Starting phenix.real_space_refine on Wed Jun 18 13:11:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t20_25607/06_2025/7t20_25607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t20_25607/06_2025/7t20_25607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t20_25607/06_2025/7t20_25607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t20_25607/06_2025/7t20_25607.map" model { file = "/net/cci-nas-00/data/ceres_data/7t20_25607/06_2025/7t20_25607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t20_25607/06_2025/7t20_25607.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 22 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 13028 2.51 5 N 3752 2.21 5 O 4222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21106 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "B" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "D" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "F" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.13, per 1000 atoms: 0.62 Number of scatterers: 21106 At special positions: 0 Unit cell: (118.08, 139.2, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 22 15.00 Mg 4 11.99 O 4222 8.00 N 3752 7.00 C 13028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.8 seconds 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 7 sheets defined 61.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.740A pdb=" N GLY A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.670A pdb=" N THR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 Processing helix chain 'A' and resid 153 through 172 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 211 through 217 Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.862A pdb=" N MET A 348 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 removed outlier: 4.336A pdb=" N GLU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.505A pdb=" N LEU A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.542A pdb=" N TYR A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.605A pdb=" N VAL B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.550A pdb=" N GLY B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.686A pdb=" N THR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 Processing helix chain 'B' and resid 153 through 171 Processing helix chain 'B' and resid 182 through 199 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 236 through 252 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 290 through 308 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.501A pdb=" N LEU B 347 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.554A pdb=" N GLN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 4.336A pdb=" N GLN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.805A pdb=" N GLY C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.737A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 Processing helix chain 'C' and resid 153 through 173 Processing helix chain 'C' and resid 182 through 199 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.517A pdb=" N ILE C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 356 through 376 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.666A pdb=" N TYR C 424 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 78 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.618A pdb=" N GLY D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 removed outlier: 3.691A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 Processing helix chain 'D' and resid 153 through 173 Processing helix chain 'D' and resid 181 through 199 removed outlier: 4.168A pdb=" N VAL D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 290 through 308 Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.599A pdb=" N TYR D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 78 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.674A pdb=" N GLY E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.713A pdb=" N THR E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 148 Processing helix chain 'E' and resid 153 through 173 Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 182 through 199 Processing helix chain 'E' and resid 213 through 218 Processing helix chain 'E' and resid 236 through 251 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 290 through 308 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 356 through 376 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.759A pdb=" N TYR E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.512A pdb=" N VAL F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 78 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 96 through 101 removed outlier: 3.565A pdb=" N GLY F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.752A pdb=" N THR F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 148 Processing helix chain 'F' and resid 153 through 172 removed outlier: 3.822A pdb=" N ARG F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.888A pdb=" N GLN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 removed outlier: 3.665A pdb=" N LYS F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 251 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 290 through 308 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 356 through 376 Processing helix chain 'F' and resid 387 through 392 removed outlier: 3.626A pdb=" N GLN F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.657A pdb=" N TYR F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.778A pdb=" N LEU B 257 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 340 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU B 382 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE B 342 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 229 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 383 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 226 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET B 416 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE B 228 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 418 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 230 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 312 removed outlier: 6.323A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 257 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE A 340 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 380 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 180 through 181 removed outlier: 3.674A pdb=" N VAL D 229 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 383 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU D 226 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET D 416 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 228 " --> pdb=" O MET D 416 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE D 418 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA D 230 " --> pdb=" O ILE D 418 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 312 through 313 removed outlier: 8.197A pdb=" N ASP C 313 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 257 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 382 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 229 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 383 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU C 226 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET C 416 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 180 through 181 removed outlier: 6.774A pdb=" N LEU F 257 " --> pdb=" O MET F 341 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL F 229 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU F 226 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET F 416 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE F 228 " --> pdb=" O MET F 416 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE F 418 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA F 230 " --> pdb=" O ILE F 418 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 310 through 313 removed outlier: 6.751A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 229 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER E 383 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU E 226 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N MET E 416 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE E 228 " --> pdb=" O MET E 416 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE E 418 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA E 230 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) 1226 hydrogen bonds defined for protein. 3570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6851 1.34 - 1.45: 2267 1.45 - 1.57: 12106 1.57 - 1.69: 40 1.69 - 1.81: 159 Bond restraints: 21423 Sorted by residual: bond pdb=" O3A ANP E1001 " pdb=" PB ANP E1001 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" O3A ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" O3A ANP D1001 " pdb=" PB ANP D1001 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" O3A ANP F1001 " pdb=" PB ANP F1001 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" N3B ANP E1001 " pdb=" PG ANP E1001 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 21418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 28959 3.90 - 7.79: 63 7.79 - 11.69: 9 11.69 - 15.59: 2 15.59 - 19.48: 2 Bond angle restraints: 29035 Sorted by residual: angle pdb=" PB ANP E1001 " pdb=" N3B ANP E1001 " pdb=" PG ANP E1001 " ideal model delta sigma weight residual 126.95 107.47 19.48 3.00e+00 1.11e-01 4.22e+01 angle pdb=" PB ANP C1001 " pdb=" N3B ANP C1001 " pdb=" PG ANP C1001 " ideal model delta sigma weight residual 126.95 109.26 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" PB ANP D1001 " pdb=" N3B ANP D1001 " pdb=" PG ANP D1001 " ideal model delta sigma weight residual 126.95 111.63 15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" PB ANP F1001 " pdb=" N3B ANP F1001 " pdb=" PG ANP F1001 " ideal model delta sigma weight residual 126.95 111.98 14.97 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C SER D 234 " pdb=" CA SER D 234 " pdb=" CB SER D 234 " ideal model delta sigma weight residual 117.23 111.21 6.02 1.36e+00 5.41e-01 1.96e+01 ... (remaining 29030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 13005 31.79 - 63.58: 245 63.58 - 95.38: 42 95.38 - 127.17: 0 127.17 - 158.96: 1 Dihedral angle restraints: 13293 sinusoidal: 5589 harmonic: 7704 Sorted by residual: dihedral pdb=" CA TYR E 344 " pdb=" C TYR E 344 " pdb=" N LEU E 345 " pdb=" CA LEU E 345 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" O1A ANP C1001 " pdb=" O3A ANP C1001 " pdb=" PA ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sinusoidal sigma weight residual 83.11 -75.85 158.96 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA TYR B 344 " pdb=" C TYR B 344 " pdb=" N LEU B 345 " pdb=" CA LEU B 345 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 13290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2788 0.055 - 0.110: 468 0.110 - 0.165: 30 0.165 - 0.220: 0 0.220 - 0.275: 4 Chirality restraints: 3290 Sorted by residual: chirality pdb=" C3' ANP E1001 " pdb=" C2' ANP E1001 " pdb=" C4' ANP E1001 " pdb=" O3' ANP E1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP C1001 " pdb=" C2' ANP C1001 " pdb=" C4' ANP C1001 " pdb=" O3' ANP C1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP F1001 " pdb=" C2' ANP F1001 " pdb=" C4' ANP F1001 " pdb=" O3' ANP F1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3287 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 232 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO D 233 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 233 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 233 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 63 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 63 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO E 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " -0.021 5.00e-02 4.00e+02 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 377 2.64 - 3.21: 19205 3.21 - 3.77: 36407 3.77 - 4.34: 48534 4.34 - 4.90: 77351 Nonbonded interactions: 181874 Sorted by model distance: nonbonded pdb=" OG1 THR D 238 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb=" OG1 THR E 238 " pdb="MG MG E1002 " model vdw 2.079 2.170 nonbonded pdb=" O2G ANP C1001 " pdb="MG MG C1002 " model vdw 2.079 2.170 nonbonded pdb=" O2B ANP D1001 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb=" O2G ANP E1001 " pdb="MG MG E1002 " model vdw 2.079 2.170 ... (remaining 181869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 25 through 464) selection = (chain 'C' and resid 25 through 464) selection = (chain 'D' and resid 25 through 464) selection = (chain 'E' and resid 25 through 464) selection = (chain 'F' and resid 25 through 464) } 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: 1.710 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: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 47.770 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.148 21423 Z= 0.204 Angle : 0.635 19.484 29035 Z= 0.350 Chirality : 0.039 0.275 3290 Planarity : 0.004 0.052 3812 Dihedral : 12.589 158.959 8301 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.27 % Favored : 97.58 % Rotamer: Outliers : 3.24 % Allowed : 4.88 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 2649 helix: 1.78 (0.13), residues: 1473 sheet: -2.17 (0.25), residues: 314 loop : -0.79 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 457 HIS 0.002 0.001 HIS D 334 PHE 0.010 0.001 PHE D 166 TYR 0.023 0.001 TYR F 344 ARG 0.002 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.13716 ( 1226) hydrogen bonds : angle 5.27944 ( 3570) covalent geometry : bond 0.00385 (21423) covalent geometry : angle 0.63482 (29035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 403 time to evaluate : 2.255 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ILE cc_start: 0.9283 (mm) cc_final: 0.9003 (pt) REVERT: A 339 LEU cc_start: 0.8704 (tp) cc_final: 0.8473 (mp) REVERT: A 347 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 50 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.9159 (p0) REVERT: B 235 MET cc_start: 0.4420 (mmt) cc_final: 0.3816 (mmm) REVERT: B 268 ILE cc_start: 0.9261 (mm) cc_final: 0.9029 (pt) REVERT: B 345 LEU cc_start: 0.9479 (mt) cc_final: 0.9258 (mt) REVERT: C 212 ASP cc_start: 0.9566 (OUTLIER) cc_final: 0.9215 (p0) REVERT: C 371 LEU cc_start: 0.9607 (tp) cc_final: 0.9306 (tp) REVERT: D 235 MET cc_start: 0.7917 (mmt) cc_final: 0.7340 (mmm) REVERT: D 240 PHE cc_start: 0.9386 (t80) cc_final: 0.9102 (t80) REVERT: D 263 MET cc_start: 0.8874 (mtp) cc_final: 0.8663 (mtt) REVERT: D 382 LEU cc_start: 0.9143 (mt) cc_final: 0.8885 (mt) REVERT: D 411 ASP cc_start: 0.7797 (m-30) cc_final: 0.7343 (t0) REVERT: E 49 ASP cc_start: 0.9578 (OUTLIER) cc_final: 0.9367 (p0) REVERT: E 315 SER cc_start: 0.8694 (m) cc_final: 0.8336 (p) REVERT: E 390 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8703 (mp0) REVERT: F 105 TYR cc_start: 0.9314 (t80) cc_final: 0.9094 (t80) REVERT: F 159 ASP cc_start: 0.9401 (m-30) cc_final: 0.9016 (p0) REVERT: F 263 MET cc_start: 0.8659 (mtt) cc_final: 0.8141 (mtt) REVERT: F 382 LEU cc_start: 0.8597 (mt) cc_final: 0.7882 (mp) REVERT: F 389 LEU cc_start: 0.9198 (tt) cc_final: 0.8948 (tt) outliers start: 73 outliers final: 15 residues processed: 471 average time/residue: 0.4033 time to fit residues: 280.8705 Evaluate side-chains 265 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 10.0000 chunk 200 optimal weight: 0.0270 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS C 96 GLN C 252 GLN C 454 ASN D 65 HIS D 252 GLN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN E 199 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 467 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.069928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.055599 restraints weight = 224464.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.057119 restraints weight = 119184.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.057389 restraints weight = 71348.475| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21423 Z= 0.166 Angle : 0.587 9.071 29035 Z= 0.304 Chirality : 0.041 0.237 3290 Planarity : 0.005 0.072 3812 Dihedral : 9.687 168.184 3150 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.91 % Favored : 96.98 % Rotamer: Outliers : 0.35 % Allowed : 1.86 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2649 helix: 2.08 (0.13), residues: 1513 sheet: -1.88 (0.26), residues: 311 loop : -0.45 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 457 HIS 0.011 0.002 HIS D 65 PHE 0.027 0.002 PHE A 460 TYR 0.018 0.001 TYR B 344 ARG 0.007 0.001 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1226) hydrogen bonds : angle 4.42988 ( 3570) covalent geometry : bond 0.00357 (21423) covalent geometry : angle 0.58743 (29035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 291 time to evaluate : 2.429 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9679 (tpt) cc_final: 0.9414 (tpp) REVERT: A 339 LEU cc_start: 0.9602 (tp) cc_final: 0.9256 (pp) REVERT: A 341 MET cc_start: 0.8053 (ttt) cc_final: 0.5915 (ppp) REVERT: B 172 ARG cc_start: 0.6970 (tpt170) cc_final: 0.6743 (tpt170) REVERT: B 270 MET cc_start: 0.9519 (mtm) cc_final: 0.9196 (mmm) REVERT: B 347 LEU cc_start: 0.9243 (mm) cc_final: 0.8746 (tt) REVERT: B 348 MET cc_start: 0.9516 (mmm) cc_final: 0.8798 (tpt) REVERT: D 411 ASP cc_start: 0.8700 (m-30) cc_final: 0.8366 (t0) REVERT: E 242 MET cc_start: 0.7807 (ttp) cc_final: 0.7540 (ptm) REVERT: F 106 LEU cc_start: 0.9871 (mt) cc_final: 0.9556 (mt) REVERT: F 240 PHE cc_start: 0.9807 (t80) cc_final: 0.9499 (t80) REVERT: F 242 MET cc_start: 0.8256 (ttp) cc_final: 0.7687 (ptm) REVERT: F 269 MET cc_start: 0.9266 (ttm) cc_final: 0.9060 (ttm) outliers start: 8 outliers final: 3 residues processed: 298 average time/residue: 0.3813 time to fit residues: 167.1305 Evaluate side-chains 210 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 186 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 182 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 249 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 63 optimal weight: 0.4980 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 281 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.065711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.051828 restraints weight = 231953.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.053328 restraints weight = 122477.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.053548 restraints weight = 73648.407| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21423 Z= 0.177 Angle : 0.593 9.313 29035 Z= 0.310 Chirality : 0.040 0.216 3290 Planarity : 0.005 0.106 3812 Dihedral : 8.522 150.178 3150 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2649 helix: 1.77 (0.13), residues: 1520 sheet: -1.57 (0.28), residues: 295 loop : -0.51 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 48 HIS 0.005 0.002 HIS D 65 PHE 0.026 0.002 PHE C 259 TYR 0.025 0.002 TYR A 344 ARG 0.010 0.001 ARG D 366 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1226) hydrogen bonds : angle 4.37322 ( 3570) covalent geometry : bond 0.00363 (21423) covalent geometry : angle 0.59339 (29035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 2.502 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9701 (tpt) cc_final: 0.9362 (tpp) REVERT: A 341 MET cc_start: 0.7767 (ttt) cc_final: 0.6174 (ppp) REVERT: B 172 ARG cc_start: 0.6919 (tpt170) cc_final: 0.6469 (tpt170) REVERT: B 235 MET cc_start: 0.3563 (mmm) cc_final: 0.3074 (mmm) REVERT: B 348 MET cc_start: 0.9542 (mmm) cc_final: 0.9144 (tpt) REVERT: C 415 ILE cc_start: 0.9790 (mt) cc_final: 0.9492 (mp) REVERT: D 105 TYR cc_start: 0.8678 (t80) cc_final: 0.8349 (t80) REVERT: D 281 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8124 (pp30) REVERT: D 348 MET cc_start: 0.9733 (mmm) cc_final: 0.9276 (tpt) REVERT: D 411 ASP cc_start: 0.9034 (m-30) cc_final: 0.8771 (t0) REVERT: E 263 MET cc_start: 0.8816 (mmp) cc_final: 0.8377 (mmm) REVERT: E 348 MET cc_start: 0.8940 (tpt) cc_final: 0.8612 (tpt) REVERT: F 105 TYR cc_start: 0.8745 (t80) cc_final: 0.8459 (t80) REVERT: F 242 MET cc_start: 0.8245 (ttp) cc_final: 0.7954 (ptm) REVERT: F 270 MET cc_start: 0.9470 (ttt) cc_final: 0.8723 (tmm) REVERT: F 418 ILE cc_start: 0.9610 (mp) cc_final: 0.9201 (mp) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.4211 time to fit residues: 168.6821 Evaluate side-chains 204 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN E 140 ASN E 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.065944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.051915 restraints weight = 233466.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.053355 restraints weight = 122115.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.053649 restraints weight = 73712.857| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21423 Z= 0.139 Angle : 0.557 9.444 29035 Z= 0.290 Chirality : 0.040 0.174 3290 Planarity : 0.004 0.058 3812 Dihedral : 7.586 144.519 3150 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2649 helix: 1.69 (0.13), residues: 1516 sheet: -1.45 (0.27), residues: 315 loop : -0.44 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 457 HIS 0.004 0.001 HIS E 29 PHE 0.027 0.002 PHE C 259 TYR 0.014 0.001 TYR A 344 ARG 0.012 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 1226) hydrogen bonds : angle 4.30255 ( 3570) covalent geometry : bond 0.00293 (21423) covalent geometry : angle 0.55717 (29035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 2.265 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9799 (tpt) cc_final: 0.9403 (tpp) REVERT: A 341 MET cc_start: 0.7849 (ttt) cc_final: 0.6063 (ppp) REVERT: B 348 MET cc_start: 0.9467 (mmm) cc_final: 0.8982 (tpt) REVERT: C 242 MET cc_start: 0.9697 (tpt) cc_final: 0.9468 (tpp) REVERT: C 415 ILE cc_start: 0.9511 (mt) cc_final: 0.9282 (mp) REVERT: C 416 MET cc_start: 0.9548 (tpt) cc_final: 0.9337 (tpp) REVERT: D 105 TYR cc_start: 0.8884 (t80) cc_final: 0.8509 (t80) REVERT: D 281 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8458 (pp30) REVERT: D 348 MET cc_start: 0.9671 (mmm) cc_final: 0.9407 (tpt) REVERT: D 411 ASP cc_start: 0.8805 (m-30) cc_final: 0.8426 (t0) REVERT: E 414 LEU cc_start: 0.9568 (mt) cc_final: 0.9350 (mt) REVERT: F 105 TYR cc_start: 0.9139 (t80) cc_final: 0.8808 (t80) REVERT: F 242 MET cc_start: 0.8703 (ttp) cc_final: 0.8438 (ptm) REVERT: F 418 ILE cc_start: 0.9623 (mp) cc_final: 0.9259 (mp) outliers start: 2 outliers final: 0 residues processed: 260 average time/residue: 0.3728 time to fit residues: 145.0308 Evaluate side-chains 194 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 195 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 155 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 140 ASN B 112 ASN B 140 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN F 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.063642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.049777 restraints weight = 237436.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.051043 restraints weight = 126098.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.051323 restraints weight = 78044.724| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21423 Z= 0.163 Angle : 0.578 10.626 29035 Z= 0.302 Chirality : 0.040 0.300 3290 Planarity : 0.004 0.096 3812 Dihedral : 7.012 141.857 3150 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2649 helix: 1.59 (0.13), residues: 1513 sheet: -1.35 (0.27), residues: 326 loop : -0.48 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 457 HIS 0.005 0.001 HIS A 67 PHE 0.015 0.002 PHE A 60 TYR 0.022 0.002 TYR A 344 ARG 0.017 0.001 ARG E 93 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 1226) hydrogen bonds : angle 4.38424 ( 3570) covalent geometry : bond 0.00337 (21423) covalent geometry : angle 0.57818 (29035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 245 time to evaluate : 2.601 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9797 (tpt) cc_final: 0.9393 (tpp) REVERT: A 341 MET cc_start: 0.7857 (ttt) cc_final: 0.6110 (ppp) REVERT: B 235 MET cc_start: 0.4624 (mmm) cc_final: 0.4241 (mmm) REVERT: B 345 LEU cc_start: 0.9671 (mt) cc_final: 0.9456 (mt) REVERT: B 348 MET cc_start: 0.9445 (mmm) cc_final: 0.9028 (tpt) REVERT: C 242 MET cc_start: 0.9666 (tpt) cc_final: 0.9454 (tpp) REVERT: C 415 ILE cc_start: 0.9582 (mt) cc_final: 0.9306 (mp) REVERT: C 416 MET cc_start: 0.9724 (tpt) cc_final: 0.9503 (tpp) REVERT: D 105 TYR cc_start: 0.8914 (t80) cc_final: 0.8549 (t80) REVERT: D 281 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8520 (pp30) REVERT: D 348 MET cc_start: 0.9685 (mmm) cc_final: 0.9458 (tpt) REVERT: D 411 ASP cc_start: 0.8796 (m-30) cc_final: 0.8411 (t0) REVERT: D 417 PHE cc_start: 0.9426 (m-80) cc_final: 0.9172 (m-80) REVERT: E 240 PHE cc_start: 0.9781 (t80) cc_final: 0.9533 (t80) REVERT: E 263 MET cc_start: 0.8851 (mmp) cc_final: 0.8283 (mmm) REVERT: E 268 ILE cc_start: 0.9729 (mm) cc_final: 0.9318 (mt) REVERT: E 271 ARG cc_start: 0.9558 (mtt180) cc_final: 0.9262 (mtt180) REVERT: E 301 MET cc_start: 0.9771 (ptp) cc_final: 0.9523 (ptp) REVERT: E 414 LEU cc_start: 0.9534 (mt) cc_final: 0.9310 (mt) REVERT: F 105 TYR cc_start: 0.9214 (t80) cc_final: 0.8901 (t80) REVERT: F 106 LEU cc_start: 0.9702 (mt) cc_final: 0.9472 (mt) REVERT: F 242 MET cc_start: 0.8619 (ttp) cc_final: 0.8361 (ptm) outliers start: 4 outliers final: 2 residues processed: 249 average time/residue: 0.4163 time to fit residues: 155.2802 Evaluate side-chains 186 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 10.0000 chunk 264 optimal weight: 40.0000 chunk 178 optimal weight: 9.9990 chunk 237 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 221 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 281 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.049778 restraints weight = 235418.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.051598 restraints weight = 122405.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.051872 restraints weight = 72374.362| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21423 Z= 0.141 Angle : 0.566 11.258 29035 Z= 0.295 Chirality : 0.040 0.264 3290 Planarity : 0.004 0.056 3812 Dihedral : 6.683 141.383 3150 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 0.09 % Allowed : 1.15 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2649 helix: 1.55 (0.13), residues: 1518 sheet: -1.10 (0.28), residues: 312 loop : -0.52 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 457 HIS 0.004 0.001 HIS E 29 PHE 0.021 0.002 PHE A 147 TYR 0.013 0.002 TYR A 344 ARG 0.007 0.000 ARG C 366 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 1226) hydrogen bonds : angle 4.36881 ( 3570) covalent geometry : bond 0.00296 (21423) covalent geometry : angle 0.56609 (29035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 3.130 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9758 (tpt) cc_final: 0.9404 (tpp) REVERT: A 339 LEU cc_start: 0.9647 (mm) cc_final: 0.9177 (pp) REVERT: A 341 MET cc_start: 0.7902 (ttt) cc_final: 0.5863 (ppp) REVERT: B 348 MET cc_start: 0.9323 (mmm) cc_final: 0.8956 (tpt) REVERT: C 242 MET cc_start: 0.9618 (tpt) cc_final: 0.9398 (tpp) REVERT: D 240 PHE cc_start: 0.9781 (t80) cc_final: 0.9564 (t80) REVERT: D 281 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8352 (pp30) REVERT: D 411 ASP cc_start: 0.8879 (m-30) cc_final: 0.8506 (t0) REVERT: D 417 PHE cc_start: 0.9384 (m-80) cc_final: 0.9160 (m-80) REVERT: E 240 PHE cc_start: 0.9734 (t80) cc_final: 0.9499 (t80) REVERT: E 263 MET cc_start: 0.8468 (mmp) cc_final: 0.7911 (mmm) REVERT: E 268 ILE cc_start: 0.9688 (mm) cc_final: 0.9309 (mt) REVERT: E 301 MET cc_start: 0.9640 (ptp) cc_final: 0.9372 (ptp) REVERT: E 348 MET cc_start: 0.9001 (tpt) cc_final: 0.8772 (tpt) REVERT: F 105 TYR cc_start: 0.9041 (t80) cc_final: 0.8765 (t80) REVERT: F 418 ILE cc_start: 0.9637 (mp) cc_final: 0.9216 (mp) outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.4186 time to fit residues: 157.2204 Evaluate side-chains 182 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 124 optimal weight: 7.9990 chunk 260 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 256 optimal weight: 40.0000 chunk 171 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN C 112 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** 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 = 0.3452 r_free = 0.3452 target = 0.062521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.048992 restraints weight = 237173.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.049965 restraints weight = 127810.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.050414 restraints weight = 84172.837| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21423 Z= 0.147 Angle : 0.574 12.882 29035 Z= 0.298 Chirality : 0.040 0.233 3290 Planarity : 0.004 0.056 3812 Dihedral : 6.769 140.814 3150 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 0.04 % Allowed : 1.02 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2649 helix: 1.47 (0.13), residues: 1520 sheet: -0.92 (0.28), residues: 316 loop : -0.52 (0.24), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 457 HIS 0.006 0.001 HIS D 65 PHE 0.018 0.002 PHE A 60 TYR 0.013 0.002 TYR F 311 ARG 0.009 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 1226) hydrogen bonds : angle 4.43423 ( 3570) covalent geometry : bond 0.00307 (21423) covalent geometry : angle 0.57356 (29035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 2.292 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9780 (tpt) cc_final: 0.9410 (tpp) REVERT: A 341 MET cc_start: 0.7900 (ttt) cc_final: 0.6172 (ppp) REVERT: B 270 MET cc_start: 0.9522 (mtm) cc_final: 0.9322 (tmm) REVERT: B 348 MET cc_start: 0.9332 (mmm) cc_final: 0.9120 (tmm) REVERT: C 348 MET cc_start: 0.9364 (mmp) cc_final: 0.8840 (tpt) REVERT: D 105 TYR cc_start: 0.9069 (t80) cc_final: 0.8863 (t80) REVERT: D 240 PHE cc_start: 0.9764 (t80) cc_final: 0.9543 (t80) REVERT: D 281 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8441 (pp30) REVERT: D 348 MET cc_start: 0.9790 (mmm) cc_final: 0.9546 (tpp) REVERT: D 411 ASP cc_start: 0.8933 (m-30) cc_final: 0.8544 (t0) REVERT: D 417 PHE cc_start: 0.9397 (m-80) cc_final: 0.9123 (m-10) REVERT: E 240 PHE cc_start: 0.9750 (t80) cc_final: 0.9445 (t80) REVERT: E 271 ARG cc_start: 0.9823 (mtt180) cc_final: 0.9510 (ptt-90) REVERT: E 301 MET cc_start: 0.9638 (ptp) cc_final: 0.9359 (ptp) REVERT: E 348 MET cc_start: 0.8986 (tpt) cc_final: 0.8774 (tpt) REVERT: F 105 TYR cc_start: 0.9084 (t80) cc_final: 0.8795 (t80) REVERT: F 235 MET cc_start: 0.8160 (ttt) cc_final: 0.7937 (tpt) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.3394 time to fit residues: 122.3838 Evaluate side-chains 181 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 113 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 238 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 247 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.060218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.046789 restraints weight = 244997.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.048199 restraints weight = 131680.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.048582 restraints weight = 79562.617| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21423 Z= 0.184 Angle : 0.630 13.545 29035 Z= 0.327 Chirality : 0.041 0.173 3290 Planarity : 0.004 0.048 3812 Dihedral : 6.944 137.904 3150 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2649 helix: 1.33 (0.13), residues: 1524 sheet: -1.05 (0.28), residues: 322 loop : -0.58 (0.24), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 48 HIS 0.006 0.002 HIS D 65 PHE 0.022 0.002 PHE B 60 TYR 0.015 0.002 TYR B 105 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 1226) hydrogen bonds : angle 4.55647 ( 3570) covalent geometry : bond 0.00376 (21423) covalent geometry : angle 0.62961 (29035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 2.260 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9752 (tpt) cc_final: 0.9364 (tpp) REVERT: A 341 MET cc_start: 0.8042 (ttt) cc_final: 0.6251 (ppp) REVERT: B 270 MET cc_start: 0.9476 (mtm) cc_final: 0.9253 (tmm) REVERT: B 348 MET cc_start: 0.9295 (mmm) cc_final: 0.8916 (tpt) REVERT: D 105 TYR cc_start: 0.9134 (t80) cc_final: 0.8905 (t80) REVERT: D 411 ASP cc_start: 0.9022 (m-30) cc_final: 0.8745 (t0) REVERT: E 240 PHE cc_start: 0.9692 (t80) cc_final: 0.9422 (t80) REVERT: E 301 MET cc_start: 0.9603 (ptp) cc_final: 0.9312 (ptp) REVERT: F 105 TYR cc_start: 0.9047 (t80) cc_final: 0.8791 (t80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3552 time to fit residues: 124.5562 Evaluate side-chains 168 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 77 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 76 optimal weight: 0.1980 chunk 59 optimal weight: 0.0770 chunk 240 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.064380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.050406 restraints weight = 233665.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.051808 restraints weight = 122084.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.052245 restraints weight = 71996.816| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 21423 Z= 0.107 Angle : 0.579 11.281 29035 Z= 0.295 Chirality : 0.042 0.175 3290 Planarity : 0.004 0.082 3812 Dihedral : 6.772 139.811 3150 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2649 helix: 1.58 (0.13), residues: 1515 sheet: -0.92 (0.29), residues: 302 loop : -0.47 (0.24), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 48 HIS 0.006 0.001 HIS D 65 PHE 0.023 0.001 PHE C 259 TYR 0.015 0.001 TYR B 105 ARG 0.016 0.000 ARG C 366 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 1226) hydrogen bonds : angle 4.33029 ( 3570) covalent geometry : bond 0.00236 (21423) covalent geometry : angle 0.57918 (29035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.602 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9789 (tpt) cc_final: 0.9407 (tpp) REVERT: A 339 LEU cc_start: 0.9636 (mm) cc_final: 0.9171 (pp) REVERT: A 341 MET cc_start: 0.7820 (ttt) cc_final: 0.5892 (ppp) REVERT: B 270 MET cc_start: 0.9460 (mtm) cc_final: 0.9258 (tmm) REVERT: B 348 MET cc_start: 0.9192 (mmm) cc_final: 0.8807 (tpt) REVERT: C 164 ARG cc_start: 0.9726 (mpt180) cc_final: 0.9490 (mmt-90) REVERT: C 242 MET cc_start: 0.9610 (tpt) cc_final: 0.9255 (ttm) REVERT: D 269 MET cc_start: 0.9705 (ttm) cc_final: 0.9459 (ttm) REVERT: D 348 MET cc_start: 0.9794 (tpt) cc_final: 0.8936 (tpt) REVERT: D 411 ASP cc_start: 0.8885 (m-30) cc_final: 0.8548 (t0) REVERT: E 142 ILE cc_start: 0.9831 (mm) cc_final: 0.9620 (mm) REVERT: E 240 PHE cc_start: 0.9746 (t80) cc_final: 0.9529 (t80) REVERT: E 301 MET cc_start: 0.9653 (ptp) cc_final: 0.9367 (ptp) REVERT: E 323 VAL cc_start: 0.9844 (t) cc_final: 0.9641 (p) REVERT: E 348 MET cc_start: 0.9148 (tpt) cc_final: 0.8722 (tpt) REVERT: F 82 ILE cc_start: 0.5919 (mt) cc_final: 0.5649 (mt) REVERT: F 105 TYR cc_start: 0.9159 (t80) cc_final: 0.8922 (t80) REVERT: F 348 MET cc_start: 0.9882 (mpp) cc_final: 0.9605 (mpp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3397 time to fit residues: 122.8429 Evaluate side-chains 172 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 175 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 chunk 229 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 chunk 237 optimal weight: 30.0000 chunk 236 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN E 443 ASN ** F 462 ASN ** 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 = 0.3466 r_free = 0.3466 target = 0.062907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.048895 restraints weight = 237002.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.050467 restraints weight = 130874.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.050891 restraints weight = 75961.506| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21423 Z= 0.123 Angle : 0.598 12.917 29035 Z= 0.305 Chirality : 0.041 0.180 3290 Planarity : 0.004 0.046 3812 Dihedral : 6.758 138.051 3150 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2649 helix: 1.57 (0.13), residues: 1519 sheet: -0.86 (0.30), residues: 302 loop : -0.43 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 48 HIS 0.003 0.001 HIS E 29 PHE 0.017 0.002 PHE F 240 TYR 0.014 0.001 TYR B 105 ARG 0.007 0.000 ARG E 152 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 1226) hydrogen bonds : angle 4.41460 ( 3570) covalent geometry : bond 0.00267 (21423) covalent geometry : angle 0.59771 (29035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 2.486 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9791 (tpt) cc_final: 0.9422 (tpp) REVERT: A 339 LEU cc_start: 0.9650 (mm) cc_final: 0.9202 (pp) REVERT: A 341 MET cc_start: 0.7810 (ttt) cc_final: 0.5915 (ppp) REVERT: B 348 MET cc_start: 0.9176 (mmm) cc_final: 0.8842 (tpt) REVERT: C 242 MET cc_start: 0.9583 (tpt) cc_final: 0.9380 (tpp) REVERT: C 345 LEU cc_start: 0.9870 (pp) cc_final: 0.9646 (pp) REVERT: C 348 MET cc_start: 0.9304 (mmp) cc_final: 0.8617 (tpp) REVERT: D 269 MET cc_start: 0.9725 (ttm) cc_final: 0.9477 (ttm) REVERT: D 411 ASP cc_start: 0.8956 (m-30) cc_final: 0.8682 (t0) REVERT: E 142 ILE cc_start: 0.9853 (mm) cc_final: 0.9406 (mm) REVERT: E 164 ARG cc_start: 0.9709 (mtm180) cc_final: 0.9502 (ptp-170) REVERT: E 240 PHE cc_start: 0.9767 (t80) cc_final: 0.9471 (t80) REVERT: E 301 MET cc_start: 0.9639 (ptp) cc_final: 0.9332 (ptp) REVERT: F 42 MET cc_start: 0.6621 (ttp) cc_final: 0.6212 (ptm) REVERT: F 105 TYR cc_start: 0.9162 (t80) cc_final: 0.8923 (t80) REVERT: F 269 MET cc_start: 0.9365 (ttm) cc_final: 0.9125 (ttm) REVERT: F 348 MET cc_start: 0.9890 (mpp) cc_final: 0.9655 (mpp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3475 time to fit residues: 126.6245 Evaluate side-chains 172 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 157 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.059175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.045856 restraints weight = 247145.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.046930 restraints weight = 140009.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.047536 restraints weight = 84826.180| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21423 Z= 0.181 Angle : 0.645 15.021 29035 Z= 0.335 Chirality : 0.041 0.174 3290 Planarity : 0.005 0.059 3812 Dihedral : 6.959 134.428 3150 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2649 helix: 1.35 (0.13), residues: 1517 sheet: -1.16 (0.29), residues: 310 loop : -0.51 (0.24), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 48 HIS 0.006 0.002 HIS E 29 PHE 0.021 0.002 PHE F 240 TYR 0.017 0.002 TYR D 344 ARG 0.008 0.001 ARG E 324 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 1226) hydrogen bonds : angle 4.60648 ( 3570) covalent geometry : bond 0.00371 (21423) covalent geometry : angle 0.64498 (29035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6225.13 seconds wall clock time: 110 minutes 50.39 seconds (6650.39 seconds total)