Starting phenix.real_space_refine on Mon Oct 26 17:21:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7b_72650/10_2026/9y7b_72650.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7b_72650/10_2026/9y7b_72650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y7b_72650/10_2026/9y7b_72650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7b_72650/10_2026/9y7b_72650.map" model { file = "/net/cci-nas-00/data/ceres_data/9y7b_72650/10_2026/9y7b_72650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7b_72650/10_2026/9y7b_72650.cif" } resolution = 3.9 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= 4.377 sd= 1.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 241 5.49 5 S 49 5.16 5 C 12755 2.51 5 N 3706 2.21 5 O 4474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21225 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 751 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 777 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 823 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "E" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1654 Classifications: {'DNA': 81} Link IDs: {'rna3p': 80} Chain: "F" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1688 Classifications: {'DNA': 82} Link IDs: {'rna3p': 81} Chain: "A" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3909 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 18, 'TRANS': 456} Chain breaks: 3 Chain: "B" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3861 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 18, 'TRANS': 450} Chain breaks: 2 Chain: "C" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3824 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 17, 'TRANS': 446} Chain breaks: 2 Chain: "D" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3196 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 12, 'TRANS': 376} Chain breaks: 3 Time building chain proxies: 4.24, per 1000 atoms: 0.20 Number of scatterers: 21225 At special positions: 0 Unit cell: (175.14, 115.92, 200.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 241 15.00 O 4474 8.00 N 3706 7.00 C 12755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 728.1 milliseconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 17 sheets defined 53.7% alpha, 12.1% beta 116 base pairs and 194 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 19 through 40 Processing helix chain 'G' and resid 84 through 92 Processing helix chain 'H' and resid 2 through 14 Processing helix chain 'H' and resid 18 through 39 Processing helix chain 'H' and resid 83 through 91 Processing helix chain 'A' and resid 44 through 65 Processing helix chain 'A' and resid 69 through 84 removed outlier: 4.159A pdb=" N GLU A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 4.399A pdb=" N VAL A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.565A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.654A pdb=" N GLN A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 167 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.816A pdb=" N TYR A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 315 through 325 removed outlier: 4.350A pdb=" N ASP A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 4.068A pdb=" N ASN A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 428 through 436 Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.809A pdb=" N ARG A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 527 Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 531 through 558 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 44 through 65 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.541A pdb=" N VAL B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 196 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 267 through 280 removed outlier: 3.575A pdb=" N GLN B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.715A pdb=" N TYR B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 removed outlier: 4.132A pdb=" N SER B 315 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 341 through 358 removed outlier: 4.561A pdb=" N ASN B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 396 Processing helix chain 'B' and resid 408 through 420 Processing helix chain 'B' and resid 429 through 437 removed outlier: 4.224A pdb=" N ASP B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 470 Processing helix chain 'B' and resid 503 through 509 removed outlier: 3.996A pdb=" N ARG B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 44 through 65 Processing helix chain 'C' and resid 69 through 84 removed outlier: 3.690A pdb=" N GLU C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Proline residue: C 75 - end of helix removed outlier: 4.554A pdb=" N VAL C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 126 through 141 Processing helix chain 'C' and resid 147 through 167 Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.732A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.696A pdb=" N TYR C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 314 Processing helix chain 'C' and resid 315 through 325 removed outlier: 3.647A pdb=" N ASP C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.791A pdb=" N LEU C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 396 Processing helix chain 'C' and resid 408 through 420 Processing helix chain 'C' and resid 428 through 437 removed outlier: 3.520A pdb=" N PHE C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 511 through 524 Processing helix chain 'D' and resid 126 through 141 Processing helix chain 'D' and resid 147 through 167 Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.685A pdb=" N VAL D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 280 removed outlier: 3.600A pdb=" N GLN D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.636A pdb=" N PHE D 313 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 314 " --> pdb=" O LYS D 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 310 through 314' Processing helix chain 'D' and resid 315 through 325 removed outlier: 4.075A pdb=" N ASP D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 381 through 396 Processing helix chain 'D' and resid 408 through 420 Processing helix chain 'D' and resid 428 through 436 Processing helix chain 'D' and resid 459 through 470 Processing helix chain 'D' and resid 503 through 509 removed outlier: 4.047A pdb=" N ARG D 509 " --> pdb=" O GLU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 528 Processing helix chain 'D' and resid 531 through 559 removed outlier: 3.831A pdb=" N ILE D 550 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL D 551 " --> pdb=" O ASP D 547 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS D 552 " --> pdb=" O ARG D 548 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'G' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 62 Processing sheet with id=AA5, first strand: chain 'A' and resid 256 through 262 removed outlier: 6.685A pdb=" N VAL A 256 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP A 250 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 258 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 305 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 232 removed outlier: 6.528A pdb=" N ALA A 231 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 438 through 443 removed outlier: 5.071A pdb=" N GLN A 475 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 450 removed outlier: 4.012A pdb=" N ILE A 449 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 256 through 262 removed outlier: 6.537A pdb=" N VAL B 256 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP B 250 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 258 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 222 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 305 " --> pdb=" O HIS B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 241 removed outlier: 6.588A pdb=" N ALA B 231 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 438 through 443 removed outlier: 5.780A pdb=" N GLN B 475 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 489 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP B 487 " --> pdb=" O LYS B 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 36 through 37 removed outlier: 3.510A pdb=" N LEU D 489 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN D 475 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 256 through 262 removed outlier: 6.331A pdb=" N VAL C 256 " --> pdb=" O ASP C 250 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP C 250 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 258 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 220 " --> pdb=" O VAL C 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 231 through 232 Processing sheet with id=AB6, first strand: chain 'C' and resid 455 through 457 removed outlier: 4.316A pdb=" N THR C 450 " --> pdb=" O GLN C 443 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN C 443 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN C 475 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 255 through 259 removed outlier: 3.615A pdb=" N ALA D 255 " --> pdb=" O ASP D 250 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 257 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU D 248 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE D 259 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR D 246 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 220 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU D 305 " --> pdb=" O HIS D 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 449 through 451 removed outlier: 3.652A pdb=" N VAL D 451 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 262 hydrogen bonds 524 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 194 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4940 1.33 - 1.45: 5593 1.45 - 1.57: 11085 1.57 - 1.69: 478 1.69 - 1.81: 71 Bond restraints: 22167 Sorted by residual: bond pdb=" C3' DG F 38 " pdb=" C2' DG F 38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC E 83 " pdb=" C2' DC E 83 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT F 7 " pdb=" C2' DT F 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 bond pdb=" C3' DT E 24 " pdb=" C2' DT E 24 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.75e+00 bond pdb=" C3' DT F 50 " pdb=" C2' DT F 50 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.66e+00 ... (remaining 22162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 28514 0.95 - 1.90: 1674 1.90 - 2.85: 742 2.85 - 3.80: 52 3.80 - 4.75: 10 Bond angle restraints: 30992 Sorted by residual: angle pdb=" N3 DT N 10 " pdb=" C4 DT N 10 " pdb=" O4 DT N 10 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT K 27 " pdb=" C4 DT K 27 " pdb=" O4 DT K 27 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT K 40 " pdb=" C4 DT K 40 " pdb=" O4 DT K 40 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT E 4 " pdb=" C4 DT E 4 " pdb=" O4 DT E 4 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT E 74 " pdb=" C4 DT E 74 " pdb=" O4 DT E 74 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 30987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 11937 35.32 - 70.64: 923 70.64 - 105.96: 11 105.96 - 141.29: 2 141.29 - 176.61: 5 Dihedral angle restraints: 12878 sinusoidal: 6998 harmonic: 5880 Sorted by residual: dihedral pdb=" C4' DA K 35 " pdb=" C3' DA K 35 " pdb=" O3' DA K 35 " pdb=" P DT K 36 " ideal model delta sinusoidal sigma weight residual -140.00 36.61 -176.61 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT F 7 " pdb=" C3' DT F 7 " pdb=" O3' DT F 7 " pdb=" P DA F 8 " ideal model delta sinusoidal sigma weight residual -140.00 35.48 -175.48 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT E 35 " pdb=" C3' DT E 35 " pdb=" O3' DT E 35 " pdb=" P DA E 36 " ideal model delta sinusoidal sigma weight residual 220.00 54.82 165.18 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 12875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1931 0.028 - 0.057: 960 0.057 - 0.085: 286 0.085 - 0.113: 193 0.113 - 0.142: 36 Chirality restraints: 3406 Sorted by residual: chirality pdb=" C3' DT E 35 " pdb=" C4' DT E 35 " pdb=" O3' DT E 35 " pdb=" C2' DT E 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" C3' DA K 35 " pdb=" C4' DA K 35 " pdb=" O3' DA K 35 " pdb=" C2' DA K 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" C3' DC K 33 " pdb=" C4' DC K 33 " pdb=" O3' DC K 33 " pdb=" C2' DC K 33 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 3403 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 43 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 44 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 71 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO G 72 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 43 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO B 44 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.016 5.00e-02 4.00e+02 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3435 2.77 - 3.31: 19862 3.31 - 3.84: 38401 3.84 - 4.37: 43184 4.37 - 4.90: 67284 Nonbonded interactions: 172166 Sorted by model distance: nonbonded pdb=" O2 DT N 31 " pdb=" NH2 ARG C 118 " model vdw 2.243 3.120 nonbonded pdb=" OP2 DA F 60 " pdb=" OH TYR B 95 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 457 " pdb=" O MET C 483 " model vdw 2.278 3.040 nonbonded pdb=" O ALA D 321 " pdb=" OG SER D 324 " model vdw 2.286 3.040 nonbonded pdb=" O TYR D 347 " pdb=" ND2 ASN D 351 " model vdw 2.291 3.120 ... (remaining 172161 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 40 through 331 or resid 341 through 358 or resid 377 throu \ gh 524)) selection = (chain 'B' and (resid 40 through 187 or resid 212 through 331 or resid 341 throu \ gh 358 or resid 377 through 524)) selection = (chain 'C' and (resid 40 through 187 or resid 212 through 524)) } 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 group one per residue 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.280 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 22167 Z= 0.358 Angle : 0.570 4.746 30992 Z= 0.497 Chirality : 0.041 0.142 3406 Planarity : 0.003 0.041 3100 Dihedral : 19.082 176.607 9078 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.28 % Allowed : 3.81 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 1952 helix: 2.62 (0.17), residues: 933 sheet: 0.37 (0.31), residues: 281 loop : -0.39 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.009 0.001 TYR C 152 PHE 0.011 0.001 PHE G 30 TRP 0.004 0.001 TRP C 487 HIS 0.003 0.000 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.36 (22167) covalent geometry : angle 0.57036 / 0.50 (30992) hydrogen bonds : bond 0.11508 / 7.45 ( 1096) hydrogen bonds : angle 4.79427 / 4.38 ( 2894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 7 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7730 (mt-10) REVERT: G 21 ARG cc_start: 0.5972 (mmt180) cc_final: 0.5601 (mtt-85) REVERT: G 85 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7331 (mp10) REVERT: H 14 GLN cc_start: 0.7546 (mm110) cc_final: 0.7277 (mm-40) REVERT: H 30 LEU cc_start: 0.8800 (mt) cc_final: 0.7918 (mt) REVERT: A 80 LEU cc_start: 0.8956 (tp) cc_final: 0.8724 (tp) REVERT: A 83 ASN cc_start: 0.7960 (t0) cc_final: 0.7698 (t0) REVERT: A 84 TYR cc_start: 0.7595 (m-80) cc_final: 0.7137 (m-80) REVERT: A 127 THR cc_start: 0.8441 (p) cc_final: 0.8166 (t) REVERT: A 483 MET cc_start: 0.8657 (mmm) cc_final: 0.8185 (mmt) REVERT: A 493 MET cc_start: 0.8521 (mmm) cc_final: 0.8197 (mmm) REVERT: A 533 ASP cc_start: 0.8541 (m-30) cc_final: 0.8239 (p0) REVERT: B 214 SER cc_start: 0.9264 (m) cc_final: 0.8923 (p) REVERT: B 268 TYR cc_start: 0.8375 (p90) cc_final: 0.8027 (p90) REVERT: B 431 GLU cc_start: 0.8696 (pt0) cc_final: 0.7549 (tp30) REVERT: B 513 TRP cc_start: 0.6259 (t-100) cc_final: 0.5324 (t-100) REVERT: B 517 TYR cc_start: 0.8077 (m-10) cc_final: 0.7870 (m-10) REVERT: C 224 HIS cc_start: 0.8041 (p-80) cc_final: 0.7747 (p-80) REVERT: C 233 HIS cc_start: 0.7638 (t-90) cc_final: 0.7237 (t-170) REVERT: C 481 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8299 (mm-30) REVERT: C 493 MET cc_start: 0.7539 (ttp) cc_final: 0.7195 (ttp) REVERT: C 506 TYR cc_start: 0.7179 (t80) cc_final: 0.6878 (t80) REVERT: C 513 TRP cc_start: 0.7011 (t-100) cc_final: 0.6752 (t-100) REVERT: D 134 GLU cc_start: 0.7937 (pt0) cc_final: 0.7686 (tp30) REVERT: D 533 ASP cc_start: 0.8863 (t70) cc_final: 0.8310 (t70) outliers start: 5 outliers final: 0 residues processed: 186 average time/residue: 0.1790 time to fit residues: 48.4449 Evaluate side-chains 127 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN A 82 GLN A 135 GLN A 247 GLN A 277 ASN A 320 GLN B 294 ASN B 403 GLN C 294 ASN C 522 GLN D 280 GLN D 320 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.101724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.081850 restraints weight = 105470.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.083532 restraints weight = 51441.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084058 restraints weight = 35087.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.084469 restraints weight = 24286.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.084592 restraints weight = 22753.384| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22167 Z= 0.133 Angle : 0.538 6.812 30992 Z= 0.320 Chirality : 0.040 0.331 3406 Planarity : 0.003 0.054 3100 Dihedral : 24.167 174.629 4975 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.56 % Allowed : 6.88 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 1952 helix: 2.33 (0.17), residues: 957 sheet: 0.30 (0.31), residues: 277 loop : -0.37 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 181 TYR 0.024 0.001 TYR H 55 PHE 0.010 0.001 PHE G 13 TRP 0.019 0.001 TRP B 244 HIS 0.010 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (22167) covalent geometry : angle 0.53835 / 0.32 (30992) hydrogen bonds : bond 0.04251 / 2.80 ( 1096) hydrogen bonds : angle 4.17877 / 3.70 ( 2894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5535 (mtm-85) REVERT: G 32 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8840 (pp20) REVERT: G 33 GLU cc_start: 0.9233 (mt-10) cc_final: 0.7673 (mm-30) REVERT: G 39 GLU cc_start: 0.8442 (pp20) cc_final: 0.7545 (tt0) REVERT: H 6 LEU cc_start: 0.7848 (tp) cc_final: 0.6943 (tt) REVERT: H 9 ARG cc_start: 0.9248 (mtt180) cc_final: 0.9010 (ttp-110) REVERT: H 10 LEU cc_start: 0.9534 (tt) cc_final: 0.9057 (tt) REVERT: H 44 GLU cc_start: 0.7703 (tt0) cc_final: 0.7191 (pt0) REVERT: H 81 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8476 (tmtt) REVERT: A 83 ASN cc_start: 0.7809 (t0) cc_final: 0.7557 (t0) REVERT: A 84 TYR cc_start: 0.7601 (m-80) cc_final: 0.7189 (m-80) REVERT: A 127 THR cc_start: 0.8531 (p) cc_final: 0.8260 (t) REVERT: A 483 MET cc_start: 0.8711 (mmm) cc_final: 0.8204 (mmt) REVERT: A 493 MET cc_start: 0.8301 (mmm) cc_final: 0.7977 (mmm) REVERT: A 533 ASP cc_start: 0.8545 (m-30) cc_final: 0.8314 (p0) REVERT: B 214 SER cc_start: 0.9394 (m) cc_final: 0.9051 (p) REVERT: B 268 TYR cc_start: 0.8753 (p90) cc_final: 0.8180 (p90) REVERT: B 276 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8497 (ptpt) REVERT: B 347 TYR cc_start: 0.7054 (m-10) cc_final: 0.6713 (m-10) REVERT: B 447 VAL cc_start: 0.5970 (OUTLIER) cc_final: 0.5762 (m) REVERT: B 513 TRP cc_start: 0.6436 (t-100) cc_final: 0.6202 (t-100) REVERT: C 224 HIS cc_start: 0.7888 (p-80) cc_final: 0.7637 (p-80) REVERT: C 233 HIS cc_start: 0.7611 (t-90) cc_final: 0.7231 (t-170) REVERT: C 493 MET cc_start: 0.7282 (ttp) cc_final: 0.6888 (ttp) REVERT: C 513 TRP cc_start: 0.6887 (t-100) cc_final: 0.6538 (t-100) outliers start: 10 outliers final: 3 residues processed: 139 average time/residue: 0.1537 time to fit residues: 32.6415 Evaluate side-chains 125 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 433 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [94, 206, 56, 6, 61, 23, 208, 45, 82, 157, 139] chunk 94 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 157 optimal weight: 0.2980 chunk 139 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 135 GLN A 346 ASN A 475 GLN D 518 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.101373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.083029 restraints weight = 106572.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083889 restraints weight = 63845.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084931 restraints weight = 38276.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.084895 restraints weight = 34191.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.084909 restraints weight = 27532.287| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22167 Z= 0.118 Angle : 0.512 6.961 30992 Z= 0.306 Chirality : 0.040 0.359 3406 Planarity : 0.003 0.058 3100 Dihedral : 24.359 175.544 4975 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.62 % Allowed : 7.39 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 1952 helix: 2.21 (0.17), residues: 973 sheet: 0.26 (0.31), residues: 285 loop : -0.34 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.011 0.001 TYR H 76 PHE 0.039 0.001 PHE G 30 TRP 0.029 0.001 TRP B 244 HIS 0.009 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.12 (22167) covalent geometry : angle 0.51221 / 0.31 (30992) hydrogen bonds : bond 0.03663 / 2.42 ( 1096) hydrogen bonds : angle 3.90951 / 3.47 ( 2894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 ARG cc_start: 0.6391 (mmt180) cc_final: 0.5550 (mtm180) REVERT: G 28 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8428 (mp0) REVERT: G 39 GLU cc_start: 0.8423 (pp20) cc_final: 0.7587 (tt0) REVERT: G 85 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8151 (mp10) REVERT: H 13 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7102 (pt0) REVERT: H 14 GLN cc_start: 0.7475 (tp40) cc_final: 0.7273 (tp-100) REVERT: H 23 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7126 (tm-30) REVERT: H 81 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8511 (tmtt) REVERT: A 83 ASN cc_start: 0.7803 (t0) cc_final: 0.7576 (t0) REVERT: A 84 TYR cc_start: 0.7576 (m-80) cc_final: 0.7220 (m-80) REVERT: A 102 ARG cc_start: 0.9172 (ptm160) cc_final: 0.8954 (ptm160) REVERT: A 117 ASP cc_start: 0.7505 (t0) cc_final: 0.7010 (t0) REVERT: A 127 THR cc_start: 0.8520 (p) cc_final: 0.8246 (t) REVERT: A 483 MET cc_start: 0.8715 (mmm) cc_final: 0.8198 (mmt) REVERT: A 533 ASP cc_start: 0.8484 (m-30) cc_final: 0.8248 (p0) REVERT: B 214 SER cc_start: 0.9371 (m) cc_final: 0.9016 (p) REVERT: B 268 TYR cc_start: 0.8641 (p90) cc_final: 0.8090 (p90) REVERT: B 276 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8560 (ptpt) REVERT: B 347 TYR cc_start: 0.7106 (m-10) cc_final: 0.6702 (m-10) REVERT: B 447 VAL cc_start: 0.5834 (OUTLIER) cc_final: 0.5618 (m) REVERT: B 513 TRP cc_start: 0.6291 (t-100) cc_final: 0.6054 (t-100) REVERT: C 224 HIS cc_start: 0.7941 (p-80) cc_final: 0.7692 (p-80) REVERT: C 233 HIS cc_start: 0.7623 (t-90) cc_final: 0.7237 (t-170) REVERT: C 433 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8768 (p0) REVERT: C 493 MET cc_start: 0.7437 (ttp) cc_final: 0.7228 (ttp) REVERT: C 513 TRP cc_start: 0.6842 (t-100) cc_final: 0.6467 (t-100) REVERT: D 134 GLU cc_start: 0.8142 (pt0) cc_final: 0.7838 (tp30) REVERT: D 289 TYR cc_start: 0.8273 (m-80) cc_final: 0.8006 (m-80) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 0.1593 time to fit residues: 33.1933 Evaluate side-chains 126 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain D residue 533 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [77, 93, 215, 180, 116, 183, 127, 55, 7, 12, 150] chunk 77 optimal weight: 0.0980 chunk 93 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 331 GLN B 309 ASN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.096780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.076415 restraints weight = 104080.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.077603 restraints weight = 62842.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.078363 restraints weight = 34351.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078351 restraints weight = 29829.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.078423 restraints weight = 26583.508| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 22167 Z= 0.222 Angle : 0.640 9.990 30992 Z= 0.365 Chirality : 0.043 0.369 3406 Planarity : 0.004 0.064 3100 Dihedral : 24.612 174.386 4975 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.01 % Allowed : 7.95 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1952 helix: 2.11 (0.17), residues: 983 sheet: -0.10 (0.30), residues: 290 loop : -0.49 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 42 TYR 0.029 0.002 TYR D 260 PHE 0.029 0.002 PHE C 313 TRP 0.046 0.002 TRP B 244 HIS 0.009 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (22167) covalent geometry : angle 0.64010 / 0.36 (30992) hydrogen bonds : bond 0.05416 / 3.64 ( 1096) hydrogen bonds : angle 4.21047 / 3.84 ( 2894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8355 (mp10) REVERT: H 23 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 83 ASN cc_start: 0.8007 (t0) cc_final: 0.7713 (t0) REVERT: A 84 TYR cc_start: 0.7631 (m-80) cc_final: 0.7254 (m-80) REVERT: A 117 ASP cc_start: 0.8184 (t0) cc_final: 0.7814 (t0) REVERT: A 483 MET cc_start: 0.8589 (mmm) cc_final: 0.7921 (mmt) REVERT: A 533 ASP cc_start: 0.8440 (m-30) cc_final: 0.8202 (p0) REVERT: B 268 TYR cc_start: 0.8743 (p90) cc_final: 0.8259 (p90) REVERT: B 347 TYR cc_start: 0.7068 (m-10) cc_final: 0.6659 (m-10) REVERT: B 447 VAL cc_start: 0.5936 (OUTLIER) cc_final: 0.5720 (m) REVERT: B 513 TRP cc_start: 0.6408 (t-100) cc_final: 0.6197 (t-100) REVERT: C 233 HIS cc_start: 0.7813 (t-90) cc_final: 0.7386 (t-170) REVERT: C 345 ARG cc_start: 0.6763 (tpt170) cc_final: 0.6335 (tpt170) REVERT: C 433 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8706 (p0) REVERT: C 493 MET cc_start: 0.7430 (ttp) cc_final: 0.7114 (ttp) REVERT: C 513 TRP cc_start: 0.7082 (t-100) cc_final: 0.6773 (t-100) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 0.1564 time to fit residues: 32.4006 Evaluate side-chains 120 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 544 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [121, 90, 203, 166, 142, 30, 64, 211, 131, 207, 31] chunk 121 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 203 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 142 optimal weight: 0.4980 chunk 30 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS D 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.097730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.077834 restraints weight = 102925.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078971 restraints weight = 50385.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.079363 restraints weight = 31834.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079452 restraints weight = 27930.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079446 restraints weight = 26251.997| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22167 Z= 0.152 Angle : 0.559 12.638 30992 Z= 0.325 Chirality : 0.041 0.342 3406 Planarity : 0.003 0.065 3100 Dihedral : 24.583 172.606 4975 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.18 % Allowed : 8.84 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.19), residues: 1952 helix: 2.25 (0.17), residues: 976 sheet: -0.07 (0.30), residues: 285 loop : -0.44 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.020 0.001 TYR G 11 PHE 0.016 0.001 PHE G 52 TRP 0.023 0.001 TRP B 244 HIS 0.009 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (22167) covalent geometry : angle 0.55947 / 0.33 (30992) hydrogen bonds : bond 0.03885 / 2.58 ( 1096) hydrogen bonds : angle 3.98802 / 3.63 ( 2894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 MET cc_start: 0.8401 (ttt) cc_final: 0.8151 (mmp) REVERT: G 39 GLU cc_start: 0.8699 (pp20) cc_final: 0.7700 (tt0) REVERT: G 85 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8352 (mp10) REVERT: H 23 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 84 TYR cc_start: 0.7628 (m-80) cc_final: 0.7320 (m-80) REVERT: A 117 ASP cc_start: 0.8181 (t0) cc_final: 0.7809 (t0) REVERT: A 483 MET cc_start: 0.8595 (mmm) cc_final: 0.7991 (mmt) REVERT: A 533 ASP cc_start: 0.8408 (m-30) cc_final: 0.8208 (p0) REVERT: B 268 TYR cc_start: 0.8747 (p90) cc_final: 0.8290 (p90) REVERT: B 276 LYS cc_start: 0.8907 (ptpp) cc_final: 0.8519 (ptpt) REVERT: B 347 TYR cc_start: 0.7096 (m-10) cc_final: 0.6624 (m-10) REVERT: B 447 VAL cc_start: 0.5942 (OUTLIER) cc_final: 0.5728 (m) REVERT: C 233 HIS cc_start: 0.7820 (t-90) cc_final: 0.7389 (t-170) REVERT: C 513 TRP cc_start: 0.7078 (t-100) cc_final: 0.6672 (t-100) REVERT: C 517 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6885 (t80) outliers start: 21 outliers final: 9 residues processed: 132 average time/residue: 0.1559 time to fit residues: 31.4772 Evaluate side-chains 121 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain D residue 533 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [130, 41, 28, 36, 59, 136, 53, 44, 124, 75, 74] chunk 130 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 36 optimal weight: 40.0000 chunk 59 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.096779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.076892 restraints weight = 103239.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.078032 restraints weight = 50204.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078179 restraints weight = 33034.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078359 restraints weight = 27873.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078367 restraints weight = 26339.649| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22167 Z= 0.180 Angle : 0.586 11.669 30992 Z= 0.337 Chirality : 0.042 0.322 3406 Planarity : 0.004 0.065 3100 Dihedral : 24.672 172.283 4975 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.06 % Allowed : 9.23 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 1952 helix: 2.21 (0.17), residues: 970 sheet: -0.21 (0.30), residues: 287 loop : -0.45 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.040 0.001 TYR G 11 PHE 0.017 0.001 PHE G 30 TRP 0.025 0.001 TRP B 244 HIS 0.008 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (22167) covalent geometry : angle 0.58639 / 0.34 (30992) hydrogen bonds : bond 0.04194 / 2.78 ( 1096) hydrogen bonds : angle 4.05735 / 3.67 ( 2894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 39 GLU cc_start: 0.8750 (pp20) cc_final: 0.7760 (tt0) REVERT: G 85 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8381 (mp10) REVERT: A 84 TYR cc_start: 0.7451 (m-80) cc_final: 0.7238 (m-80) REVERT: A 117 ASP cc_start: 0.8215 (t0) cc_final: 0.7844 (t0) REVERT: A 483 MET cc_start: 0.8612 (mmm) cc_final: 0.7994 (mmt) REVERT: B 268 TYR cc_start: 0.8792 (p90) cc_final: 0.8318 (p90) REVERT: B 276 LYS cc_start: 0.9051 (ptpp) cc_final: 0.8804 (ptpt) REVERT: B 347 TYR cc_start: 0.7020 (m-10) cc_final: 0.6603 (m-10) REVERT: B 447 VAL cc_start: 0.5954 (OUTLIER) cc_final: 0.5730 (m) REVERT: C 493 MET cc_start: 0.7315 (ttp) cc_final: 0.6886 (ttp) REVERT: C 513 TRP cc_start: 0.7052 (t-100) cc_final: 0.6539 (t-100) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.1578 time to fit residues: 31.4921 Evaluate side-chains 121 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 533 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [10, 92, 194, 55, 201, 151, 0, 203, 90, 155, 20] chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 203 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.096883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075666 restraints weight = 103078.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.077638 restraints weight = 51918.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077968 restraints weight = 32808.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.078355 restraints weight = 26062.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.078453 restraints weight = 23598.167| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22167 Z= 0.160 Angle : 0.586 13.488 30992 Z= 0.334 Chirality : 0.041 0.315 3406 Planarity : 0.003 0.066 3100 Dihedral : 24.702 172.953 4975 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.06 % Allowed : 9.57 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1952 helix: 2.22 (0.17), residues: 965 sheet: -0.22 (0.30), residues: 281 loop : -0.54 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.029 0.001 TYR G 11 PHE 0.012 0.001 PHE G 52 TRP 0.025 0.001 TRP B 244 HIS 0.008 0.001 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (22167) covalent geometry : angle 0.58629 / 0.33 (30992) hydrogen bonds : bond 0.03879 / 2.57 ( 1096) hydrogen bonds : angle 4.00206 / 3.62 ( 2894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8448 (mp10) REVERT: H 1 MET cc_start: 0.3853 (tpp) cc_final: 0.3649 (tpt) REVERT: H 29 MET cc_start: 0.8138 (ppp) cc_final: 0.7934 (ppp) REVERT: A 84 TYR cc_start: 0.7449 (m-80) cc_final: 0.7227 (m-80) REVERT: A 117 ASP cc_start: 0.8271 (t0) cc_final: 0.7900 (t0) REVERT: A 483 MET cc_start: 0.8480 (mmm) cc_final: 0.7751 (mmm) REVERT: B 268 TYR cc_start: 0.8678 (p90) cc_final: 0.8266 (p90) REVERT: B 276 LYS cc_start: 0.9006 (ptpp) cc_final: 0.8547 (ptpt) REVERT: B 347 TYR cc_start: 0.6968 (m-10) cc_final: 0.6546 (m-10) REVERT: B 447 VAL cc_start: 0.6000 (OUTLIER) cc_final: 0.5798 (m) REVERT: B 513 TRP cc_start: 0.6572 (t-100) cc_final: 0.6360 (t-100) REVERT: C 493 MET cc_start: 0.7617 (ttp) cc_final: 0.7221 (ttp) REVERT: C 513 TRP cc_start: 0.7077 (t-100) cc_final: 0.6436 (t-100) REVERT: D 512 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6771 (tt) outliers start: 19 outliers final: 10 residues processed: 128 average time/residue: 0.1694 time to fit residues: 32.9396 Evaluate side-chains 122 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 533 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [86, 182, 127, 128, 94, 166, 124, 183, 30, 26, 139] chunk 86 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 26 optimal weight: 10.9990 chunk 139 optimal weight: 0.0570 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS D 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.095006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.074895 restraints weight = 102221.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.075926 restraints weight = 52012.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076375 restraints weight = 32247.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076397 restraints weight = 27803.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076437 restraints weight = 26574.887| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22167 Z= 0.244 Angle : 0.669 15.098 30992 Z= 0.376 Chirality : 0.044 0.308 3406 Planarity : 0.004 0.063 3100 Dihedral : 24.854 171.434 4975 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.01 % Allowed : 10.13 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1952 helix: 2.02 (0.17), residues: 970 sheet: -0.33 (0.32), residues: 252 loop : -0.72 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 181 TYR 0.033 0.002 TYR B 517 PHE 0.019 0.002 PHE H 80 TRP 0.021 0.002 TRP B 244 HIS 0.010 0.001 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (22167) covalent geometry : angle 0.66888 / 0.38 (30992) hydrogen bonds : bond 0.05066 / 3.38 ( 1096) hydrogen bonds : angle 4.26685 / 3.89 ( 2894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8426 (mp10) REVERT: H 33 MET cc_start: 0.8542 (ptm) cc_final: 0.8332 (ptp) REVERT: A 84 TYR cc_start: 0.7412 (m-80) cc_final: 0.7202 (m-80) REVERT: A 117 ASP cc_start: 0.8324 (t0) cc_final: 0.7994 (t0) REVERT: A 483 MET cc_start: 0.8554 (mmm) cc_final: 0.8057 (mmm) REVERT: B 268 TYR cc_start: 0.8723 (p90) cc_final: 0.8334 (p90) REVERT: B 276 LYS cc_start: 0.8985 (ptpp) cc_final: 0.8436 (ptpp) REVERT: B 447 VAL cc_start: 0.5805 (OUTLIER) cc_final: 0.5605 (m) REVERT: C 233 HIS cc_start: 0.7949 (t-90) cc_final: 0.7518 (t70) REVERT: C 493 MET cc_start: 0.7576 (ttp) cc_final: 0.7153 (ttp) outliers start: 18 outliers final: 14 residues processed: 122 average time/residue: 0.1660 time to fit residues: 30.5417 Evaluate side-chains 119 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain D residue 533 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [59, 152, 217, 56, 166, 32, 22, 96, 2, 106, 213] chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 GLN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.095698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073621 restraints weight = 101947.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.075400 restraints weight = 50420.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076451 restraints weight = 33251.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.077058 restraints weight = 25938.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077389 restraints weight = 22372.078| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22167 Z= 0.180 Angle : 0.612 15.072 30992 Z= 0.350 Chirality : 0.043 0.315 3406 Planarity : 0.004 0.065 3100 Dihedral : 24.860 172.557 4975 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.01 % Allowed : 10.41 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1952 helix: 2.05 (0.17), residues: 965 sheet: -0.24 (0.30), residues: 280 loop : -0.70 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 9 TYR 0.029 0.001 TYR G 11 PHE 0.025 0.002 PHE H 80 TRP 0.021 0.001 TRP B 244 HIS 0.007 0.001 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (22167) covalent geometry : angle 0.61249 / 0.35 (30992) hydrogen bonds : bond 0.04176 / 2.77 ( 1096) hydrogen bonds : angle 4.13348 / 3.76 ( 2894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 85 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8581 (mp10) REVERT: H 33 MET cc_start: 0.8443 (ptm) cc_final: 0.8046 (ptp) REVERT: A 84 TYR cc_start: 0.7379 (m-80) cc_final: 0.7150 (m-80) REVERT: A 483 MET cc_start: 0.8547 (mmm) cc_final: 0.8021 (mmt) REVERT: B 268 TYR cc_start: 0.8748 (p90) cc_final: 0.8368 (p90) REVERT: B 276 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8589 (ptpt) REVERT: B 347 TYR cc_start: 0.7009 (m-10) cc_final: 0.6723 (m-10) REVERT: C 233 HIS cc_start: 0.8006 (t-90) cc_final: 0.7510 (t70) REVERT: C 493 MET cc_start: 0.7560 (ttp) cc_final: 0.7324 (ttp) outliers start: 18 outliers final: 14 residues processed: 118 average time/residue: 0.1636 time to fit residues: 29.1042 Evaluate side-chains 117 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain D residue 533 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [197, 161, 213, 26, 105, 111, 201, 138, 160, 115, 28] chunk 197 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.095857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.075894 restraints weight = 103334.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.077019 restraints weight = 51867.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.077283 restraints weight = 33247.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.077576 restraints weight = 28726.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.077535 restraints weight = 26122.011| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22167 Z= 0.166 Angle : 0.614 17.170 30992 Z= 0.346 Chirality : 0.043 0.359 3406 Planarity : 0.004 0.067 3100 Dihedral : 24.890 173.047 4975 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.95 % Allowed : 10.52 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1952 helix: 2.07 (0.17), residues: 964 sheet: -0.14 (0.30), residues: 270 loop : -0.67 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 9 TYR 0.041 0.001 TYR B 517 PHE 0.012 0.001 PHE G 52 TRP 0.032 0.002 TRP B 244 HIS 0.009 0.001 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (22167) covalent geometry : angle 0.61406 / 0.35 (30992) hydrogen bonds : bond 0.04045 / 2.68 ( 1096) hydrogen bonds : angle 4.05494 / 3.69 ( 2894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 85 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8492 (mp10) REVERT: H 33 MET cc_start: 0.8488 (ptm) cc_final: 0.8237 (ptp) REVERT: A 84 TYR cc_start: 0.7392 (m-80) cc_final: 0.7086 (m-80) REVERT: A 483 MET cc_start: 0.8542 (mmm) cc_final: 0.8057 (mmm) REVERT: A 533 ASP cc_start: 0.8626 (p0) cc_final: 0.8350 (p0) REVERT: B 268 TYR cc_start: 0.8739 (p90) cc_final: 0.8371 (p90) REVERT: B 276 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8315 (ptpp) REVERT: B 347 TYR cc_start: 0.7075 (m-10) cc_final: 0.6804 (m-10) REVERT: C 233 HIS cc_start: 0.7984 (t-90) cc_final: 0.7448 (t-170) REVERT: C 493 MET cc_start: 0.7574 (ttp) cc_final: 0.7322 (ttp) outliers start: 17 outliers final: 15 residues processed: 111 average time/residue: 0.1564 time to fit residues: 26.4195 Evaluate side-chains 111 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain D residue 533 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: [69, 50, 130, 173, 162, 196, 112, 149, 134, 73, 103] chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS D 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.095275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.075035 restraints weight = 103704.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076109 restraints weight = 52512.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.076534 restraints weight = 32961.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076593 restraints weight = 29180.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076632 restraints weight = 26734.995| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22167 Z= 0.192 Angle : 0.630 14.846 30992 Z= 0.356 Chirality : 0.043 0.318 3406 Planarity : 0.004 0.068 3100 Dihedral : 24.948 172.333 4975 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.06 % Allowed : 10.86 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1952 helix: 2.03 (0.17), residues: 965 sheet: -0.17 (0.31), residues: 262 loop : -0.76 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 9 TYR 0.047 0.001 TYR G 11 PHE 0.027 0.002 PHE H 80 TRP 0.023 0.002 TRP B 244 HIS 0.009 0.001 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (22167) covalent geometry : angle 0.62985 / 0.36 (30992) hydrogen bonds : bond 0.04341 / 2.88 ( 1096) hydrogen bonds : angle 4.12645 / 3.76 ( 2894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.33 seconds wall clock time: 59 minutes 54.97 seconds (3594.97 seconds total)