ND1 HIS C 270 " pdb=" OD1 ASP C 272 " model vdw 2.296 3.120 nonbonded pdb=" ND2 ASN B 261 " pdb=" O ILE B 420 " model vdw 2.307 3.120 nonbonded pdb=" ND2 ASN B 49 " pdb=" O VAL B 216 " model vdw 2.316 3.120 ... (remaining 90147 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 530 or resid 601)) selection = (chain 'B' and resid 27 through 601) selection = chain 'C' } 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: 15.170 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.640 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 0.076 12118 Z= 0.123 Angle : 0.623 11.321 16612 Z= 0.324 Chirality : 0.046 0.222 1892 Planarity : 0.007 0.140 2174 Dihedral : 17.272 86.950 4347 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.58 % Favored : 94.22 % Rotamer: Outliers : 5.19 % Allowed : 22.41 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1523 helix: -0.25 (0.66), residues: 50 sheet: 0.06 (0.24), residues: 406 loop : -1.18 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.016 0.001 TYR A 217 PHE 0.017 0.001 PHE C 80 TRP 0.011 0.001 TRP C 169 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (12118) covalent geometry : angle 0.62278 / 0.32 (16612) hydrogen bonds : bond 0.17064 / 11.28 ( 305) hydrogen bonds : angle 6.60433 / 4.58 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 0.402 Fit side-chains outliers start: 66 outliers final: 64 residues processed: 214 average time/residue: 0.4555 time to fit residues: 106.6404 Evaluate side-chains 208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 144 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 334 GLN B 367 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.179611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113573 restraints weight = 11779.869| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.54 r_work: 0.3238 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12118 Z= 0.165 Angle : 0.685 11.768 16612 Z= 0.352 Chirality : 0.048 0.228 1892 Planarity : 0.007 0.141 2174 Dihedral : 8.987 59.998 1743 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.58 % Favored : 94.22 % Rotamer: Outliers : 7.23 % Allowed : 19.58 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.15 (0.20), residues: 1523 helix: -0.79 (0.64), residues: 52 sheet: 0.04 (0.25), residues: 412 loop : -1.15 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 437 TYR 0.019 0.002 TYR A 217 PHE 0.019 0.002 PHE C 80 TRP 0.010 0.002 TRP B 520 HIS 0.002 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (12118) covalent geometry : angle 0.68478 / 0.35 (16612) hydrogen bonds : bond 0.04623 / 3.20 ( 305) hydrogen bonds : angle 5.55815 / 3.87 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 150 time to evaluate : 0.388 Fit side-chains REVERT: A 238 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7035 (mtp85) REVERT: A 338 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: A 340 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7010 (tp40) REVERT: B 22 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7696 (t) REVERT: B 367 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6443 (mt0) REVERT: C 175 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7905 (tp40) REVERT: C 289 PHE cc_start: 0.8138 (p90) cc_final: 0.7893 (p90) REVERT: C 390 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6677 (ttp-170) REVERT: C 416 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7543 (pp) outliers start: 92 outliers final: 56 residues processed: 216 average time/residue: 0.4817 time to fit residues: 113.5480 Evaluate side-chains 213 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 129 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 261 ASN B 334 GLN B 367 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.179604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116642 restraints weight = 11936.918| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.67 r_work: 0.3228 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12118 Z= 0.151 Angle : 0.668 11.593 16612 Z= 0.342 Chirality : 0.047 0.224 1892 Planarity : 0.007 0.141 2174 Dihedral : 8.143 59.215 1705 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 6.13 % Allowed : 20.36 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.13 (0.20), residues: 1523 helix: -0.85 (0.64), residues: 52 sheet: 0.07 (0.24), residues: 410 loop : -1.14 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 478 TYR 0.019 0.002 TYR A 217 PHE 0.018 0.002 PHE C 80 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (12118) covalent geometry : angle 0.66835 / 0.34 (16612) hydrogen bonds : bond 0.04151 / 2.92 ( 305) hydrogen bonds : angle 5.44018 / 3.78 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 151 time to evaluate : 0.413 Fit side-chains REVERT: A 224 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.6968 (mtt-85) REVERT: A 238 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7105 (mtp85) REVERT: A 340 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7026 (tp40) REVERT: B 22 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7696 (t) REVERT: B 342 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: B 367 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6697 (mt0) REVERT: C 175 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: C 289 PHE cc_start: 0.8260 (p90) cc_final: 0.8030 (p90) REVERT: C 390 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6645 (ttp-170) outliers start: 78 outliers final: 46 residues processed: 204 average time/residue: 0.5194 time to fit residues: 115.4312 Evaluate side-chains 204 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 chunk 110 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 261 ASN B 402 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.180663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117027 restraints weight = 11919.042| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.66 r_work: 0.3243 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12118 Z= 0.121 Angle : 0.620 10.959 16612 Z= 0.315 Chirality : 0.046 0.220 1892 Planarity : 0.007 0.141 2174 Dihedral : 7.575 58.417 1695 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 5.50 % Allowed : 21.31 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.06 (0.20), residues: 1523 helix: -0.70 (0.65), residues: 52 sheet: 0.08 (0.24), residues: 416 loop : -1.08 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 478 TYR 0.014 0.001 TYR A 217 PHE 0.019 0.001 PHE C 80 TRP 0.010 0.001 TRP C 169 HIS 0.002 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (12118) covalent geometry : angle 0.62000 / 0.32 (16612) hydrogen bonds : bond 0.03657 / 2.57 ( 305) hydrogen bonds : angle 5.28664 / 3.66 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 151 time to evaluate : 0.428 Fit side-chains REVERT: A 224 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6939 (mtt-85) REVERT: A 238 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7101 (mtp85) REVERT: A 340 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6987 (tp40) REVERT: B 20 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6912 (p0) REVERT: B 22 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7679 (t) REVERT: B 254 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 407 GLU cc_start: 0.6955 (pm20) cc_final: 0.6357 (pt0) REVERT: B 512 ASP cc_start: 0.7781 (m-30) cc_final: 0.7324 (m-30) REVERT: C 155 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: C 175 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7884 (tp40) REVERT: C 289 PHE cc_start: 0.8268 (p90) cc_final: 0.8062 (p90) REVERT: C 390 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6652 (ttp-170) REVERT: C 416 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7686 (pp) outliers start: 70 outliers final: 42 residues processed: 198 average time/residue: 0.5105 time to fit residues: 109.9631 Evaluate side-chains 198 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 50.0000 chunk 107 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 261 ASN B 334 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112558 restraints weight = 11808.601| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.62 r_work: 0.3185 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12118 Z= 0.230 Angle : 0.775 12.454 16612 Z= 0.395 Chirality : 0.052 0.231 1892 Planarity : 0.008 0.145 2174 Dihedral : 7.780 58.152 1686 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.16 % Rotamer: Outliers : 6.29 % Allowed : 20.91 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.25 (0.19), residues: 1523 helix: -1.05 (0.64), residues: 52 sheet: 0.01 (0.24), residues: 409 loop : -1.23 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 180 TYR 0.027 0.002 TYR A 217 PHE 0.017 0.003 PHE B 59 TRP 0.010 0.002 TRP C 169 HIS 0.005 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.23 (12118) covalent geometry : angle 0.77471 / 0.40 (16612) hydrogen bonds : bond 0.04754 / 3.36 ( 305) hydrogen bonds : angle 5.50112 / 3.85 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 150 time to evaluate : 0.437 Fit side-chains REVERT: A 107 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8677 (mt-10) REVERT: A 238 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7017 (mtp85) REVERT: A 340 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: B 20 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7018 (p0) REVERT: B 22 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7694 (t) REVERT: B 28 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.5732 (mm-40) REVERT: B 166 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8375 (ptt90) REVERT: C 289 PHE cc_start: 0.8230 (p90) cc_final: 0.7996 (p90) REVERT: C 390 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6720 (ttp-170) REVERT: C 416 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7601 (pp) outliers start: 80 outliers final: 51 residues processed: 206 average time/residue: 0.5365 time to fit residues: 120.3231 Evaluate side-chains 209 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 261 ASN B 334 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.179032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117322 restraints weight = 11816.886| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.64 r_work: 0.3213 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12118 Z= 0.173 Angle : 0.705 11.998 16612 Z= 0.359 Chirality : 0.049 0.230 1892 Planarity : 0.007 0.143 2174 Dihedral : 7.484 57.994 1682 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.16 % Rotamer: Outliers : 5.90 % Allowed : 21.46 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.26 (0.20), residues: 1523 helix: -1.03 (0.63), residues: 52 sheet: -0.02 (0.24), residues: 414 loop : -1.22 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 180 TYR 0.022 0.002 TYR A 217 PHE 0.017 0.002 PHE C 80 TRP 0.010 0.002 TRP C 169 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.17 (12118) covalent geometry : angle 0.70465 / 0.36 (16612) hydrogen bonds : bond 0.04248 / 3.01 ( 305) hydrogen bonds : angle 5.43467 / 3.79 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 146 time to evaluate : 0.435 Fit side-chains REVERT: A 100 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8550 (t) REVERT: A 238 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: A 340 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7061 (tp40) REVERT: B 20 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6950 (OUTLIER) REVERT: B 22 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7722 (t) REVERT: B 166 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8403 (ptt90) REVERT: B 254 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8311 (p) REVERT: C 289 PHE cc_start: 0.8335 (p90) cc_final: 0.8108 (p90) REVERT: C 292 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6185 (mm-30) REVERT: C 390 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6183 (ttp-170) REVERT: C 416 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7838 (pp) outliers start: 75 outliers final: 51 residues processed: 202 average time/residue: 0.4961 time to fit residues: 109.2328 Evaluate side-chains 205 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 53 optimal weight: 0.0770 chunk 82 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 109 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 261 ASN B 402 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119085 restraints weight = 11933.156| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.74 r_work: 0.3246 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 12118 Z= 0.103 Angle : 0.595 11.850 16612 Z= 0.300 Chirality : 0.045 0.217 1892 Planarity : 0.007 0.140 2174 Dihedral : 6.813 56.136 1682 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.25 % Favored : 94.55 % Rotamer: Outliers : 4.56 % Allowed : 22.88 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.04 (0.20), residues: 1523 helix: -0.66 (0.66), residues: 52 sheet: 0.08 (0.24), residues: 417 loop : -1.06 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 478 TYR 0.014 0.001 TYR A 217 PHE 0.020 0.001 PHE C 80 TRP 0.010 0.001 TRP C 169 HIS 0.002 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (12118) covalent geometry : angle 0.59496 / 0.30 (16612) hydrogen bonds : bond 0.03294 / 2.32 ( 305) hydrogen bonds : angle 5.16152 / 3.58 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 153 time to evaluate : 0.402 Fit side-chains REVERT: A 238 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7041 (mtp85) REVERT: B 166 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8476 (ptt90) REVERT: B 357 MET cc_start: 0.8249 (ptt) cc_final: 0.7907 (ptt) REVERT: C 155 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: C 175 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7873 (tp40) REVERT: C 390 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6611 (ttp-170) REVERT: C 416 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7694 (pp) outliers start: 58 outliers final: 34 residues processed: 189 average time/residue: 0.5321 time to fit residues: 109.2851 Evaluate side-chains 189 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 99 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 88 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 138 optimal weight: 40.0000 chunk 107 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 261 ASN B 334 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.177901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112269 restraints weight = 11797.539| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.65 r_work: 0.3197 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12118 Z= 0.219 Angle : 0.764 12.368 16612 Z= 0.389 Chirality : 0.052 0.236 1892 Planarity : 0.008 0.144 2174 Dihedral : 6.915 56.301 1672 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.71 % Favored : 94.09 % Rotamer: Outliers : 5.03 % Allowed : 22.80 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.22 (0.20), residues: 1523 helix: -1.04 (0.63), residues: 52 sheet: 0.02 (0.24), residues: 409 loop : -1.20 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 152 TYR 0.026 0.002 TYR C 217 PHE 0.017 0.002 PHE B 59 TRP 0.009 0.002 TRP C 169 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (12118) covalent geometry : angle 0.76387 / 0.39 (16612) hydrogen bonds : bond 0.04630 / 3.29 ( 305) hydrogen bonds : angle 5.42774 / 3.80 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 146 time to evaluate : 0.424 Fit side-chains REVERT: A 100 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8431 (m) REVERT: A 238 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6978 (mtp85) REVERT: B 20 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7049 (p0) REVERT: B 22 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7661 (t) REVERT: B 28 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5827 (mm-40) REVERT: B 166 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8352 (ptt90) REVERT: C 175 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7950 (tp40) REVERT: C 390 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6736 (ttp-170) REVERT: C 416 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7534 (pp) outliers start: 64 outliers final: 42 residues processed: 194 average time/residue: 0.5162 time to fit residues: 109.3165 Evaluate side-chains 194 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 261 ASN B 402 GLN B 438 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.180240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114542 restraints weight = 11719.664| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.47 r_work: 0.3238 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12118 Z= 0.126 Angle : 0.641 11.350 16612 Z= 0.324 Chirality : 0.046 0.221 1892 Planarity : 0.007 0.141 2174 Dihedral : 6.530 55.639 1671 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 4.17 % Allowed : 23.66 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.20), residues: 1523 helix: -0.84 (0.64), residues: 52 sheet: 0.04 (0.24), residues: 419 loop : -1.13 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 478 TYR 0.016 0.001 TYR A 217 PHE 0.019 0.001 PHE C 80 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12118) covalent geometry : angle 0.64128 / 0.32 (16612) hydrogen bonds : bond 0.03673 / 2.60 ( 305) hydrogen bonds : angle 5.25249 / 3.65 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.438 Fit side-chains REVERT: A 238 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.7011 (mtp85) REVERT: A 340 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6943 (tp40) REVERT: B 166 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8433 (ptt90) REVERT: B 512 ASP cc_start: 0.7649 (m-30) cc_final: 0.7222 (m-30) REVERT: C 175 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7914 (tp40) REVERT: C 390 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6619 (ttp-170) outliers start: 53 outliers final: 38 residues processed: 190 average time/residue: 0.5434 time to fit residues: 112.3855 Evaluate side-chains 196 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 122 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118678 restraints weight = 11961.506| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.69 r_work: 0.3266 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 12118 Z= 0.098 Angle : 0.588 11.914 16612 Z= 0.294 Chirality : 0.045 0.217 1892 Planarity : 0.006 0.139 2174 Dihedral : 6.046 53.251 1671 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 3.14 % Allowed : 24.53 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -0.97 (0.20), residues: 1523 helix: -0.45 (0.67), residues: 52 sheet: 0.10 (0.24), residues: 414 loop : -1.00 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 478 TYR 0.013 0.001 TYR A 217 PHE 0.019 0.001 PHE C 80 TRP 0.011 0.001 TRP B 520 HIS 0.002 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (12118) covalent geometry : angle 0.58804 / 0.29 (16612) hydrogen bonds : bond 0.03101 / 2.19 ( 305) hydrogen bonds : angle 5.04107 / 3.49 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.488 Fit side-chains REVERT: A 238 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6602 (mtp85) REVERT: A 340 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6982 (tp40) REVERT: A 456 GLU cc_start: 0.7268 (mp0) cc_final: 0.6929 (mp0) REVERT: B 64 LEU cc_start: 0.8488 (tt) cc_final: 0.8266 (tp) REVERT: C 175 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: C 390 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6441 (ttp-170) outliers start: 40 outliers final: 32 residues processed: 178 average time/residue: 0.5702 time to fit residues: 110.0672 Evaluate side-chains 187 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 20.0000 chunk 129 optimal weight: 50.0000 chunk 151 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 402 GLN A 479 ASN B 402 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.179525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122831 restraints weight = 11883.863| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.29 r_work: 0.3228 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12118 Z= 0.163 Angle : 0.690 11.753 16612 Z= 0.349 Chirality : 0.048 0.232 1892 Planarity : 0.007 0.142 2174 Dihedral : 6.272 53.365 1667 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 3.85 % Allowed : 23.35 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.09 (0.20), residues: 1523 helix: -0.73 (0.65), residues: 52 sheet: 0.01 (0.24), residues: 413 loop : -1.08 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 478 TYR 0.022 0.002 TYR A 217 PHE 0.016 0.002 PHE C 80 TRP 0.009 0.002 TRP C 169 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (12118) covalent geometry : angle 0.69038 / 0.35 (16612) hydrogen bonds : bond 0.04006 / 2.85 ( 305) hydrogen bonds : angle 5.21968 / 3.64 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5221.06 seconds wall clock time: 89 minutes 24.30 seconds (5364.30 seconds total)