Starting phenix.real_space_refine on Tue Sep 24 21:23:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/09_2024/7z0z_14435.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/09_2024/7z0z_14435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/09_2024/7z0z_14435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/09_2024/7z0z_14435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/09_2024/7z0z_14435.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0z_14435/09_2024/7z0z_14435.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 29130 atoms to isotropic. 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 114 5.16 5 C 19122 2.51 5 N 4722 2.21 5 O 5508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 29466 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 9.07, per 1000 atoms: 0.31 Number of scatterers: 29466 At special positions: 0 Unit cell: (163.18, 147.6, 115.62, 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 114 16.00 O 5508 8.00 N 4722 7.00 C 19122 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: 5.39 Conformation dependent library (CDL) restraints added in 2.7 seconds 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 64.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 0 through 13 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR A 282 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 310 through 331 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 402 Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 435 through 449 Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'B' and resid 1 through 13 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 273 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 402 Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 517 through 530 Processing helix chain 'B' and resid 534 through 545 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'C' and resid 1 through 13 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 273 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 310 through 331 Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 354 through 364 Processing helix chain 'C' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 402 Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 435 through 449 Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 517 through 530 Processing helix chain 'C' and resid 534 through 545 Processing helix chain 'C' and resid 559 through 564 Processing helix chain 'C' and resid 570 through 582 Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 273 Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR D 282 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 310 through 331 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 354 through 364 Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 402 Processing helix chain 'D' and resid 404 through 419 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 517 through 530 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 559 through 564 Processing helix chain 'D' and resid 570 through 582 Processing helix chain 'E' and resid 1 through 13 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 122 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.198A pdb=" N TRP E 178 " --> pdb=" O HIS E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG E 221 " --> pdb=" O ASN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 273 Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR E 282 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 310 through 331 Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'E' and resid 354 through 364 Processing helix chain 'E' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 402 Processing helix chain 'E' and resid 404 through 419 Processing helix chain 'E' and resid 419 through 434 Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 504 removed outlier: 3.538A pdb=" N LYS E 494 " --> pdb=" O LYS E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 517 through 530 Processing helix chain 'E' and resid 534 through 545 Processing helix chain 'E' and resid 559 through 564 Processing helix chain 'E' and resid 570 through 582 Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.826A pdb=" N SER F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG F 221 " --> pdb=" O ASN F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 273 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR F 282 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 310 through 331 Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 354 through 364 Processing helix chain 'F' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 402 Processing helix chain 'F' and resid 404 through 419 Processing helix chain 'F' and resid 419 through 434 Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 462 through 464 No H-bonds generated for 'chain 'F' and resid 462 through 464' Processing helix chain 'F' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS F 494 " --> pdb=" O LYS F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 517 through 530 Processing helix chain 'F' and resid 534 through 545 Processing helix chain 'F' and resid 559 through 564 Processing helix chain 'F' and resid 570 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 245 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 89 Processing sheet with id=AA6, first strand: chain 'C' and resid 243 through 245 Processing sheet with id=AA7, first strand: chain 'D' and resid 84 through 89 Processing sheet with id=AA8, first strand: chain 'D' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'E' and resid 84 through 89 Processing sheet with id=AB1, first strand: chain 'E' and resid 243 through 245 Processing sheet with id=AB2, first strand: chain 'F' and resid 84 through 89 Processing sheet with id=AB3, first strand: chain 'F' and resid 243 through 245 1567 hydrogen bonds defined for protein. 4485 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: 7.39 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4865 1.31 - 1.43: 8737 1.43 - 1.56: 16404 1.56 - 1.68: 0 1.68 - 1.81: 174 Bond restraints: 30180 Sorted by residual: bond pdb=" C TYR D 245 " pdb=" O TYR D 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" C TYR F 245 " pdb=" O TYR F 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.81e+01 bond pdb=" C TYR A 245 " pdb=" O TYR A 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.80e+01 bond pdb=" C TYR C 245 " pdb=" O TYR C 245 " ideal model delta sigma weight residual 1.236 1.186 0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" C TYR E 245 " pdb=" O TYR E 245 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.17e-02 7.31e+03 1.76e+01 ... (remaining 30175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 40142 2.37 - 4.75: 429 4.75 - 7.12: 79 7.12 - 9.49: 6 9.49 - 11.87: 12 Bond angle restraints: 40668 Sorted by residual: angle pdb=" N GLU B 489 " pdb=" CA GLU B 489 " pdb=" C GLU B 489 " ideal model delta sigma weight residual 114.56 102.69 11.87 1.27e+00 6.20e-01 8.73e+01 angle pdb=" N GLU A 489 " pdb=" CA GLU A 489 " pdb=" C GLU A 489 " ideal model delta sigma weight residual 114.56 102.70 11.86 1.27e+00 6.20e-01 8.72e+01 angle pdb=" N GLU E 489 " pdb=" CA GLU E 489 " pdb=" C GLU E 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.71e+01 angle pdb=" N GLU C 489 " pdb=" CA GLU C 489 " pdb=" C GLU C 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.70e+01 angle pdb=" N GLU D 489 " pdb=" CA GLU D 489 " pdb=" C GLU D 489 " ideal model delta sigma weight residual 114.56 102.72 11.84 1.27e+00 6.20e-01 8.69e+01 ... (remaining 40663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 16137 18.02 - 36.04: 1404 36.04 - 54.06: 246 54.06 - 72.08: 63 72.08 - 90.10: 54 Dihedral angle restraints: 17904 sinusoidal: 7398 harmonic: 10506 Sorted by residual: dihedral pdb=" C VAL A 246 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " pdb=" CB VAL A 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL F 246 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " pdb=" CB VAL F 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL E 246 " pdb=" N VAL E 246 " pdb=" CA VAL E 246 " pdb=" CB VAL E 246 " ideal model delta harmonic sigma weight residual -122.00 -135.84 13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 17901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3829 0.078 - 0.155: 429 0.155 - 0.233: 32 0.233 - 0.311: 6 0.311 - 0.389: 6 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CA VAL E 246 " pdb=" N VAL E 246 " pdb=" C VAL E 246 " pdb=" CB VAL E 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL B 246 " pdb=" N VAL B 246 " pdb=" C VAL B 246 " pdb=" CB VAL B 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA VAL F 246 " pdb=" N VAL F 246 " pdb=" C VAL F 246 " pdb=" CB VAL F 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 4299 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA D 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA D 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER D 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA E 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA E 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER E 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 185 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ALA A 185 " 0.071 2.00e-02 2.50e+03 pdb=" O ALA A 185 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 186 " -0.024 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 372 2.65 - 3.22: 28315 3.22 - 3.78: 47268 3.78 - 4.34: 70523 4.34 - 4.90: 112653 Nonbonded interactions: 259131 Sorted by model distance: nonbonded pdb=" OH TYR E 522 " pdb=" O VAL E 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR F 522 " pdb=" O VAL F 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR C 522 " pdb=" O VAL C 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR A 522 " pdb=" O VAL A 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR D 522 " pdb=" O VAL D 584 " model vdw 2.092 3.040 ... (remaining 259126 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 44.610 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.006 0.072 30180 Z= 0.378 Angle : 0.718 11.868 40668 Z= 0.446 Chirality : 0.053 0.389 4302 Planarity : 0.004 0.041 5190 Dihedral : 14.672 90.096 11112 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.87 % Favored : 97.96 % Rotamer: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.91 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3474 helix: 0.82 (0.11), residues: 2124 sheet: 0.80 (0.41), residues: 156 loop : -0.59 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 585 HIS 0.005 0.001 HIS D 67 PHE 0.026 0.002 PHE E 44 TYR 0.029 0.002 TYR E 106 ARG 0.003 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 558 time to evaluate : 2.700 Fit side-chains REVERT: A 208 ASP cc_start: 0.8174 (m-30) cc_final: 0.7971 (m-30) REVERT: B 3 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8247 (tttm) REVERT: B 488 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7764 (mt) REVERT: B 548 ASN cc_start: 0.7717 (t0) cc_final: 0.7493 (t0) REVERT: C 228 MET cc_start: 0.8932 (mmp) cc_final: 0.8717 (mmp) REVERT: C 280 ASN cc_start: 0.7940 (m110) cc_final: 0.7586 (m-40) REVERT: C 488 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7783 (mt) REVERT: D 248 ASP cc_start: 0.6629 (t0) cc_final: 0.6427 (t0) REVERT: D 280 ASN cc_start: 0.7774 (m110) cc_final: 0.7506 (m110) REVERT: E 21 TYR cc_start: 0.8994 (m-80) cc_final: 0.8701 (m-80) REVERT: E 488 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7646 (mt) REVERT: F 3 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8353 (tttm) REVERT: F 488 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7755 (mt) REVERT: F 548 ASN cc_start: 0.7705 (t0) cc_final: 0.7496 (t0) outliers start: 18 outliers final: 2 residues processed: 561 average time/residue: 1.2867 time to fit residues: 831.2948 Evaluate side-chains 400 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 394 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 537 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 389 ASN A 399 ASN A 433 ASN A 436 ASN A 505 ASN B 30 ASN B 399 ASN B 433 ASN B 436 ASN C 30 ASN C 87 ASN C 389 ASN C 399 ASN C 433 ASN C 436 ASN C 548 ASN D 30 ASN D 87 ASN D 280 ASN D 286 ASN D 389 ASN D 399 ASN D 433 ASN D 436 ASN D 543 GLN D 548 ASN E 30 ASN E 87 ASN E 110 ASN E 399 ASN E 433 ASN E 436 ASN F 30 ASN F 67 HIS F 110 ASN F 399 ASN F 433 ASN F 436 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30180 Z= 0.205 Angle : 0.486 5.731 40668 Z= 0.270 Chirality : 0.041 0.148 4302 Planarity : 0.003 0.043 5190 Dihedral : 4.555 39.313 3812 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.38 % Favored : 98.45 % Rotamer: Outliers : 1.30 % Allowed : 8.71 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3474 helix: 1.17 (0.11), residues: 2166 sheet: 0.66 (0.44), residues: 156 loop : -0.61 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 585 HIS 0.005 0.001 HIS F 67 PHE 0.016 0.002 PHE D 231 TYR 0.018 0.002 TYR C 525 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 451 time to evaluate : 2.680 Fit side-chains REVERT: A 29 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7181 (mmtt) REVERT: A 568 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8224 (pmtt) REVERT: B 3 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8254 (tttm) REVERT: B 233 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7953 (tttt) REVERT: B 548 ASN cc_start: 0.7779 (t0) cc_final: 0.7558 (t0) REVERT: B 568 LYS cc_start: 0.8812 (ptmm) cc_final: 0.8305 (pmtt) REVERT: B 591 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6636 (mt-10) REVERT: C 2 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7337 (mptm) REVERT: C 29 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7548 (tptt) REVERT: C 280 ASN cc_start: 0.8020 (m110) cc_final: 0.7617 (m-40) REVERT: D 146 GLN cc_start: 0.7983 (mm110) cc_final: 0.7678 (mm-40) REVERT: D 280 ASN cc_start: 0.7935 (m-40) cc_final: 0.7659 (m110) REVERT: D 568 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8198 (pmtt) REVERT: E 21 TYR cc_start: 0.8994 (m-80) cc_final: 0.8695 (m-80) REVERT: E 317 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7589 (mm-30) REVERT: F 3 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8314 (tttm) REVERT: F 29 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7292 (mmtt) REVERT: F 356 LYS cc_start: 0.8231 (mppt) cc_final: 0.7950 (mppt) REVERT: F 360 ASN cc_start: 0.7983 (t0) cc_final: 0.7770 (t0) REVERT: F 568 LYS cc_start: 0.8812 (ptmm) cc_final: 0.8231 (pmtt) outliers start: 43 outliers final: 13 residues processed: 470 average time/residue: 1.2754 time to fit residues: 707.7791 Evaluate side-chains 409 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 392 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 236 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 263 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 316 optimal weight: 0.6980 chunk 342 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 chunk 313 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 110 ASN A 217 ASN A 436 ASN B 30 ASN B 217 ASN B 311 ASN B 360 ASN B 543 GLN C 30 ASN C 110 ASN C 217 ASN C 311 ASN C 548 ASN D 30 ASN D 110 ASN D 217 ASN D 311 ASN D 389 ASN D 548 ASN E 30 ASN E 110 ASN E 311 ASN E 360 ASN E 548 ASN F 30 ASN F 67 HIS F 110 ASN F 217 ASN F 543 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30180 Z= 0.158 Angle : 0.444 13.143 40668 Z= 0.244 Chirality : 0.040 0.145 4302 Planarity : 0.003 0.041 5190 Dihedral : 4.088 21.675 3798 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.44 % Favored : 98.39 % Rotamer: Outliers : 1.66 % Allowed : 9.65 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3474 helix: 1.39 (0.11), residues: 2190 sheet: 0.33 (0.43), residues: 156 loop : -0.51 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 585 HIS 0.003 0.001 HIS D 230 PHE 0.012 0.001 PHE D 231 TYR 0.012 0.001 TYR B 227 ARG 0.003 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 441 time to evaluate : 2.671 Fit side-chains REVERT: A 543 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: A 568 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8231 (pmtt) REVERT: B 3 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8265 (tttm) REVERT: B 169 HIS cc_start: 0.7852 (m-70) cc_final: 0.7649 (m-70) REVERT: B 233 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7948 (ttpp) REVERT: B 356 LYS cc_start: 0.8208 (mppt) cc_final: 0.7918 (mptt) REVERT: B 548 ASN cc_start: 0.7752 (t0) cc_final: 0.7523 (t0) REVERT: B 568 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8325 (pmtt) REVERT: B 591 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6651 (mt-10) REVERT: C 2 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7479 (mptm) REVERT: C 280 ASN cc_start: 0.8066 (m110) cc_final: 0.7676 (m-40) REVERT: C 356 LYS cc_start: 0.8019 (mppt) cc_final: 0.7586 (mmtm) REVERT: D 146 GLN cc_start: 0.7984 (mm110) cc_final: 0.7705 (mm-40) REVERT: D 280 ASN cc_start: 0.8000 (m-40) cc_final: 0.7743 (m110) REVERT: D 568 LYS cc_start: 0.8651 (ptmm) cc_final: 0.8178 (pmtt) REVERT: E 317 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7596 (mm-30) REVERT: F 1 MET cc_start: 0.7718 (ttm) cc_final: 0.7466 (ttm) REVERT: F 3 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8296 (tttm) REVERT: F 209 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: F 356 LYS cc_start: 0.8238 (mppt) cc_final: 0.8008 (mptt) REVERT: F 568 LYS cc_start: 0.8763 (ptmm) cc_final: 0.8209 (pmtt) outliers start: 55 outliers final: 13 residues processed: 472 average time/residue: 1.1715 time to fit residues: 646.5541 Evaluate side-chains 405 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 389 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.0070 chunk 238 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 165 optimal weight: 0.0470 chunk 301 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 110 ASN A 217 ASN A 311 ASN A 436 ASN B 30 ASN B 217 ASN B 543 GLN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 110 ASN E 280 ASN E 548 ASN F 30 ASN F 67 HIS F 110 ASN F 217 ASN F 311 ASN F 543 GLN F 548 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 30180 Z= 0.133 Angle : 0.427 9.543 40668 Z= 0.234 Chirality : 0.039 0.140 4302 Planarity : 0.003 0.039 5190 Dihedral : 3.899 19.682 3798 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.50 % Favored : 98.33 % Rotamer: Outliers : 1.72 % Allowed : 10.53 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3474 helix: 1.57 (0.11), residues: 2190 sheet: 0.12 (0.42), residues: 156 loop : -0.47 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 585 HIS 0.003 0.000 HIS F 67 PHE 0.012 0.001 PHE D 231 TYR 0.013 0.001 TYR B 227 ARG 0.003 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 418 time to evaluate : 2.660 Fit side-chains REVERT: A 568 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8225 (pmtt) REVERT: B 3 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8253 (tttm) REVERT: B 233 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7944 (ttpp) REVERT: B 356 LYS cc_start: 0.8199 (mppt) cc_final: 0.7904 (mptt) REVERT: B 548 ASN cc_start: 0.7802 (t0) cc_final: 0.7565 (t0) REVERT: B 568 LYS cc_start: 0.8735 (ptmm) cc_final: 0.8319 (pmtt) REVERT: C 2 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7474 (mptm) REVERT: C 256 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7622 (mm-30) REVERT: C 280 ASN cc_start: 0.8073 (m110) cc_final: 0.7691 (m-40) REVERT: C 356 LYS cc_start: 0.8047 (mppt) cc_final: 0.7599 (mmtm) REVERT: C 497 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: C 561 ASN cc_start: 0.8687 (m-40) cc_final: 0.8404 (m-40) REVERT: D 146 GLN cc_start: 0.7951 (mm110) cc_final: 0.7651 (mm-40) REVERT: D 280 ASN cc_start: 0.8007 (m-40) cc_final: 0.7759 (m110) REVERT: D 568 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8219 (pmtt) REVERT: D 591 GLU cc_start: 0.7194 (pt0) cc_final: 0.6857 (mp0) REVERT: E 4 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: E 317 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7600 (mm-30) REVERT: E 334 LYS cc_start: 0.8300 (mtmp) cc_final: 0.8009 (mmpt) REVERT: F 209 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: F 233 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7978 (ttpp) REVERT: F 356 LYS cc_start: 0.8244 (mppt) cc_final: 0.8009 (mptt) REVERT: F 568 LYS cc_start: 0.8755 (ptmm) cc_final: 0.8223 (pmtt) outliers start: 57 outliers final: 8 residues processed: 448 average time/residue: 1.1234 time to fit residues: 590.6407 Evaluate side-chains 400 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 389 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 287 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 505 ASN A 548 ASN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 67 HIS D 217 ASN D 548 ASN E 280 ASN E 548 ASN F 67 HIS F 217 ASN F 543 GLN F 548 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30180 Z= 0.235 Angle : 0.465 6.205 40668 Z= 0.255 Chirality : 0.041 0.147 4302 Planarity : 0.003 0.039 5190 Dihedral : 4.025 22.997 3798 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.87 % Favored : 97.96 % Rotamer: Outliers : 1.36 % Allowed : 11.34 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3474 helix: 1.54 (0.11), residues: 2178 sheet: -0.01 (0.42), residues: 156 loop : -0.51 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 585 HIS 0.005 0.001 HIS D 230 PHE 0.016 0.002 PHE E 231 TYR 0.013 0.001 TYR C 227 ARG 0.003 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 409 time to evaluate : 2.682 Fit side-chains REVERT: A 568 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8232 (pmtt) REVERT: B 356 LYS cc_start: 0.8277 (mppt) cc_final: 0.8038 (mptt) REVERT: B 548 ASN cc_start: 0.7800 (t0) cc_final: 0.7552 (t0) REVERT: B 568 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8366 (pmtt) REVERT: C 2 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7480 (mptm) REVERT: C 561 ASN cc_start: 0.8757 (m-40) cc_final: 0.8480 (m-40) REVERT: D 118 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8253 (mptt) REVERT: D 146 GLN cc_start: 0.8046 (mm110) cc_final: 0.7748 (mm-40) REVERT: D 568 LYS cc_start: 0.8698 (ptmm) cc_final: 0.8246 (pmtt) REVERT: D 591 GLU cc_start: 0.7257 (pt0) cc_final: 0.6915 (mp0) REVERT: E 4 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: E 317 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7622 (mm-30) REVERT: E 334 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8002 (mmpt) REVERT: F 146 GLN cc_start: 0.7876 (mm110) cc_final: 0.7493 (mm-40) REVERT: F 209 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: F 233 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7951 (ttpp) REVERT: F 356 LYS cc_start: 0.8248 (mppt) cc_final: 0.7951 (mptt) REVERT: F 490 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: F 568 LYS cc_start: 0.8762 (ptmm) cc_final: 0.8233 (pmtt) REVERT: F 591 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6422 (mp0) outliers start: 45 outliers final: 20 residues processed: 441 average time/residue: 1.1859 time to fit residues: 610.4088 Evaluate side-chains 413 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 388 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 334 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 490 LYS Chi-restraints excluded: chain F residue 591 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 111 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 110 ASN A 217 ASN A 257 ASN B 110 ASN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 280 ASN D 548 ASN E 548 ASN F 67 HIS F 110 ASN F 548 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 30180 Z= 0.417 Angle : 0.540 6.233 40668 Z= 0.294 Chirality : 0.045 0.157 4302 Planarity : 0.003 0.040 5190 Dihedral : 4.301 25.957 3798 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.33 % Favored : 97.50 % Rotamer: Outliers : 2.06 % Allowed : 10.77 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3474 helix: 1.29 (0.11), residues: 2172 sheet: -0.02 (0.41), residues: 156 loop : -0.54 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 585 HIS 0.006 0.001 HIS C 230 PHE 0.020 0.002 PHE E 231 TYR 0.015 0.002 TYR D 227 ARG 0.004 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 378 time to evaluate : 2.718 Fit side-chains REVERT: A 276 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8510 (mm) REVERT: B 1 MET cc_start: 0.7836 (ttm) cc_final: 0.7511 (ttm) REVERT: B 431 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8016 (mtp-110) REVERT: B 490 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8331 (mtmt) REVERT: B 548 ASN cc_start: 0.7812 (t0) cc_final: 0.7607 (t0) REVERT: B 568 LYS cc_start: 0.8739 (ptmm) cc_final: 0.8375 (pmtt) REVERT: B 591 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: C 2 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7413 (mptm) REVERT: C 579 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8228 (mp) REVERT: C 591 GLU cc_start: 0.7073 (pt0) cc_final: 0.6850 (mp0) REVERT: D 4 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: D 146 GLN cc_start: 0.8041 (mm110) cc_final: 0.7714 (mm-40) REVERT: D 257 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7441 (p0) REVERT: D 568 LYS cc_start: 0.8737 (ptmm) cc_final: 0.8272 (pmtt) REVERT: E 4 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: E 334 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8093 (mmpt) REVERT: E 490 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8597 (mtpt) REVERT: E 591 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: F 4 GLU cc_start: 0.7477 (mp0) cc_final: 0.6980 (mp0) REVERT: F 209 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: F 431 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8024 (mtp-110) REVERT: F 490 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8375 (mtmt) REVERT: F 568 LYS cc_start: 0.8764 (ptmm) cc_final: 0.8224 (pmtt) outliers start: 68 outliers final: 25 residues processed: 418 average time/residue: 1.2584 time to fit residues: 608.8798 Evaluate side-chains 400 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 361 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 561 ASN Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 334 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 490 LYS Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 490 LYS Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 190 optimal weight: 0.0070 chunk 283 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 335 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 257 ASN A 548 ASN B 87 ASN B 217 ASN C 30 ASN C 217 ASN C 260 GLN C 548 ASN D 217 ASN D 548 ASN E 217 ASN E 548 ASN F 67 HIS F 217 ASN F 260 GLN F 548 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30180 Z= 0.170 Angle : 0.442 7.100 40668 Z= 0.243 Chirality : 0.039 0.150 4302 Planarity : 0.003 0.041 5190 Dihedral : 4.038 24.071 3798 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.90 % Favored : 97.93 % Rotamer: Outliers : 1.97 % Allowed : 11.52 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3474 helix: 1.50 (0.11), residues: 2178 sheet: -0.03 (0.42), residues: 156 loop : -0.60 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 585 HIS 0.003 0.001 HIS C 230 PHE 0.013 0.001 PHE E 231 TYR 0.014 0.001 TYR F 227 ARG 0.002 0.000 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 385 time to evaluate : 2.690 Fit side-chains REVERT: A 568 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8288 (pmtt) REVERT: B 169 HIS cc_start: 0.7833 (m-70) cc_final: 0.7633 (m-70) REVERT: B 356 LYS cc_start: 0.8242 (mppt) cc_final: 0.8032 (mptt) REVERT: B 548 ASN cc_start: 0.7800 (t0) cc_final: 0.7586 (t0) REVERT: B 568 LYS cc_start: 0.8726 (ptmm) cc_final: 0.8365 (pmtt) REVERT: B 591 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: C 2 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7459 (mptm) REVERT: C 356 LYS cc_start: 0.8140 (mppt) cc_final: 0.7881 (mptp) REVERT: C 497 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: C 591 GLU cc_start: 0.7027 (pt0) cc_final: 0.6810 (mp0) REVERT: D 4 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: D 118 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8268 (mptt) REVERT: D 146 GLN cc_start: 0.8007 (mm110) cc_final: 0.7691 (mm-40) REVERT: D 356 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8023 (mppt) REVERT: D 568 LYS cc_start: 0.8722 (ptmm) cc_final: 0.8264 (pmtt) REVERT: D 591 GLU cc_start: 0.7266 (pt0) cc_final: 0.6934 (mp0) REVERT: E 4 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: E 356 LYS cc_start: 0.8196 (mppt) cc_final: 0.7918 (mptp) REVERT: E 591 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: F 169 HIS cc_start: 0.7828 (m-70) cc_final: 0.7624 (m-70) REVERT: F 209 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: F 356 LYS cc_start: 0.8252 (mppt) cc_final: 0.8050 (mptt) REVERT: F 568 LYS cc_start: 0.8754 (ptmm) cc_final: 0.8253 (pmtt) outliers start: 65 outliers final: 18 residues processed: 426 average time/residue: 1.2033 time to fit residues: 600.9388 Evaluate side-chains 397 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 373 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 561 ASN Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 200 optimal weight: 0.0970 chunk 101 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 263 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 257 ASN A 548 ASN B 217 ASN C 30 ASN C 110 ASN C 217 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 30 ASN E 110 ASN F 67 HIS F 217 ASN F 548 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30180 Z= 0.155 Angle : 0.438 6.738 40668 Z= 0.239 Chirality : 0.039 0.144 4302 Planarity : 0.003 0.042 5190 Dihedral : 3.865 20.308 3798 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.01 % Favored : 97.81 % Rotamer: Outliers : 1.24 % Allowed : 12.55 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3474 helix: 1.56 (0.11), residues: 2196 sheet: -0.04 (0.42), residues: 156 loop : -0.47 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 585 HIS 0.004 0.001 HIS F 67 PHE 0.015 0.001 PHE E 231 TYR 0.012 0.001 TYR F 227 ARG 0.002 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 390 time to evaluate : 2.664 Fit side-chains REVERT: A 29 LYS cc_start: 0.7832 (mmpt) cc_final: 0.7573 (tppt) REVERT: A 146 GLN cc_start: 0.7987 (mm110) cc_final: 0.7664 (mm-40) REVERT: A 568 LYS cc_start: 0.8708 (ptmm) cc_final: 0.8272 (pmtt) REVERT: B 146 GLN cc_start: 0.7786 (mm110) cc_final: 0.7482 (mm-40) REVERT: B 356 LYS cc_start: 0.8208 (mppt) cc_final: 0.7943 (mptt) REVERT: B 548 ASN cc_start: 0.7789 (t0) cc_final: 0.7521 (t0) REVERT: B 568 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8296 (pmtt) REVERT: C 2 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7489 (mptm) REVERT: C 125 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7223 (pt) REVERT: C 146 GLN cc_start: 0.7935 (mm110) cc_final: 0.7647 (mm-40) REVERT: C 356 LYS cc_start: 0.8152 (mppt) cc_final: 0.7898 (mptp) REVERT: C 497 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: C 591 GLU cc_start: 0.7002 (pt0) cc_final: 0.6793 (mp0) REVERT: D 118 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8276 (mptt) REVERT: D 146 GLN cc_start: 0.7964 (mm110) cc_final: 0.7667 (mm-40) REVERT: D 568 LYS cc_start: 0.8732 (ptmm) cc_final: 0.8290 (pmtt) REVERT: D 591 GLU cc_start: 0.7263 (pt0) cc_final: 0.6927 (mp0) REVERT: E 4 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: E 356 LYS cc_start: 0.8179 (mppt) cc_final: 0.7902 (mptp) REVERT: E 591 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: F 146 GLN cc_start: 0.7838 (mm110) cc_final: 0.7524 (mm-40) REVERT: F 209 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: F 356 LYS cc_start: 0.8226 (mppt) cc_final: 0.7943 (mptt) REVERT: F 568 LYS cc_start: 0.8733 (ptmm) cc_final: 0.8220 (pmtt) outliers start: 41 outliers final: 17 residues processed: 420 average time/residue: 1.1744 time to fit residues: 576.8838 Evaluate side-chains 393 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 371 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.5980 chunk 321 optimal weight: 0.9980 chunk 293 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 295 optimal weight: 0.6980 chunk 311 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 257 ASN B 217 ASN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 110 ASN E 548 ASN F 67 HIS F 169 HIS F 217 ASN F 548 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30180 Z= 0.182 Angle : 0.450 7.026 40668 Z= 0.245 Chirality : 0.039 0.146 4302 Planarity : 0.003 0.040 5190 Dihedral : 3.883 21.189 3798 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.04 % Favored : 97.78 % Rotamer: Outliers : 1.06 % Allowed : 12.95 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3474 helix: 1.53 (0.11), residues: 2196 sheet: -0.10 (0.41), residues: 156 loop : -0.46 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 585 HIS 0.005 0.001 HIS F 67 PHE 0.014 0.001 PHE C 231 TYR 0.014 0.001 TYR C 227 ARG 0.003 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 381 time to evaluate : 2.797 Fit side-chains REVERT: A 29 LYS cc_start: 0.7840 (mmpt) cc_final: 0.7577 (tppt) REVERT: A 146 GLN cc_start: 0.8008 (mm110) cc_final: 0.7681 (mm-40) REVERT: A 568 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8278 (pmtt) REVERT: B 146 GLN cc_start: 0.7795 (mm110) cc_final: 0.7481 (mm-40) REVERT: B 356 LYS cc_start: 0.8217 (mppt) cc_final: 0.7945 (mptt) REVERT: B 548 ASN cc_start: 0.7845 (t0) cc_final: 0.7629 (t0) REVERT: B 568 LYS cc_start: 0.8732 (ptmm) cc_final: 0.8289 (pmtt) REVERT: C 2 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7412 (mptm) REVERT: C 146 GLN cc_start: 0.7942 (mm110) cc_final: 0.7637 (mm-40) REVERT: C 356 LYS cc_start: 0.8149 (mppt) cc_final: 0.7820 (mmtm) REVERT: C 591 GLU cc_start: 0.7014 (pt0) cc_final: 0.6801 (mp0) REVERT: D 2 LYS cc_start: 0.8178 (tttm) cc_final: 0.7623 (mptm) REVERT: D 146 GLN cc_start: 0.7972 (mm110) cc_final: 0.7672 (mm-40) REVERT: D 257 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7450 (p0) REVERT: D 568 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8293 (pmtt) REVERT: D 591 GLU cc_start: 0.7261 (pt0) cc_final: 0.6930 (mp0) REVERT: E 4 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: E 356 LYS cc_start: 0.8182 (mppt) cc_final: 0.7889 (mptp) REVERT: F 146 GLN cc_start: 0.7845 (mm110) cc_final: 0.7526 (mm-40) REVERT: F 209 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: F 356 LYS cc_start: 0.8236 (mppt) cc_final: 0.7948 (mptt) REVERT: F 431 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7856 (mtp-110) REVERT: F 568 LYS cc_start: 0.8730 (ptmm) cc_final: 0.8224 (pmtt) outliers start: 35 outliers final: 15 residues processed: 406 average time/residue: 1.1730 time to fit residues: 557.3682 Evaluate side-chains 392 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 373 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.7980 chunk 330 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 346 optimal weight: 0.7980 chunk 319 optimal weight: 0.4980 chunk 276 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 213 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 257 ASN A 548 ASN B 110 ASN B 169 HIS B 217 ASN C 110 ASN D 30 ASN D 217 ASN D 548 ASN E 30 ASN F 67 HIS F 169 HIS F 217 ASN F 548 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30180 Z= 0.153 Angle : 0.439 7.189 40668 Z= 0.239 Chirality : 0.039 0.144 4302 Planarity : 0.003 0.041 5190 Dihedral : 3.805 20.429 3798 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 1.12 % Allowed : 12.76 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.15), residues: 3474 helix: 1.58 (0.11), residues: 2196 sheet: -0.09 (0.41), residues: 156 loop : -0.44 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 585 HIS 0.005 0.001 HIS F 67 PHE 0.013 0.001 PHE C 231 TYR 0.015 0.001 TYR E 111 ARG 0.004 0.000 ARG F 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 377 time to evaluate : 2.690 Fit side-chains REVERT: A 29 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7580 (tppt) REVERT: A 146 GLN cc_start: 0.7991 (mm110) cc_final: 0.7671 (mm-40) REVERT: A 568 LYS cc_start: 0.8712 (ptmm) cc_final: 0.8283 (pmtt) REVERT: B 146 GLN cc_start: 0.7794 (mm110) cc_final: 0.7493 (mm-40) REVERT: B 356 LYS cc_start: 0.8182 (mppt) cc_final: 0.7920 (mptt) REVERT: B 548 ASN cc_start: 0.7844 (t0) cc_final: 0.7582 (t0) REVERT: B 568 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8238 (pmtt) REVERT: C 2 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7459 (mptm) REVERT: C 146 GLN cc_start: 0.7930 (mm110) cc_final: 0.7637 (mm-40) REVERT: C 356 LYS cc_start: 0.8155 (mppt) cc_final: 0.7781 (mmtm) REVERT: C 497 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: D 2 LYS cc_start: 0.8150 (tttm) cc_final: 0.7658 (mptm) REVERT: D 3 LYS cc_start: 0.8372 (ttpm) cc_final: 0.8135 (tttm) REVERT: D 146 GLN cc_start: 0.7953 (mm110) cc_final: 0.7632 (mm-40) REVERT: D 257 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7437 (p0) REVERT: D 568 LYS cc_start: 0.8730 (ptmm) cc_final: 0.8322 (pmtt) REVERT: D 591 GLU cc_start: 0.7235 (pt0) cc_final: 0.6912 (mp0) REVERT: E 4 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: E 356 LYS cc_start: 0.8173 (mppt) cc_final: 0.7886 (mptp) REVERT: F 1 MET cc_start: 0.7915 (ttm) cc_final: 0.7624 (ttm) REVERT: F 146 GLN cc_start: 0.7832 (mm110) cc_final: 0.7525 (mm-40) REVERT: F 209 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: F 356 LYS cc_start: 0.8232 (mppt) cc_final: 0.7949 (mptt) REVERT: F 568 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8215 (pmtt) outliers start: 37 outliers final: 15 residues processed: 405 average time/residue: 1.1884 time to fit residues: 562.8368 Evaluate side-chains 383 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 364 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.1980 chunk 294 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 254 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 276 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 283 optimal weight: 0.5980 chunk 35 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 217 ASN A 257 ASN B 30 ASN B 67 HIS B 169 HIS B 217 ASN C 110 ASN C 548 ASN D 30 ASN D 217 ASN D 548 ASN E 30 ASN E 217 ASN E 548 ASN F 67 HIS F 169 HIS F 217 ASN F 548 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103921 restraints weight = 36701.360| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.80 r_work: 0.3093 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30180 Z= 0.132 Angle : 0.427 7.244 40668 Z= 0.232 Chirality : 0.038 0.141 4302 Planarity : 0.003 0.040 5190 Dihedral : 3.683 18.353 3798 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 0.97 % Allowed : 12.86 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.15), residues: 3474 helix: 1.65 (0.11), residues: 2196 sheet: -0.06 (0.42), residues: 156 loop : -0.38 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 585 HIS 0.005 0.000 HIS F 67 PHE 0.013 0.001 PHE C 533 TYR 0.019 0.001 TYR E 111 ARG 0.005 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9540.40 seconds wall clock time: 164 minutes 33.39 seconds (9873.39 seconds total)