Starting phenix.real_space_refine on Wed Sep 17 22:23:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eaq_47840/09_2025/9eaq_47840.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eaq_47840/09_2025/9eaq_47840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eaq_47840/09_2025/9eaq_47840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eaq_47840/09_2025/9eaq_47840.map" model { file = "/net/cci-nas-00/data/ceres_data/9eaq_47840/09_2025/9eaq_47840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eaq_47840/09_2025/9eaq_47840.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7604 2.51 5 N 1942 2.21 5 O 2205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11799 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3953 Classifications: {'peptide': 515} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} 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: "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} Time building chain proxies: 2.66, per 1000 atoms: 0.23 Number of scatterers: 11799 At special positions: 0 Unit cell: (118.8, 117.7, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2205 8.00 N 1942 7.00 C 7604 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: 1.32 Conformation dependent library (CDL) restraints added in 832.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 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: 26 helices and 19 sheets defined 9.8% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.550A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.995A pdb=" N ASN A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.537A pdb=" N LEU A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' 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: 3.792A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.520A pdb=" N CYS A 240 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 52 through 58 removed outlier: 4.076A pdb=" N ASN B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.525A 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 140 through 144 removed outlier: 3.560A 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: 3.693A pdb=" N TRP B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.798A 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 454 through 465 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.612A 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: 3.632A pdb=" N GLN C 57 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 3.777A 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 137 through 142 removed outlier: 4.014A pdb=" N THR C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.519A pdb=" N TRP C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 282 through 286' 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: 12.550A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.550A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 6.829A pdb=" N CYS A 183 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A 81 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A 181 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 121 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 119 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451 removed outlier: 4.412A pdb=" N LEU A 252 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451 removed outlier: 5.212A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 496 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 487 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 472 " --> pdb=" O TRP A 520 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP A 520 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 6.786A 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 296 removed outlier: 4.144A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 303 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER A 332 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 400 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN A 334 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE A 398 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU A 336 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 394 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN A 340 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG A 392 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.658A 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: 12.826A pdb=" N GLN B 61 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N SER B 207 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 5.045A 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: 6.937A pdb=" N ILE B 78 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 185 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 80 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS B 121 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA B 119 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 103 removed outlier: 6.335A pdb=" N TYR B 99 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 218 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY B 101 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 448 through 451 removed outlier: 4.241A pdb=" N LEU B 252 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 448 through 451 removed outlier: 5.339A pdb=" N ILE B 497 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR B 477 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 488 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 475 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS B 490 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 473 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 474 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 358 removed outlier: 4.538A pdb=" N GLN B 334 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY B 400 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 336 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 398 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU B 338 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG B 396 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N GLN B 340 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N VAL B 394 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N GLU B 342 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 13.258A pdb=" N ARG B 392 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.692A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.692A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.725A pdb=" N ILE C 78 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 185 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 449 through 451 removed outlier: 3.510A pdb=" N GLY C 251 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU C 252 " --> pdb=" O PHE C 509 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 351 through 358 removed outlier: 3.819A pdb=" N THR C 353 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 339 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLN C 334 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLY C 400 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU C 336 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 398 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N GLU C 338 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG C 396 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN C 340 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N VAL C 394 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 427 through 429 removed outlier: 3.768A pdb=" N ALA C 472 " --> pdb=" O VAL C 521 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 485 through 487 removed outlier: 7.161A pdb=" N TYR C 477 " --> pdb=" O LEU C 486 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3845 1.34 - 1.46: 2510 1.46 - 1.58: 5698 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 12125 Sorted by residual: bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 bond pdb=" CA ASP B 174 " pdb=" CB ASP B 174 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.59e+00 bond pdb=" CG PRO B 23 " pdb=" CD PRO B 23 " ideal model delta sigma weight residual 1.503 1.546 -0.043 3.40e-02 8.65e+02 1.57e+00 bond pdb=" CB ASP B 174 " pdb=" CG ASP B 174 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" C VAL B 22 " pdb=" N PRO B 23 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.12e+00 ... (remaining 12120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 16580 3.27 - 6.53: 42 6.53 - 9.80: 2 9.80 - 13.06: 1 13.06 - 16.33: 1 Bond angle restraints: 16626 Sorted by residual: angle pdb=" CA LEU B 64 " pdb=" CB LEU B 64 " pdb=" CG LEU B 64 " ideal model delta sigma weight residual 116.30 132.63 -16.33 3.50e+00 8.16e-02 2.18e+01 angle pdb=" CA PRO B 23 " pdb=" N PRO B 23 " pdb=" CD PRO B 23 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA LEU B 112 " pdb=" CB LEU B 112 " pdb=" CG LEU B 112 " ideal model delta sigma weight residual 116.30 127.60 -11.30 3.50e+00 8.16e-02 1.04e+01 angle pdb=" C GLN B 173 " pdb=" N ASP B 174 " pdb=" CA ASP B 174 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" N PRO B 23 " pdb=" CA PRO B 23 " pdb=" C PRO B 23 " ideal model delta sigma weight residual 112.47 117.60 -5.13 2.06e+00 2.36e-01 6.20e+00 ... (remaining 16621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 6143 17.29 - 34.58: 746 34.58 - 51.87: 212 51.87 - 69.16: 72 69.16 - 86.45: 20 Dihedral angle restraints: 7193 sinusoidal: 2762 harmonic: 4431 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 180.00 146.96 33.04 0 5.00e+00 4.00e-02 4.37e+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 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+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 -24.55 24.55 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 7190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1445 0.044 - 0.088: 287 0.088 - 0.133: 158 0.133 - 0.177: 1 0.177 - 0.221: 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 1.22e+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 -2.45 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE A 157 " pdb=" N ILE A 157 " pdb=" C ILE A 157 " pdb=" CB ILE A 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1889 not shown) Planarity restraints: 2178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 22 " -0.091 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO B 23 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 196 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" CG ASP B 196 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP B 196 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 196 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 128 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO C 129 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.032 5.00e-02 4.00e+02 ... (remaining 2175 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3017 2.80 - 3.33: 9250 3.33 - 3.85: 18218 3.85 - 4.38: 21308 4.38 - 4.90: 37830 Nonbonded interactions: 89623 Sorted by model distance: nonbonded pdb=" NH1 ARG A 224 " pdb=" O SER A 463 " model vdw 2.279 3.120 nonbonded pdb=" OH TYR A 501 " pdb=" O GLY A 505 " model vdw 2.293 3.040 nonbonded pdb=" O ASP C 150 " pdb=" OG1 THR C 153 " model vdw 2.355 3.040 nonbonded pdb=" O ASP A 150 " pdb=" OG1 THR A 153 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG C 244 " pdb=" OD1 ASP C 330 " model vdw 2.384 3.120 ... (remaining 89618 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) selection = (chain 'B' and resid 27 through 530) 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: 13.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.002 0.074 12125 Z= 0.103 Angle : 0.572 16.328 16626 Z= 0.289 Chirality : 0.044 0.221 1892 Planarity : 0.006 0.137 2178 Dihedral : 17.465 86.445 4351 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 4.09 % Allowed : 24.29 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1529 helix: -0.06 (0.70), residues: 51 sheet: 0.30 (0.23), residues: 458 loop : -1.00 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.012 0.001 TYR C 496 PHE 0.020 0.001 PHE C 80 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00233 (12125) covalent geometry : angle 0.57190 (16626) hydrogen bonds : bond 0.16964 ( 304) hydrogen bonds : angle 7.85689 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 0.448 Fit side-chains REVERT: A 437 ARG cc_start: 0.7158 (mtm-85) cc_final: 0.5385 (ttt-90) REVERT: B 310 ILE cc_start: 0.5471 (OUTLIER) cc_final: 0.5182 (pp) REVERT: C 523 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7527 (ttm170) outliers start: 52 outliers final: 45 residues processed: 159 average time/residue: 0.5764 time to fit residues: 99.6363 Evaluate side-chains 150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 138 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 530 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 270 HIS A 469 GLN A 493 ASN B 340 GLN B 438 GLN C 261 ASN C 263 GLN C 265 GLN C 270 HIS C 493 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.222218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.148477 restraints weight = 10728.383| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 5.73 r_work: 0.2753 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12125 Z= 0.158 Angle : 0.655 13.297 16626 Z= 0.332 Chirality : 0.047 0.233 1892 Planarity : 0.007 0.138 2178 Dihedral : 7.791 69.449 1723 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 4.80 % Allowed : 22.80 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.20), residues: 1529 helix: -0.82 (0.62), residues: 52 sheet: 0.30 (0.23), residues: 436 loop : -1.04 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 392 TYR 0.019 0.002 TYR B 217 PHE 0.020 0.002 PHE C 80 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00389 (12125) covalent geometry : angle 0.65469 (16626) hydrogen bonds : bond 0.04016 ( 304) hydrogen bonds : angle 6.09952 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 105 time to evaluate : 0.488 Fit side-chains REVERT: A 437 ARG cc_start: 0.6002 (mtm-85) cc_final: 0.3325 (ttt-90) REVERT: A 501 TYR cc_start: 0.6751 (t80) cc_final: 0.6519 (t80) REVERT: B 175 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: B 516 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: C 176 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: C 238 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6334 (ptp90) REVERT: C 523 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.7139 (ttm170) outliers start: 61 outliers final: 35 residues processed: 155 average time/residue: 0.5953 time to fit residues: 100.4643 Evaluate side-chains 138 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE 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 154 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 530 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 0.0370 chunk 127 optimal weight: 0.0870 chunk 33 optimal weight: 30.0000 chunk 109 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 129 optimal weight: 40.0000 chunk 15 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 42 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 overall best weight: 4.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 438 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.222042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.151701 restraints weight = 10828.599| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.82 r_work: 0.2791 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12125 Z= 0.167 Angle : 0.664 14.319 16626 Z= 0.337 Chirality : 0.047 0.235 1892 Planarity : 0.007 0.139 2178 Dihedral : 6.993 58.506 1686 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.56 % Favored : 94.31 % Rotamer: Outliers : 4.72 % Allowed : 22.72 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.20), residues: 1529 helix: -1.15 (0.60), residues: 52 sheet: 0.25 (0.24), residues: 438 loop : -1.08 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.021 0.002 TYR A 217 PHE 0.018 0.002 PHE C 80 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00416 (12125) covalent geometry : angle 0.66382 (16626) hydrogen bonds : bond 0.04004 ( 304) hydrogen bonds : angle 5.90429 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 102 time to evaluate : 0.457 Fit side-chains REVERT: A 349 LYS cc_start: 0.4371 (OUTLIER) cc_final: 0.2940 (pttp) REVERT: B 175 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: B 371 GLN cc_start: 0.4314 (OUTLIER) cc_final: 0.4022 (pm20) REVERT: B 516 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: C 523 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7171 (ttm170) outliers start: 60 outliers final: 34 residues processed: 152 average time/residue: 0.6219 time to fit residues: 102.5715 Evaluate side-chains 140 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE 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 154 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 40.0000 chunk 125 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 105 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 438 GLN C 270 HIS C 493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.223036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.154384 restraints weight = 10776.068| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.71 r_work: 0.2811 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12125 Z= 0.124 Angle : 0.610 14.471 16626 Z= 0.308 Chirality : 0.045 0.225 1892 Planarity : 0.006 0.138 2178 Dihedral : 6.458 58.477 1676 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 4.40 % Allowed : 22.80 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1529 helix: -0.91 (0.62), residues: 52 sheet: 0.26 (0.24), residues: 437 loop : -1.04 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.015 0.001 TYR A 217 PHE 0.020 0.001 PHE C 80 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00304 (12125) covalent geometry : angle 0.61042 (16626) hydrogen bonds : bond 0.03440 ( 304) hydrogen bonds : angle 5.70092 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 109 time to evaluate : 0.470 Fit side-chains REVERT: A 106 MET cc_start: 0.9104 (mtp) cc_final: 0.8816 (mtm) REVERT: A 349 LYS cc_start: 0.4258 (OUTLIER) cc_final: 0.2857 (pttp) REVERT: B 371 GLN cc_start: 0.4095 (OUTLIER) cc_final: 0.3868 (pm20) REVERT: B 516 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: C 397 SER cc_start: 0.7435 (OUTLIER) cc_final: 0.7172 (t) REVERT: C 412 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6599 (pp) REVERT: C 523 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7167 (ttm170) outliers start: 56 outliers final: 34 residues processed: 157 average time/residue: 0.6241 time to fit residues: 106.3885 Evaluate side-chains 143 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE 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 138 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 86 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 438 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.222786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.130365 restraints weight = 10789.334| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 10.47 r_work: 0.2779 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12125 Z= 0.127 Angle : 0.615 15.203 16626 Z= 0.309 Chirality : 0.045 0.230 1892 Planarity : 0.006 0.138 2178 Dihedral : 6.411 59.789 1676 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 4.01 % Allowed : 23.90 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.20), residues: 1529 helix: -0.87 (0.63), residues: 52 sheet: 0.29 (0.24), residues: 436 loop : -1.04 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 166 TYR 0.017 0.001 TYR A 217 PHE 0.019 0.001 PHE C 80 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00312 (12125) covalent geometry : angle 0.61491 (16626) hydrogen bonds : bond 0.03419 ( 304) hydrogen bonds : angle 5.59157 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 0.458 Fit side-chains REVERT: A 106 MET cc_start: 0.9163 (mtp) cc_final: 0.8872 (mtm) REVERT: A 349 LYS cc_start: 0.4224 (OUTLIER) cc_final: 0.2834 (pttm) REVERT: A 437 ARG cc_start: 0.5918 (mtm-85) cc_final: 0.5070 (ptt90) REVERT: B 371 GLN cc_start: 0.4112 (OUTLIER) cc_final: 0.3816 (pm20) REVERT: B 516 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6299 (mp0) REVERT: C 397 SER cc_start: 0.7500 (OUTLIER) cc_final: 0.7199 (t) outliers start: 51 outliers final: 33 residues processed: 150 average time/residue: 0.5759 time to fit residues: 94.2596 Evaluate side-chains 141 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 138 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 120 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 94 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 438 GLN C 270 HIS C 493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.220623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.150131 restraints weight = 10743.459| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.79 r_work: 0.2764 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 12125 Z= 0.224 Angle : 0.733 15.386 16626 Z= 0.372 Chirality : 0.050 0.247 1892 Planarity : 0.007 0.140 2178 Dihedral : 6.729 57.786 1674 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % Rotamer: Outliers : 4.95 % Allowed : 22.80 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.20), residues: 1529 helix: -1.44 (0.61), residues: 52 sheet: 0.25 (0.24), residues: 436 loop : -1.16 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 523 TYR 0.027 0.002 TYR A 217 PHE 0.018 0.002 PHE C 80 TRP 0.011 0.002 TRP B 102 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00560 (12125) covalent geometry : angle 0.73250 (16626) hydrogen bonds : bond 0.04295 ( 304) hydrogen bonds : angle 5.81633 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 102 time to evaluate : 0.421 Fit side-chains REVERT: A 82 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8550 (mt) REVERT: A 349 LYS cc_start: 0.4251 (OUTLIER) cc_final: 0.2776 (pttm) REVERT: B 142 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8426 (m) REVERT: B 175 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: B 512 ASP cc_start: 0.8059 (m-30) cc_final: 0.7341 (m-30) REVERT: B 516 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: C 238 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6028 (ptp90) REVERT: C 523 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.7274 (ttm170) outliers start: 63 outliers final: 38 residues processed: 154 average time/residue: 0.6014 time to fit residues: 100.8022 Evaluate side-chains 145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 82 LEU 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 138 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 530 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 238 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 139 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 109 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 chunk 12 optimal weight: 0.1980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 493 ASN B 438 GLN C 270 HIS C 493 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.224413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.158447 restraints weight = 10801.978| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 4.57 r_work: 0.2845 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 12125 Z= 0.095 Angle : 0.572 16.038 16626 Z= 0.286 Chirality : 0.044 0.225 1892 Planarity : 0.006 0.137 2178 Dihedral : 5.851 56.975 1671 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 2.99 % Allowed : 24.92 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.20), residues: 1529 helix: -0.75 (0.64), residues: 52 sheet: 0.28 (0.24), residues: 437 loop : -1.00 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.013 0.001 TYR A 496 PHE 0.025 0.001 PHE C 80 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00228 (12125) covalent geometry : angle 0.57180 (16626) hydrogen bonds : bond 0.02942 ( 304) hydrogen bonds : angle 5.44083 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.462 Fit side-chains REVERT: A 349 LYS cc_start: 0.4329 (OUTLIER) cc_final: 0.2950 (pttm) REVERT: A 437 ARG cc_start: 0.5966 (mtm-85) cc_final: 0.5308 (ptt90) REVERT: B 21 LEU cc_start: 0.7921 (mt) cc_final: 0.7530 (mt) REVERT: B 142 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 175 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: C 317 TYR cc_start: 0.7503 (t80) cc_final: 0.7234 (t80) REVERT: C 397 SER cc_start: 0.7632 (OUTLIER) cc_final: 0.7305 (t) REVERT: C 457 PHE cc_start: 0.7487 (m-10) cc_final: 0.7286 (m-80) REVERT: C 523 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7249 (ttm170) outliers start: 38 outliers final: 23 residues processed: 144 average time/residue: 0.6071 time to fit residues: 94.8495 Evaluate side-chains 137 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 154 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 530 VAL 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 397 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 88 optimal weight: 50.0000 chunk 4 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 493 ASN B 438 GLN C 270 HIS C 493 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.224611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157647 restraints weight = 10752.316| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.68 r_work: 0.2840 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 12125 Z= 0.096 Angle : 0.570 15.613 16626 Z= 0.285 Chirality : 0.044 0.225 1892 Planarity : 0.006 0.137 2178 Dihedral : 5.678 57.389 1670 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 3.14 % Allowed : 24.92 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1529 helix: -0.49 (0.64), residues: 52 sheet: 0.34 (0.24), residues: 433 loop : -0.96 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.018 0.001 TYR A 496 PHE 0.021 0.001 PHE C 80 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00231 (12125) covalent geometry : angle 0.57037 (16626) hydrogen bonds : bond 0.02943 ( 304) hydrogen bonds : angle 5.35342 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.374 Fit side-chains REVERT: A 349 LYS cc_start: 0.4174 (OUTLIER) cc_final: 0.2898 (pttm) REVERT: A 437 ARG cc_start: 0.5873 (mtm-85) cc_final: 0.5268 (ptt90) REVERT: B 21 LEU cc_start: 0.7975 (mt) cc_final: 0.7555 (mt) REVERT: B 142 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8454 (p) REVERT: B 175 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: B 512 ASP cc_start: 0.8083 (m-30) cc_final: 0.7736 (m-30) REVERT: C 317 TYR cc_start: 0.7451 (t80) cc_final: 0.7176 (t80) REVERT: C 397 SER cc_start: 0.7602 (OUTLIER) cc_final: 0.7246 (t) REVERT: C 457 PHE cc_start: 0.7435 (m-10) cc_final: 0.7196 (m-10) REVERT: C 523 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7218 (ttm170) outliers start: 40 outliers final: 27 residues processed: 145 average time/residue: 0.5558 time to fit residues: 88.0491 Evaluate side-chains 143 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 530 VAL 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 397 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 4 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 73 optimal weight: 0.0370 chunk 151 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 20 optimal weight: 0.7980 chunk 78 optimal weight: 50.0000 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 438 GLN C 270 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.224289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.131656 restraints weight = 10707.549| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 11.22 r_work: 0.2820 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12125 Z= 0.104 Angle : 0.583 16.164 16626 Z= 0.291 Chirality : 0.044 0.225 1892 Planarity : 0.006 0.136 2178 Dihedral : 5.647 57.401 1669 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.10 % Favored : 94.77 % Rotamer: Outliers : 3.07 % Allowed : 25.16 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.20), residues: 1529 helix: -0.41 (0.65), residues: 52 sheet: 0.32 (0.24), residues: 437 loop : -0.94 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.019 0.001 TYR A 496 PHE 0.020 0.001 PHE C 80 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00252 (12125) covalent geometry : angle 0.58295 (16626) hydrogen bonds : bond 0.03031 ( 304) hydrogen bonds : angle 5.34255 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.510 Fit side-chains REVERT: A 349 LYS cc_start: 0.3886 (OUTLIER) cc_final: 0.2752 (pttm) REVERT: A 437 ARG cc_start: 0.5777 (mtm-85) cc_final: 0.5052 (ptt90) REVERT: B 21 LEU cc_start: 0.8097 (mt) cc_final: 0.7666 (mt) REVERT: B 142 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8438 (m) REVERT: B 175 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: C 317 TYR cc_start: 0.7447 (t80) cc_final: 0.7156 (t80) REVERT: C 397 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7206 (t) REVERT: C 457 PHE cc_start: 0.7413 (m-10) cc_final: 0.7169 (m-10) REVERT: C 523 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.7138 (ttm170) outliers start: 39 outliers final: 28 residues processed: 145 average time/residue: 0.6027 time to fit residues: 94.9684 Evaluate side-chains 145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 530 VAL 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 397 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 chunk 59 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 438 GLN C 270 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.224819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.160910 restraints weight = 10864.673| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 4.40 r_work: 0.2840 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 12125 Z= 0.097 Angle : 0.570 15.924 16626 Z= 0.284 Chirality : 0.044 0.222 1892 Planarity : 0.006 0.136 2178 Dihedral : 5.542 57.524 1669 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.90 % Rotamer: Outliers : 2.83 % Allowed : 25.31 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.21), residues: 1529 helix: -0.26 (0.66), residues: 52 sheet: 0.31 (0.24), residues: 439 loop : -0.91 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.021 0.001 TYR A 496 PHE 0.021 0.001 PHE C 80 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00233 (12125) covalent geometry : angle 0.56997 (16626) hydrogen bonds : bond 0.02917 ( 304) hydrogen bonds : angle 5.29279 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.351 Fit side-chains REVERT: A 241 THR cc_start: 0.5696 (OUTLIER) cc_final: 0.5265 (t) REVERT: A 311 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6972 (mm-30) REVERT: A 349 LYS cc_start: 0.3885 (OUTLIER) cc_final: 0.2818 (pttm) REVERT: A 437 ARG cc_start: 0.6153 (mtm-85) cc_final: 0.5395 (ptt90) REVERT: B 21 LEU cc_start: 0.7984 (mt) cc_final: 0.7544 (mt) REVERT: B 142 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8403 (m) REVERT: B 512 ASP cc_start: 0.8002 (m-30) cc_final: 0.7719 (m-30) REVERT: C 317 TYR cc_start: 0.7532 (t80) cc_final: 0.7265 (t80) REVERT: C 397 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7324 (t) REVERT: C 457 PHE cc_start: 0.7585 (m-10) cc_final: 0.7345 (m-80) REVERT: C 523 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7230 (ttm170) outliers start: 36 outliers final: 25 residues processed: 143 average time/residue: 0.5753 time to fit residues: 89.3188 Evaluate side-chains 140 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 530 VAL 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 397 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 0.0170 chunk 132 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 overall best weight: 4.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN C 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.222016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.156312 restraints weight = 10827.061| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 4.74 r_work: 0.2773 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12125 Z= 0.167 Angle : 0.669 15.903 16626 Z= 0.336 Chirality : 0.047 0.237 1892 Planarity : 0.006 0.138 2178 Dihedral : 5.979 57.025 1669 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.51 % Rotamer: Outliers : 2.99 % Allowed : 25.16 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.20), residues: 1529 helix: -0.82 (0.63), residues: 52 sheet: 0.30 (0.24), residues: 438 loop : -1.01 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 523 TYR 0.020 0.002 TYR A 496 PHE 0.015 0.002 PHE C 80 TRP 0.011 0.002 TRP B 102 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00415 (12125) covalent geometry : angle 0.66879 (16626) hydrogen bonds : bond 0.03717 ( 304) hydrogen bonds : angle 5.54324 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4860.34 seconds wall clock time: 83 minutes 19.45 seconds (4999.45 seconds total)