Starting phenix.real_space_refine on Sat Aug 23 12:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eap_47839/08_2025/9eap_47839.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eap_47839/08_2025/9eap_47839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eap_47839/08_2025/9eap_47839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eap_47839/08_2025/9eap_47839.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eap_47839/08_2025/9eap_47839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eap_47839/08_2025/9eap_47839.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7673 2.51 5 N 1944 2.21 5 O 2218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11883 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3949 Classifications: {'peptide': 514} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 467} Chain: "B" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3963 Classifications: {'peptide': 516} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 469} Chain: "C" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3875 Classifications: {'peptide': 504} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 458} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'CHO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'CHO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'CHO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.24 Number of scatterers: 11883 At special positions: 0 Unit cell: (124.3, 115.5, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2218 8.00 N 1944 7.00 C 7673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 411.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 23 sheets defined 8.1% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 4.132A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.776A pdb=" N LEU A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.672A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.532A pdb=" N ALA B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.719A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.529A pdb=" N ILE B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 142' Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 37 through 42 removed outlier: 4.177A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 85 through 88 removed outlier: 3.686A pdb=" N LEU C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.771A pdb=" N PHE C 144 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 454 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 7.116A pdb=" N ILE A 78 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 185 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 80 " --> pdb=" O CYS A 183 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N CYS A 183 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA A 125 " --> pdb=" O CYS A 183 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU A 185 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 123 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 121 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A 189 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 119 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 3.643A pdb=" N HIS A 170 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 102 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 296 removed outlier: 4.231A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER A 332 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 401 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU A 338 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLN A 340 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA A 393 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N GLU A 342 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N VAL A 391 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 429 removed outlier: 7.090A pdb=" N TYR A 477 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.757A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG A 476 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL A 517 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 478 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE A 515 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 69 removed outlier: 12.584A pdb=" N GLN B 61 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N SER B 207 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLY B 65 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.740A pdb=" N ILE B 78 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 185 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 181 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 127 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N CYS B 183 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA B 125 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 185 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 123 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 121 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 189 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 119 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 99 through 103 removed outlier: 6.627A pdb=" N TYR B 99 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 218 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY B 101 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 214 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 449 through 451 removed outlier: 4.215A pdb=" N LEU B 252 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 449 through 451 removed outlier: 5.701A pdb=" N ILE B 497 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B 487 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 474 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 476 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 478 " --> pdb=" O ILE B 514 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 289 through 298 removed outlier: 4.002A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 377 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 356 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER B 332 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY B 400 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN B 334 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 398 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU B 336 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 394 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLN B 340 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG B 392 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU B 342 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N ARG B 390 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.449A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.763A pdb=" N ILE C 78 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 185 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 181 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 127 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N CYS C 183 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA C 125 " --> pdb=" O CYS C 183 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU C 185 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL C 123 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171 removed outlier: 3.744A pdb=" N HIS C 170 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP C 102 " --> pdb=" O HIS C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 449 through 451 removed outlier: 4.346A pdb=" N LEU C 252 " --> pdb=" O PHE C 509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 290 through 297 removed outlier: 4.161A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 357 through 358 removed outlier: 7.252A pdb=" N SER C 332 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE C 401 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER C 397 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C 338 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 341 through 342 Processing sheet with id=AC4, first strand: chain 'C' and resid 428 through 429 removed outlier: 4.077A pdb=" N TYR C 496 " --> pdb=" O TYR C 492 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 487 " --> pdb=" O TYR C 477 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 428 through 429 removed outlier: 4.077A pdb=" N TYR C 496 " --> pdb=" O TYR C 492 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA C 472 " --> pdb=" O TRP C 520 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP C 520 " --> pdb=" O ALA C 472 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 474 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 478 " --> pdb=" O ILE C 514 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3853 1.34 - 1.46: 1981 1.46 - 1.57: 6311 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 12217 Sorted by residual: bond pdb=" CA ASP B 196 " pdb=" CB ASP B 196 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.69e-02 3.50e+03 1.82e+00 bond pdb=" CB GLN A 469 " pdb=" CG GLN A 469 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" CA GLN A 469 " pdb=" CB GLN A 469 " ideal model delta sigma weight residual 1.530 1.552 -0.021 1.69e-02 3.50e+03 1.60e+00 bond pdb=" CB ASP B 196 " pdb=" CG ASP B 196 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" CA ASP B 174 " pdb=" CB ASP B 174 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.16e+00 ... (remaining 12212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 16354 2.08 - 4.17: 354 4.17 - 6.25: 49 6.25 - 8.34: 10 8.34 - 10.42: 3 Bond angle restraints: 16770 Sorted by residual: angle pdb=" CA GLN A 469 " pdb=" CB GLN A 469 " pdb=" CG GLN A 469 " ideal model delta sigma weight residual 114.10 123.31 -9.21 2.00e+00 2.50e-01 2.12e+01 angle pdb=" C GLU C 447 " pdb=" N ALA C 448 " pdb=" CA ALA C 448 " ideal model delta sigma weight residual 121.70 128.24 -6.54 1.80e+00 3.09e-01 1.32e+01 angle pdb=" CB LYS A 351 " pdb=" CG LYS A 351 " pdb=" CD LYS A 351 " ideal model delta sigma weight residual 111.30 119.11 -7.81 2.30e+00 1.89e-01 1.15e+01 angle pdb=" CA ASP B 196 " pdb=" CB ASP B 196 " pdb=" CG ASP B 196 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" C ASP B 366 " pdb=" N GLN B 367 " pdb=" CA GLN B 367 " ideal model delta sigma weight residual 121.70 127.74 -6.04 1.80e+00 3.09e-01 1.13e+01 ... (remaining 16765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 6595 22.36 - 44.73: 638 44.73 - 67.09: 134 67.09 - 89.46: 22 89.46 - 111.82: 11 Dihedral angle restraints: 7400 sinusoidal: 2973 harmonic: 4427 Sorted by residual: dihedral pdb=" CA VAL B 22 " pdb=" C VAL B 22 " pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta harmonic sigma weight residual -180.00 -138.81 -41.19 0 5.00e+00 4.00e-02 6.79e+01 dihedral pdb=" CA PRO B 361 " pdb=" C PRO B 361 " pdb=" N THR B 362 " pdb=" CA THR B 362 " ideal model delta harmonic sigma weight residual 180.00 -139.67 -40.33 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N ASP B 196 " pdb=" CA ASP B 196 " ideal model delta harmonic sigma weight residual 180.00 145.50 34.50 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 7397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1100 0.030 - 0.061: 506 0.061 - 0.091: 175 0.091 - 0.121: 125 0.121 - 0.152: 15 Chirality restraints: 1921 Sorted by residual: chirality pdb=" CG LEU C 258 " pdb=" CB LEU C 258 " pdb=" CD1 LEU C 258 " pdb=" CD2 LEU C 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA VAL A 378 " pdb=" N VAL A 378 " pdb=" C VAL A 378 " pdb=" CB VAL A 378 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CB ILE C 358 " pdb=" CA ILE C 358 " pdb=" CG1 ILE C 358 " pdb=" CG2 ILE C 358 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1918 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 22 " -0.047 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO B 23 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 196 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C ASP B 196 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP B 196 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 197 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 469 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.83e+00 pdb=" C GLN A 469 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 469 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 470 " 0.014 2.00e-02 2.50e+03 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 408 2.70 - 3.25: 10797 3.25 - 3.80: 17057 3.80 - 4.35: 20428 4.35 - 4.90: 36790 Nonbonded interactions: 85480 Sorted by model distance: nonbonded pdb=" O ALA B 25 " pdb=" N GLU B 27 " model vdw 2.148 3.120 nonbonded pdb=" O SER C 96 " pdb=" OG SER C 96 " model vdw 2.187 3.040 nonbonded pdb=" OG1 THR C 482 " pdb=" OE1 GLN C 484 " model vdw 2.217 3.040 nonbonded pdb=" N GLU B 456 " pdb=" OE1 GLU B 456 " model vdw 2.243 3.120 nonbonded pdb=" O PRO B 63 " pdb=" OG SER B 519 " model vdw 2.252 3.040 ... (remaining 85475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 90 or (resid 91 and (name N or name CA or name \ C or name O )) or resid 92 through 530 or resid 601)) selection = (chain 'B' and (resid 27 through 90 or (resid 91 and (name N or name CA or name \ C or name O )) or resid 92 through 601)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 11.330 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5275 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 : 0.004 0.040 12217 Z= 0.180 Angle : 0.729 10.424 16770 Z= 0.374 Chirality : 0.045 0.152 1921 Planarity : 0.005 0.072 2182 Dihedral : 18.584 111.820 4560 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.85 % Favored : 92.02 % Rotamer: Outliers : 4.25 % Allowed : 33.52 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.21 % Twisted Proline : 0.75 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.21), residues: 1528 helix: -0.63 (0.71), residues: 56 sheet: -0.23 (0.26), residues: 421 loop : -1.39 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 523 TYR 0.021 0.001 TYR B 435 PHE 0.030 0.001 PHE C 401 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00408 (12217) covalent geometry : angle 0.72920 (16770) hydrogen bonds : bond 0.16397 ( 272) hydrogen bonds : angle 6.99735 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.439 Fit side-chains REVERT: A 27 GLU cc_start: 0.6068 (pm20) cc_final: 0.5307 (mm-30) REVERT: A 88 LEU cc_start: 0.5290 (mt) cc_final: 0.5042 (mt) REVERT: A 105 ASN cc_start: 0.6381 (OUTLIER) cc_final: 0.6039 (m110) REVERT: A 117 PHE cc_start: 0.6189 (m-10) cc_final: 0.5929 (m-80) REVERT: A 149 CYS cc_start: 0.6261 (t) cc_final: 0.6035 (m) REVERT: A 181 LEU cc_start: 0.5060 (tt) cc_final: 0.4825 (tp) REVERT: A 214 ASN cc_start: 0.6263 (OUTLIER) cc_final: 0.5929 (p0) REVERT: A 222 ILE cc_start: 0.5822 (pt) cc_final: 0.5457 (mp) REVERT: A 328 TYR cc_start: 0.5934 (t80) cc_final: 0.5352 (t80) REVERT: A 402 GLN cc_start: 0.4486 (mp10) cc_final: 0.4259 (mp10) REVERT: A 519 SER cc_start: 0.7063 (m) cc_final: 0.6752 (p) REVERT: A 523 ARG cc_start: 0.5996 (tpp80) cc_final: 0.5165 (ttp-110) REVERT: B 48 ILE cc_start: 0.5677 (pt) cc_final: 0.5344 (mt) REVERT: B 58 ASN cc_start: 0.5713 (p0) cc_final: 0.5459 (p0) REVERT: B 106 MET cc_start: 0.6243 (mtm) cc_final: 0.6041 (tpp) REVERT: B 235 ILE cc_start: 0.7009 (pt) cc_final: 0.6785 (pp) REVERT: B 329 PRO cc_start: 0.6170 (Cg_exo) cc_final: 0.5913 (Cg_endo) REVERT: B 394 VAL cc_start: 0.4784 (OUTLIER) cc_final: 0.4391 (t) REVERT: B 436 MET cc_start: 0.1932 (mpp) cc_final: -0.0170 (mtt) REVERT: B 464 ASN cc_start: 0.5411 (OUTLIER) cc_final: 0.4104 (m-40) REVERT: B 493 ASN cc_start: 0.6261 (p0) cc_final: 0.5912 (p0) REVERT: B 512 ASP cc_start: 0.7010 (m-30) cc_final: 0.6654 (t0) REVERT: B 514 ILE cc_start: 0.7417 (pt) cc_final: 0.7007 (pp) REVERT: C 33 GLN cc_start: 0.6378 (mt0) cc_final: 0.6007 (mt0) REVERT: C 49 ASN cc_start: 0.7127 (m110) cc_final: 0.6803 (m110) REVERT: C 61 GLN cc_start: 0.5935 (tt0) cc_final: 0.5583 (tp40) REVERT: C 74 THR cc_start: 0.7040 (p) cc_final: 0.6788 (t) REVERT: C 137 THR cc_start: 0.6173 (p) cc_final: 0.5921 (p) REVERT: C 174 ASP cc_start: 0.6610 (m-30) cc_final: 0.6222 (p0) REVERT: C 222 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6257 (pt) REVERT: C 432 PHE cc_start: 0.5072 (m-80) cc_final: 0.4564 (m-80) REVERT: C 436 MET cc_start: 0.5735 (mmm) cc_final: 0.5245 (mmt) REVERT: C 471 GLU cc_start: 0.7449 (tp30) cc_final: 0.6926 (tp30) REVERT: C 516 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6390 (mt-10) outliers start: 54 outliers final: 15 residues processed: 267 average time/residue: 0.4364 time to fit residues: 129.2386 Evaluate side-chains 153 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 514 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN B 105 ASN B 270 HIS C 105 ASN C 265 GLN C 455 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.232682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.205755 restraints weight = 12118.198| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.14 r_work: 0.3887 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.3786 rms_B_bonded: 3.17 restraints_weight: 0.1250 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 12217 Z= 0.148 Angle : 0.701 8.604 16770 Z= 0.351 Chirality : 0.047 0.187 1921 Planarity : 0.006 0.056 2182 Dihedral : 7.644 98.381 1897 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.41 % Favored : 93.39 % Rotamer: Outliers : 4.48 % Allowed : 28.48 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.21 % Twisted Proline : 0.75 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.21), residues: 1528 helix: -0.65 (0.62), residues: 59 sheet: -0.18 (0.25), residues: 429 loop : -1.42 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 433 TYR 0.019 0.001 TYR B 317 PHE 0.026 0.002 PHE C 487 TRP 0.013 0.001 TRP B 264 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00330 (12217) covalent geometry : angle 0.70100 (16770) hydrogen bonds : bond 0.03657 ( 272) hydrogen bonds : angle 5.88890 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.435 Fit side-chains REVERT: A 214 ASN cc_start: 0.8052 (p0) cc_final: 0.7839 (p0) REVERT: A 219 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7778 (m) REVERT: A 328 TYR cc_start: 0.5867 (t80) cc_final: 0.5522 (t80) REVERT: A 335 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5310 (mp) REVERT: B 212 ASP cc_start: 0.6918 (m-30) cc_final: 0.6673 (p0) REVERT: B 357 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.4866 (ptm) REVERT: B 359 LEU cc_start: 0.3845 (OUTLIER) cc_final: 0.3556 (tm) REVERT: C 33 GLN cc_start: 0.8258 (mt0) cc_final: 0.7887 (mt0) REVERT: C 106 MET cc_start: 0.8741 (mtm) cc_final: 0.8412 (mtp) REVERT: C 155 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: C 197 GLU cc_start: 0.3869 (OUTLIER) cc_final: 0.3647 (tt0) REVERT: C 238 ARG cc_start: 0.5411 (tmt170) cc_final: 0.5198 (ptp90) outliers start: 57 outliers final: 11 residues processed: 185 average time/residue: 0.5091 time to fit residues: 103.5817 Evaluate side-chains 130 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 137 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 261 ASN B 270 HIS C 50 GLN C 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.227238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.199688 restraints weight = 12111.357| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.16 r_work: 0.3807 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work: 0.3678 rms_B_bonded: 3.62 restraints_weight: 0.1250 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12217 Z= 0.141 Angle : 0.661 10.907 16770 Z= 0.332 Chirality : 0.047 0.239 1921 Planarity : 0.006 0.058 2182 Dihedral : 6.417 57.601 1871 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.41 % Favored : 93.32 % Rotamer: Outliers : 5.19 % Allowed : 26.59 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.21 % Twisted Proline : 0.75 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.21), residues: 1528 helix: -0.45 (0.64), residues: 59 sheet: -0.25 (0.25), residues: 437 loop : -1.34 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 228 TYR 0.012 0.001 TYR B 227 PHE 0.020 0.002 PHE C 199 TRP 0.013 0.002 TRP A 169 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00326 (12217) covalent geometry : angle 0.66137 (16770) hydrogen bonds : bond 0.04084 ( 272) hydrogen bonds : angle 5.67217 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 126 time to evaluate : 0.453 Fit side-chains REVERT: A 335 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5436 (mp) REVERT: A 456 GLU cc_start: 0.6586 (mp0) cc_final: 0.6371 (mp0) REVERT: A 471 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: B 72 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7918 (mpp80) REVERT: B 196 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6449 (p0) REVERT: B 359 LEU cc_start: 0.3981 (OUTLIER) cc_final: 0.3776 (tm) REVERT: B 484 GLN cc_start: 0.8214 (pt0) cc_final: 0.7985 (pt0) REVERT: C 33 GLN cc_start: 0.8643 (mt0) cc_final: 0.8386 (mt0) REVERT: C 106 MET cc_start: 0.8887 (mtm) cc_final: 0.8676 (mtp) REVERT: C 155 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: C 174 ASP cc_start: 0.8401 (m-30) cc_final: 0.8024 (t0) REVERT: C 197 GLU cc_start: 0.3990 (OUTLIER) cc_final: 0.3775 (tt0) REVERT: C 235 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8448 (mm) REVERT: C 312 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7156 (mt0) outliers start: 66 outliers final: 22 residues processed: 175 average time/residue: 0.5479 time to fit residues: 104.7141 Evaluate side-chains 146 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 508 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.224453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.173968 restraints weight = 11960.232| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 4.12 r_work: 0.3105 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12217 Z= 0.134 Angle : 0.644 7.959 16770 Z= 0.329 Chirality : 0.046 0.187 1921 Planarity : 0.006 0.057 2182 Dihedral : 6.458 59.259 1871 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.28 % Favored : 93.52 % Rotamer: Outliers : 4.41 % Allowed : 26.51 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.21 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.21), residues: 1528 helix: -0.26 (0.66), residues: 53 sheet: -0.36 (0.24), residues: 444 loop : -1.27 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 224 TYR 0.014 0.001 TYR B 227 PHE 0.018 0.002 PHE C 199 TRP 0.013 0.001 TRP A 169 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00313 (12217) covalent geometry : angle 0.64420 (16770) hydrogen bonds : bond 0.03558 ( 272) hydrogen bonds : angle 5.62134 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 0.459 Fit side-chains REVERT: A 148 MET cc_start: 0.8885 (ttm) cc_final: 0.8471 (tpp) REVERT: A 478 ARG cc_start: 0.6949 (ptp-170) cc_final: 0.6358 (mtp85) REVERT: A 523 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7439 (ttp-110) REVERT: B 196 ASP cc_start: 0.7024 (p0) cc_final: 0.6776 (p0) REVERT: B 329 PRO cc_start: 0.6702 (Cg_exo) cc_final: 0.6138 (Cg_endo) REVERT: B 359 LEU cc_start: 0.3296 (OUTLIER) cc_final: 0.2939 (tm) REVERT: B 456 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: B 512 ASP cc_start: 0.7994 (t0) cc_final: 0.7690 (t0) REVERT: C 33 GLN cc_start: 0.8700 (mt0) cc_final: 0.8401 (mt0) REVERT: C 106 MET cc_start: 0.9002 (mtm) cc_final: 0.8785 (mtp) REVERT: C 174 ASP cc_start: 0.8350 (m-30) cc_final: 0.7846 (t0) REVERT: C 197 GLU cc_start: 0.3490 (OUTLIER) cc_final: 0.3110 (tt0) REVERT: C 228 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: C 235 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8374 (mm) REVERT: C 264 TRP cc_start: 0.8133 (m-10) cc_final: 0.7823 (m-10) REVERT: C 275 LEU cc_start: 0.8320 (mp) cc_final: 0.8052 (mt) REVERT: C 407 GLU cc_start: 0.6613 (mp0) cc_final: 0.6067 (tt0) REVERT: C 450 ASP cc_start: 0.7071 (m-30) cc_final: 0.6791 (t0) outliers start: 56 outliers final: 22 residues processed: 167 average time/residue: 0.5601 time to fit residues: 101.9250 Evaluate side-chains 143 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 405 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 265 GLN B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.221767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.150528 restraints weight = 11916.859| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 8.13 r_work: 0.2991 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12217 Z= 0.152 Angle : 0.667 7.584 16770 Z= 0.341 Chirality : 0.047 0.190 1921 Planarity : 0.006 0.056 2182 Dihedral : 6.512 56.482 1871 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.02 % Favored : 93.72 % Rotamer: Outliers : 4.56 % Allowed : 25.89 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.21 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.20), residues: 1528 helix: -0.35 (0.64), residues: 53 sheet: -0.25 (0.25), residues: 421 loop : -1.32 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 433 TYR 0.018 0.002 TYR B 227 PHE 0.022 0.002 PHE A 401 TRP 0.012 0.002 TRP A 169 HIS 0.005 0.002 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00364 (12217) covalent geometry : angle 0.66688 (16770) hydrogen bonds : bond 0.03890 ( 272) hydrogen bonds : angle 5.66756 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 125 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8977 (ttm) cc_final: 0.8542 (tpp) REVERT: A 478 ARG cc_start: 0.6950 (ptp-170) cc_final: 0.6478 (mtp85) REVERT: A 523 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7413 (ttp-110) REVERT: B 40 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8942 (mt) REVERT: B 72 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8499 (mpp80) REVERT: B 112 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7296 (mt) REVERT: B 359 LEU cc_start: 0.3066 (OUTLIER) cc_final: 0.2751 (tm) REVERT: B 437 ARG cc_start: 0.1617 (OUTLIER) cc_final: 0.1089 (pmt170) REVERT: B 512 ASP cc_start: 0.7935 (t0) cc_final: 0.7639 (t0) REVERT: C 106 MET cc_start: 0.9067 (mtm) cc_final: 0.8842 (mtp) REVERT: C 155 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: C 174 ASP cc_start: 0.8337 (m-30) cc_final: 0.7825 (t0) REVERT: C 197 GLU cc_start: 0.3081 (OUTLIER) cc_final: 0.2574 (tt0) REVERT: C 228 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: C 235 ILE cc_start: 0.8461 (mm) cc_final: 0.8232 (mm) REVERT: C 407 GLU cc_start: 0.6668 (mp0) cc_final: 0.6105 (tt0) REVERT: C 438 GLN cc_start: 0.5393 (OUTLIER) cc_final: 0.5134 (tt0) REVERT: C 450 ASP cc_start: 0.7295 (m-30) cc_final: 0.6927 (t0) outliers start: 58 outliers final: 25 residues processed: 171 average time/residue: 0.5965 time to fit residues: 111.1809 Evaluate side-chains 148 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 438 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.220895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.166823 restraints weight = 11842.581| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 4.36 r_work: 0.3006 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12217 Z= 0.165 Angle : 0.691 8.742 16770 Z= 0.352 Chirality : 0.048 0.187 1921 Planarity : 0.006 0.056 2182 Dihedral : 6.649 53.618 1871 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.69 % Favored : 94.11 % Rotamer: Outliers : 5.19 % Allowed : 24.78 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.21 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.20), residues: 1528 helix: -0.76 (0.62), residues: 53 sheet: -0.14 (0.25), residues: 417 loop : -1.38 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.017 0.002 TYR B 227 PHE 0.016 0.002 PHE C 80 TRP 0.013 0.002 TRP A 169 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00400 (12217) covalent geometry : angle 0.69125 (16770) hydrogen bonds : bond 0.03911 ( 272) hydrogen bonds : angle 5.64803 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 123 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8981 (ttm) cc_final: 0.8558 (tpp) REVERT: A 154 LEU cc_start: 0.8846 (mp) cc_final: 0.8444 (mt) REVERT: A 471 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: A 478 ARG cc_start: 0.7229 (ptp-170) cc_final: 0.6708 (mtp85) REVERT: A 497 ILE cc_start: 0.7288 (mm) cc_final: 0.6975 (mt) REVERT: A 526 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: B 112 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7236 (mt) REVERT: B 359 LEU cc_start: 0.2964 (OUTLIER) cc_final: 0.2619 (tm) REVERT: B 437 ARG cc_start: 0.1799 (OUTLIER) cc_final: 0.1371 (pmt170) REVERT: B 512 ASP cc_start: 0.7924 (t0) cc_final: 0.7607 (t0) REVERT: C 174 ASP cc_start: 0.8309 (m-30) cc_final: 0.7784 (t0) REVERT: C 196 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6767 (p0) REVERT: C 197 GLU cc_start: 0.3103 (OUTLIER) cc_final: 0.2599 (tt0) REVERT: C 228 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: C 275 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8272 (mt) REVERT: C 384 LEU cc_start: 0.4659 (OUTLIER) cc_final: 0.4082 (pt) REVERT: C 407 GLU cc_start: 0.6925 (mp0) cc_final: 0.6105 (tt0) REVERT: C 410 ASP cc_start: 0.5778 (m-30) cc_final: 0.5200 (m-30) REVERT: C 436 MET cc_start: 0.5697 (mmm) cc_final: 0.5192 (mmt) outliers start: 66 outliers final: 32 residues processed: 173 average time/residue: 0.5961 time to fit residues: 112.2120 Evaluate side-chains 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 134 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.220900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.166859 restraints weight = 11839.355| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 4.31 r_work: 0.3019 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12217 Z= 0.152 Angle : 0.667 9.221 16770 Z= 0.341 Chirality : 0.047 0.177 1921 Planarity : 0.006 0.055 2182 Dihedral : 6.596 52.515 1871 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.54 % Favored : 93.26 % Rotamer: Outliers : 4.33 % Allowed : 25.57 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.21 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.20), residues: 1528 helix: -0.82 (0.62), residues: 53 sheet: -0.12 (0.25), residues: 413 loop : -1.38 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.016 0.001 TYR B 227 PHE 0.015 0.002 PHE C 80 TRP 0.013 0.002 TRP A 169 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00366 (12217) covalent geometry : angle 0.66712 (16770) hydrogen bonds : bond 0.03789 ( 272) hydrogen bonds : angle 5.59447 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8970 (ttm) cc_final: 0.8530 (tpp) REVERT: A 154 LEU cc_start: 0.8835 (mp) cc_final: 0.8440 (mt) REVERT: A 402 GLN cc_start: 0.5146 (mp10) cc_final: 0.4774 (mp10) REVERT: A 471 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: A 478 ARG cc_start: 0.7344 (ptp-170) cc_final: 0.6831 (mtp85) REVERT: A 497 ILE cc_start: 0.7313 (mm) cc_final: 0.7022 (mt) REVERT: A 526 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: B 112 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7106 (mt) REVERT: B 359 LEU cc_start: 0.3064 (OUTLIER) cc_final: 0.2732 (tm) REVERT: B 512 ASP cc_start: 0.7871 (t0) cc_final: 0.7553 (t0) REVERT: C 155 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: C 174 ASP cc_start: 0.8290 (m-30) cc_final: 0.7785 (t0) REVERT: C 197 GLU cc_start: 0.3096 (OUTLIER) cc_final: 0.2355 (tt0) REVERT: C 228 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7685 (ttm170) REVERT: C 407 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6182 (tt0) REVERT: C 410 ASP cc_start: 0.5878 (m-30) cc_final: 0.5189 (m-30) REVERT: C 436 MET cc_start: 0.6375 (mmm) cc_final: 0.5883 (mmt) outliers start: 55 outliers final: 29 residues processed: 157 average time/residue: 0.6203 time to fit residues: 106.1373 Evaluate side-chains 149 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 471 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7583 > 50: distance: 8 - 10: 27.880 distance: 10 - 11: 19.196 distance: 11 - 12: 15.530 distance: 11 - 14: 7.217 distance: 12 - 13: 19.962 distance: 12 - 19: 15.427 distance: 14 - 15: 12.022 distance: 15 - 16: 3.571 distance: 16 - 17: 8.275 distance: 16 - 18: 21.110 distance: 19 - 20: 12.708 distance: 19 - 167: 21.284 distance: 20 - 21: 25.465 distance: 20 - 23: 16.271 distance: 21 - 22: 10.636 distance: 21 - 30: 18.739 distance: 22 - 164: 26.309 distance: 23 - 24: 20.541 distance: 24 - 25: 10.630 distance: 24 - 26: 13.531 distance: 25 - 27: 18.991 distance: 26 - 28: 15.686 distance: 27 - 29: 18.761 distance: 28 - 29: 9.480 distance: 30 - 31: 37.752 distance: 31 - 32: 40.279 distance: 31 - 34: 39.159 distance: 32 - 33: 8.883 distance: 32 - 36: 21.705 distance: 34 - 35: 27.322 distance: 36 - 37: 15.289 distance: 36 - 154: 22.946 distance: 37 - 38: 21.496 distance: 37 - 40: 16.032 distance: 38 - 39: 7.479 distance: 38 - 44: 11.781 distance: 39 - 151: 17.319 distance: 40 - 41: 37.129 distance: 40 - 42: 44.201 distance: 41 - 43: 43.099 distance: 44 - 45: 19.392 distance: 45 - 46: 19.681 distance: 45 - 48: 16.817 distance: 46 - 47: 22.762 distance: 46 - 50: 27.550 distance: 48 - 49: 7.688 distance: 50 - 51: 13.573 distance: 50 - 56: 21.146 distance: 51 - 52: 17.172 distance: 51 - 54: 10.529 distance: 52 - 53: 23.937 distance: 52 - 57: 12.382 distance: 54 - 55: 5.629 distance: 55 - 56: 18.525 distance: 57 - 58: 24.612 distance: 58 - 59: 23.283 distance: 58 - 61: 16.070 distance: 59 - 60: 4.010 distance: 59 - 68: 51.558 distance: 61 - 62: 27.484 distance: 62 - 63: 34.477 distance: 63 - 64: 25.286 distance: 64 - 65: 25.431 distance: 65 - 66: 9.259 distance: 65 - 67: 14.511 distance: 68 - 69: 25.179 distance: 69 - 70: 26.381 distance: 69 - 72: 24.595 distance: 70 - 71: 25.638 distance: 70 - 76: 15.456 distance: 72 - 73: 35.263 distance: 73 - 75: 4.635 distance: 76 - 77: 28.608 distance: 77 - 78: 27.600 distance: 77 - 80: 36.716 distance: 78 - 79: 23.702 distance: 78 - 83: 9.408 distance: 80 - 81: 41.012 distance: 80 - 82: 9.371 distance: 83 - 89: 36.007 distance: 84 - 85: 3.253 distance: 84 - 87: 32.042 distance: 85 - 86: 30.765 distance: 85 - 90: 29.816 distance: 88 - 89: 20.180