Starting phenix.real_space_refine on Tue Jun 10 15:01:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eao_47838/06_2025/9eao_47838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eao_47838/06_2025/9eao_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9eao_47838/06_2025/9eao_47838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eao_47838/06_2025/9eao_47838.map" model { file = "/net/cci-nas-00/data/ceres_data/9eao_47838/06_2025/9eao_47838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eao_47838/06_2025/9eao_47838.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.04, per 1000 atoms: 0.85 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: 2.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.50 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: 4.47 Time building geometry restraints manager: 3.19 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 530 or resid 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: 21.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.380 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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:15.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 4.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.19), 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 TRP 0.011 0.001 TRP C 169 HIS 0.002 0.001 HIS A 170 PHE 0.017 0.001 PHE C 80 TYR 0.016 0.001 TYR A 217 ARG 0.002 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.17064 ( 305) hydrogen bonds : angle 6.60433 ( 786) covalent geometry : bond 0.00286 (12118) covalent geometry : angle 0.62278 (16612) *********************** 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 : 1.287 Fit side-chains outliers start: 66 outliers final: 64 residues processed: 214 average time/residue: 1.1375 time to fit residues: 266.8329 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 : 1.232 ------------------------------------------------------------------------------- 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 128 optimal weight: 30.0000 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN B 334 GLN B 367 GLN B 402 GLN B 438 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 = 0.4006 r_free = 0.4006 target = 0.179381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114280 restraints weight = 11768.312| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.67 r_work: 0.3222 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0496 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= 0.160 Angle : 0.683 11.708 16612 Z= 0.350 Chirality : 0.048 0.227 1892 Planarity : 0.007 0.141 2174 Dihedral : 8.922 59.939 1743 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 7.31 % Allowed : 19.42 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1523 helix: -0.82 (0.64), residues: 52 sheet: 0.04 (0.24), residues: 430 loop : -1.14 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 520 HIS 0.002 0.001 HIS A 270 PHE 0.019 0.002 PHE C 80 TYR 0.019 0.002 TYR A 217 ARG 0.004 0.000 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 305) hydrogen bonds : angle 5.50012 ( 786) covalent geometry : bond 0.00388 (12118) covalent geometry : angle 0.68324 (16612) *********************** 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 243 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 150 time to evaluate : 1.470 Fit side-chains REVERT: A 238 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7029 (mtp85) REVERT: A 340 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7023 (tp40) REVERT: B 22 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7710 (t) REVERT: B 367 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: C 175 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7923 (tp40) REVERT: C 289 PHE cc_start: 0.8154 (p90) cc_final: 0.7909 (p90) REVERT: C 390 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6659 (ttp-170) REVERT: C 416 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7571 (pp) outliers start: 93 outliers final: 51 residues processed: 217 average time/residue: 1.1962 time to fit residues: 283.4407 Evaluate side-chains 206 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 279 THR 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 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 147 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 28 optimal weight: 30.0000 chunk 109 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3991 r_free = 0.3991 target = 0.177886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111620 restraints weight = 11902.776| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.47 r_work: 0.3197 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0733 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= 0.213 Angle : 0.758 12.484 16612 Z= 0.389 Chirality : 0.051 0.233 1892 Planarity : 0.008 0.143 2174 Dihedral : 8.432 59.280 1704 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.52 % Favored : 94.29 % Rotamer: Outliers : 6.76 % Allowed : 19.58 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1523 helix: -1.05 (0.63), residues: 52 sheet: 0.03 (0.24), residues: 408 loop : -1.24 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 169 HIS 0.004 0.001 HIS C 170 PHE 0.017 0.002 PHE C 80 TYR 0.025 0.002 TYR C 217 ARG 0.004 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 305) hydrogen bonds : angle 5.57912 ( 786) covalent geometry : bond 0.00528 (12118) covalent geometry : angle 0.75794 (16612) *********************** 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 237 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 151 time to evaluate : 1.202 Fit side-chains REVERT: A 100 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8415 (m) REVERT: A 224 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6895 (mtt-85) REVERT: A 238 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6974 (mtp85) REVERT: A 340 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: B 22 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7665 (t) REVERT: B 342 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: B 367 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6625 (mt0) REVERT: C 289 PHE cc_start: 0.8166 (p90) cc_final: 0.7946 (p90) REVERT: C 390 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6686 (ttp-170) outliers start: 86 outliers final: 53 residues processed: 209 average time/residue: 1.3211 time to fit residues: 301.8030 Evaluate side-chains 208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 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 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 A residue 530 VAL 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 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 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 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 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 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 353 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 387 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 Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN B 261 ASN 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 = 0.4005 r_free = 0.4005 target = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114374 restraints weight = 11828.568| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.73 r_work: 0.3216 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12118 Z= 0.149 Angle : 0.670 11.852 16612 Z= 0.342 Chirality : 0.047 0.225 1892 Planarity : 0.007 0.142 2174 Dihedral : 7.823 58.547 1694 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.58 % Favored : 94.22 % Rotamer: Outliers : 6.13 % Allowed : 20.91 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1523 helix: -0.93 (0.64), residues: 52 sheet: 0.02 (0.24), residues: 413 loop : -1.18 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 170 PHE 0.018 0.002 PHE C 80 TYR 0.019 0.002 TYR A 217 ARG 0.003 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 305) hydrogen bonds : angle 5.42352 ( 786) covalent geometry : bond 0.00361 (12118) covalent geometry : angle 0.66974 (16612) *********************** 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 225 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 147 time to evaluate : 1.431 Fit side-chains REVERT: A 224 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.6867 (mtt-85) REVERT: A 238 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.7093 (mtp85) REVERT: A 340 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.6975 (tp40) REVERT: B 20 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6914 (OUTLIER) REVERT: B 22 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7691 (t) REVERT: B 166 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8402 (ptt90) REVERT: B 342 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: B 367 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6587 (mt0) REVERT: C 289 PHE cc_start: 0.8204 (p90) cc_final: 0.8003 (p90) REVERT: C 390 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6681 (ttp-170) REVERT: C 416 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7605 (pp) outliers start: 78 outliers final: 51 residues processed: 201 average time/residue: 1.6255 time to fit residues: 356.7285 Evaluate side-chains 208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 224 ARG Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 253 LEU 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 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 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 162 LEU Chi-restraints excluded: chain B residue 166 ARG 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 253 LEU 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 342 GLU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 405 ILE 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 303 GLU 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 387 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 0.0070 chunk 141 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 6.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3987 r_free = 0.3987 target = 0.177487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111361 restraints weight = 11807.925| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.51 r_work: 0.3200 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0852 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= 0.225 Angle : 0.776 12.724 16612 Z= 0.397 Chirality : 0.052 0.235 1892 Planarity : 0.008 0.144 2174 Dihedral : 7.814 58.284 1685 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.84 % Favored : 93.96 % Rotamer: Outliers : 7.23 % Allowed : 19.73 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1523 helix: -1.14 (0.63), residues: 52 sheet: -0.02 (0.24), residues: 409 loop : -1.28 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 169 HIS 0.005 0.001 HIS C 170 PHE 0.017 0.002 PHE B 59 TYR 0.027 0.002 TYR A 217 ARG 0.004 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 305) hydrogen bonds : angle 5.55039 ( 786) covalent geometry : bond 0.00559 (12118) covalent geometry : angle 0.77615 (16612) *********************** 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 241 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 149 time to evaluate : 1.419 Fit side-chains REVERT: A 107 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8657 (mt-10) REVERT: A 238 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7003 (mtp85) REVERT: A 340 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: B 20 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7003 (p0) REVERT: B 22 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7677 (t) REVERT: B 28 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5724 (mm-40) REVERT: B 166 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8374 (ptt90) REVERT: B 342 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: C 289 PHE cc_start: 0.8216 (p90) cc_final: 0.7987 (p90) REVERT: C 292 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6104 (mm-30) REVERT: C 390 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6266 (ttp-170) REVERT: C 416 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7571 (pp) outliers start: 92 outliers final: 64 residues processed: 216 average time/residue: 1.2793 time to fit residues: 302.1635 Evaluate side-chains 224 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 149 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR 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 387 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 516 GLU 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 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 162 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 174 ASP 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 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 341 THR Chi-restraints excluded: chain B residue 342 GLU 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 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 292 GLU Chi-restraints excluded: chain C residue 303 GLU 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 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 387 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 508 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 530 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 127 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4009 r_free = 0.4009 target = 0.179698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113964 restraints weight = 11923.435| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.56 r_work: 0.3227 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0745 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= 0.131 Angle : 0.648 11.680 16612 Z= 0.329 Chirality : 0.046 0.224 1892 Planarity : 0.007 0.142 2174 Dihedral : 7.360 57.283 1685 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.32 % Favored : 94.48 % Rotamer: Outliers : 6.13 % Allowed : 20.83 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1523 helix: -0.87 (0.65), residues: 52 sheet: 0.01 (0.24), residues: 419 loop : -1.18 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 170 PHE 0.019 0.002 PHE C 80 TYR 0.018 0.001 TYR A 217 ARG 0.003 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 305) hydrogen bonds : angle 5.34779 ( 786) covalent geometry : bond 0.00312 (12118) covalent geometry : angle 0.64752 (16612) *********************** 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 234 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 156 time to evaluate : 1.197 Fit side-chains REVERT: A 238 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.7023 (mtp85) REVERT: A 338 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 20 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6846 (OUTLIER) REVERT: B 22 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7656 (t) REVERT: B 166 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8459 (ptt90) REVERT: B 254 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8211 (p) REVERT: B 342 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: B 512 ASP cc_start: 0.7684 (m-30) cc_final: 0.7213 (m-30) REVERT: C 158 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8366 (mm-40) REVERT: C 175 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (tp40) REVERT: C 289 PHE cc_start: 0.8162 (p90) cc_final: 0.7954 (p90) REVERT: C 390 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6676 (ttp-170) outliers start: 78 outliers final: 52 residues processed: 209 average time/residue: 1.2522 time to fit residues: 286.8765 Evaluate side-chains 210 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 149 CYS 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 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 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 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 141 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 166 ARG 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 341 THR Chi-restraints excluded: chain B residue 342 GLU 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 158 GLN 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 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 374 VAL Chi-restraints excluded: chain C residue 387 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 82 optimal weight: 0.2980 chunk 22 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 28 optimal weight: 50.0000 chunk 67 optimal weight: 10.0000 chunk 77 optimal weight: 0.0270 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 371 GLN A 402 GLN B 261 ASN 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 = 0.4065 r_free = 0.4065 target = 0.185118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120992 restraints weight = 12137.799| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.62 r_work: 0.3326 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 12118 Z= 0.087 Angle : 0.552 11.196 16612 Z= 0.275 Chirality : 0.044 0.210 1892 Planarity : 0.006 0.138 2174 Dihedral : 6.285 54.543 1682 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.79 % Favored : 95.01 % Rotamer: Outliers : 4.09 % Allowed : 22.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1523 helix: -0.30 (0.67), residues: 52 sheet: 0.16 (0.24), residues: 428 loop : -0.93 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.001 0.000 HIS B 170 PHE 0.020 0.001 PHE C 80 TYR 0.011 0.001 TYR A 217 ARG 0.004 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 305) hydrogen bonds : angle 4.98968 ( 786) covalent geometry : bond 0.00203 (12118) covalent geometry : angle 0.55191 (16612) *********************** 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 207 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 1.312 Fit side-chains REVERT: A 214 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7924 (p0) REVERT: A 338 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 340 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6927 (tp40) REVERT: A 456 GLU cc_start: 0.7230 (mp0) cc_final: 0.6890 (mp0) REVERT: B 342 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: C 207 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8701 (t) REVERT: C 218 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8341 (mt) REVERT: C 390 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6377 (ttp-170) outliers start: 52 outliers final: 21 residues processed: 190 average time/residue: 1.2824 time to fit residues: 265.7275 Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 70 SER 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 162 LEU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 405 ILE 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 122 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 9.9990 chunk 51 optimal weight: 0.0020 chunk 13 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 20 optimal weight: 0.0050 chunk 138 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 chunk 112 optimal weight: 0.5980 chunk 126 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 overall best weight: 2.9206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 371 GLN A 402 GLN A 479 ASN B 334 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 = 0.4023 r_free = 0.4023 target = 0.180883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115633 restraints weight = 11970.433| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.56 r_work: 0.3239 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12118 Z= 0.131 Angle : 0.631 11.150 16612 Z= 0.319 Chirality : 0.046 0.226 1892 Planarity : 0.007 0.141 2174 Dihedral : 5.907 53.892 1665 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 3.38 % Allowed : 23.58 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.20), residues: 1523 helix: -0.45 (0.67), residues: 52 sheet: 0.08 (0.24), residues: 418 loop : -0.97 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 520 HIS 0.003 0.001 HIS C 170 PHE 0.016 0.002 PHE C 80 TYR 0.015 0.001 TYR A 217 ARG 0.003 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 305) hydrogen bonds : angle 5.10828 ( 786) covalent geometry : bond 0.00317 (12118) covalent geometry : angle 0.63139 (16612) *********************** 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 196 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 1.436 Fit side-chains REVERT: A 340 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6874 (tp40) REVERT: A 359 LEU cc_start: 0.7834 (mt) cc_final: 0.7621 (mt) REVERT: B 166 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8473 (ptt90) REVERT: B 342 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: B 357 MET cc_start: 0.8163 (ptt) cc_final: 0.7837 (ptt) REVERT: C 155 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: C 175 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7879 (tp40) REVERT: C 390 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6668 (ttp-170) outliers start: 43 outliers final: 26 residues processed: 184 average time/residue: 1.4944 time to fit residues: 297.3849 Evaluate side-chains 182 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 362 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 453 LEU 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 148 MET Chi-restraints excluded: chain B residue 162 LEU 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 342 GLU 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 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 260 SER Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 485 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 371 GLN A 402 GLN A 479 ASN B 261 ASN B 334 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116799 restraints weight = 11903.171| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.76 r_work: 0.3217 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12118 Z= 0.137 Angle : 0.652 11.313 16612 Z= 0.330 Chirality : 0.047 0.230 1892 Planarity : 0.007 0.141 2174 Dihedral : 6.029 53.013 1665 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.32 % Favored : 94.48 % Rotamer: Outliers : 4.48 % Allowed : 22.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1523 helix: -0.65 (0.65), residues: 52 sheet: 0.08 (0.25), residues: 403 loop : -1.00 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.003 0.001 HIS C 170 PHE 0.016 0.002 PHE C 80 TYR 0.016 0.001 TYR A 217 ARG 0.003 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 305) hydrogen bonds : angle 5.17215 ( 786) covalent geometry : bond 0.00330 (12118) covalent geometry : angle 0.65219 (16612) *********************** 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 208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 1.338 Fit side-chains REVERT: A 238 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6646 (mtp85) REVERT: A 340 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6930 (tp40) REVERT: A 359 LEU cc_start: 0.7909 (mt) cc_final: 0.7697 (mt) REVERT: B 166 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8485 (ptt90) REVERT: C 155 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: C 175 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7886 (tp40) REVERT: C 390 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6660 (ttp-170) outliers start: 57 outliers final: 35 residues processed: 191 average time/residue: 1.7873 time to fit residues: 373.2629 Evaluate side-chains 190 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 335 LEU 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 362 THR Chi-restraints excluded: chain A residue 374 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 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 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 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 70 SER Chi-restraints excluded: chain C residue 103 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 260 SER Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 119 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 371 GLN A 402 GLN A 479 ASN 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 = 0.4039 r_free = 0.4039 target = 0.182467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117114 restraints weight = 11915.118| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.48 r_work: 0.3277 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 12118 Z= 0.100 Angle : 0.583 10.751 16612 Z= 0.294 Chirality : 0.045 0.225 1892 Planarity : 0.006 0.140 2174 Dihedral : 5.715 51.221 1665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.06 % Favored : 94.75 % Rotamer: Outliers : 3.54 % Allowed : 23.35 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1523 helix: -0.40 (0.67), residues: 52 sheet: 0.09 (0.24), residues: 416 loop : -0.93 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 520 HIS 0.003 0.001 HIS C 170 PHE 0.018 0.001 PHE C 80 TYR 0.013 0.001 TYR A 217 ARG 0.003 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 305) hydrogen bonds : angle 5.03615 ( 786) covalent geometry : bond 0.00235 (12118) covalent geometry : angle 0.58250 (16612) ********************** 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 197 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.383 Fit side-chains REVERT: A 238 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6401 (mtp85) REVERT: A 340 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6853 (tp40) REVERT: A 359 LEU cc_start: 0.7788 (mt) cc_final: 0.7576 (mt) REVERT: C 175 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7823 (tp40) REVERT: C 390 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6576 (ttp-170) outliers start: 45 outliers final: 34 residues processed: 183 average time/residue: 1.3341 time to fit residues: 264.3677 Evaluate side-chains 185 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 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 362 THR Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 385 ASP 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 28 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 ARG 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 162 LEU 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 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 122 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 30.0000 chunk 129 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN A 479 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 = 0.4012 r_free = 0.4012 target = 0.179891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113952 restraints weight = 11850.940| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.55 r_work: 0.3237 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12118 Z= 0.159 Angle : 0.686 11.702 16612 Z= 0.347 Chirality : 0.048 0.231 1892 Planarity : 0.007 0.141 2174 Dihedral : 5.974 51.786 1663 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 3.69 % Allowed : 23.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1523 helix: -0.69 (0.65), residues: 52 sheet: 0.04 (0.24), residues: 413 loop : -1.02 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.004 0.001 HIS C 170 PHE 0.016 0.002 PHE C 80 TYR 0.021 0.002 TYR A 217 ARG 0.007 0.000 ARG C 478 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 305) hydrogen bonds : angle 5.16472 ( 786) covalent geometry : bond 0.00387 (12118) covalent geometry : angle 0.68557 (16612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12814.58 seconds wall clock time: 227 minutes 1.52 seconds (13621.52 seconds total)