Starting phenix.real_space_refine on Sun Sep 29 03:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/09_2024/7t20_25607.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/09_2024/7t20_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/09_2024/7t20_25607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/09_2024/7t20_25607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/09_2024/7t20_25607.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t20_25607/09_2024/7t20_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-5461/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: 10.77, per 1000 atoms: 0.51 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: 5.45 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: 2.47 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: 7.00 Time building geometry restraints manager: 6.30 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: 0.010 Normalize map: mean=0, sd=1: 12.110 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.760 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.610 ------------------------------------------------------------------------------- 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= 0.258 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 *********************** 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 fitting. rotamer outliers: 73 poor density : 403 time to evaluate : 2.403 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: 0.3585 time to fit residues: 248.7095 Evaluate side-chains 265 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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= 0.238 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 291 time to evaluate : 2.459 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 339 LEU cc_start: 0.8650 (tp) cc_final: 0.8348 (pp) REVERT: A 341 MET cc_start: 0.5534 (ttt) cc_final: 0.4599 (ppp) REVERT: A 416 MET cc_start: 0.8941 (mmp) cc_final: 0.8708 (mmp) REVERT: B 235 MET cc_start: 0.4815 (mmt) cc_final: 0.4251 (mmm) REVERT: B 242 MET cc_start: 0.7924 (ptt) cc_final: 0.7588 (ppp) REVERT: B 268 ILE cc_start: 0.9302 (mm) cc_final: 0.9060 (pt) REVERT: B 347 LEU cc_start: 0.9166 (mm) cc_final: 0.8883 (tt) REVERT: B 348 MET cc_start: 0.9131 (mmm) cc_final: 0.8799 (tpt) REVERT: C 257 LEU cc_start: 0.9551 (tp) cc_final: 0.9298 (tt) REVERT: C 371 LEU cc_start: 0.9673 (tp) cc_final: 0.9427 (tp) REVERT: D 105 TYR cc_start: 0.8644 (t80) cc_final: 0.8382 (t80) REVERT: D 235 MET cc_start: 0.7975 (mmt) cc_final: 0.7424 (mmm) REVERT: D 240 PHE cc_start: 0.9405 (t80) cc_final: 0.9032 (t80) REVERT: D 263 MET cc_start: 0.8849 (mtp) cc_final: 0.8563 (mtm) REVERT: D 291 ASP cc_start: 0.9313 (t0) cc_final: 0.8941 (p0) REVERT: D 411 ASP cc_start: 0.7745 (m-30) cc_final: 0.7222 (t0) REVERT: E 291 ASP cc_start: 0.9256 (t0) cc_final: 0.8836 (p0) REVERT: E 315 SER cc_start: 0.8877 (m) cc_final: 0.8596 (p) REVERT: F 105 TYR cc_start: 0.9362 (t80) cc_final: 0.9084 (t80) REVERT: F 235 MET cc_start: 0.7776 (tpt) cc_final: 0.7567 (mmm) REVERT: F 240 PHE cc_start: 0.9542 (t80) cc_final: 0.9324 (t80) REVERT: F 242 MET cc_start: 0.9087 (ttp) cc_final: 0.8884 (ptm) REVERT: F 263 MET cc_start: 0.8229 (mtt) cc_final: 0.7982 (mtt) REVERT: F 389 LEU cc_start: 0.9263 (tt) cc_final: 0.9039 (tt) outliers start: 8 outliers final: 3 residues processed: 298 average time/residue: 0.3711 time to fit residues: 163.6484 Evaluate side-chains 211 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 208 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 260 optimal weight: 0.0030 chunk 214 optimal weight: 30.0000 chunk 239 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN F 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21423 Z= 0.219 Angle : 0.573 9.144 29035 Z= 0.297 Chirality : 0.040 0.203 3290 Planarity : 0.005 0.113 3812 Dihedral : 8.549 152.625 3150 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.17), residues: 2649 helix: 1.81 (0.13), residues: 1515 sheet: -1.60 (0.27), residues: 315 loop : -0.43 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 48 HIS 0.004 0.001 HIS E 67 PHE 0.015 0.002 PHE C 60 TYR 0.024 0.002 TYR A 344 ARG 0.010 0.001 ARG D 366 *********************** 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 fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 2.418 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: A 341 MET cc_start: 0.5203 (ttt) cc_final: 0.4767 (ppp) REVERT: B 235 MET cc_start: 0.4784 (mmt) cc_final: 0.4297 (mmm) REVERT: B 242 MET cc_start: 0.7979 (ptt) cc_final: 0.7659 (ppp) REVERT: B 347 LEU cc_start: 0.9402 (mm) cc_final: 0.8978 (tt) REVERT: B 467 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7685 (mm-40) REVERT: C 415 ILE cc_start: 0.9823 (mt) cc_final: 0.9457 (mp) REVERT: D 105 TYR cc_start: 0.8669 (t80) cc_final: 0.8231 (t80) REVERT: D 235 MET cc_start: 0.8076 (mmt) cc_final: 0.7613 (mmm) REVERT: D 240 PHE cc_start: 0.9391 (t80) cc_final: 0.8951 (t80) REVERT: D 263 MET cc_start: 0.8830 (mtp) cc_final: 0.8560 (mtm) REVERT: D 376 ASN cc_start: 0.9433 (t0) cc_final: 0.9181 (m-40) REVERT: E 142 ILE cc_start: 0.9285 (mm) cc_final: 0.8677 (mm) REVERT: E 240 PHE cc_start: 0.8936 (t80) cc_final: 0.8727 (t80) REVERT: E 291 ASP cc_start: 0.9284 (t0) cc_final: 0.8831 (p0) REVERT: E 315 SER cc_start: 0.8924 (m) cc_final: 0.8630 (p) REVERT: E 348 MET cc_start: 0.8105 (tpt) cc_final: 0.7824 (tpt) REVERT: E 414 LEU cc_start: 0.8607 (mt) cc_final: 0.8326 (mt) REVERT: F 105 TYR cc_start: 0.9389 (t80) cc_final: 0.9013 (t80) REVERT: F 229 VAL cc_start: 0.9455 (t) cc_final: 0.9239 (t) REVERT: F 263 MET cc_start: 0.8216 (mtt) cc_final: 0.7986 (mtt) REVERT: F 389 LEU cc_start: 0.9284 (tt) cc_final: 0.9046 (tt) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.3994 time to fit residues: 160.6674 Evaluate side-chains 205 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 140 ASN D 281 GLN E 140 ASN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN E 410 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3660 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= 0.224 Angle : 0.580 13.739 29035 Z= 0.304 Chirality : 0.040 0.196 3290 Planarity : 0.004 0.098 3812 Dihedral : 7.615 143.243 3150 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % 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: 1.61 (0.13), residues: 1516 sheet: -1.41 (0.27), residues: 315 loop : -0.49 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 457 HIS 0.005 0.001 HIS E 29 PHE 0.020 0.002 PHE E 60 TYR 0.015 0.002 TYR A 344 ARG 0.010 0.001 ARG C 152 *********************** 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 253 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 251 time to evaluate : 2.472 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 341 MET cc_start: 0.5439 (ttt) cc_final: 0.4902 (ppp) REVERT: B 235 MET cc_start: 0.4862 (mmt) cc_final: 0.4400 (mmm) REVERT: B 348 MET cc_start: 0.9242 (tpt) cc_final: 0.8948 (tpt) REVERT: C 155 GLU cc_start: 0.9436 (mp0) cc_final: 0.9226 (mp0) REVERT: C 415 ILE cc_start: 0.9462 (mt) cc_final: 0.9196 (mp) REVERT: C 416 MET cc_start: 0.9278 (tpt) cc_final: 0.8888 (tpp) REVERT: D 105 TYR cc_start: 0.8725 (t80) cc_final: 0.8331 (t80) REVERT: D 235 MET cc_start: 0.8191 (mmt) cc_final: 0.7642 (mmm) REVERT: D 240 PHE cc_start: 0.9316 (t80) cc_final: 0.9096 (t80) REVERT: D 263 MET cc_start: 0.8788 (mtp) cc_final: 0.8505 (mtm) REVERT: D 382 LEU cc_start: 0.9229 (mt) cc_final: 0.9004 (mt) REVERT: E 164 ARG cc_start: 0.9500 (mtm180) cc_final: 0.9106 (mtm180) REVERT: E 240 PHE cc_start: 0.9014 (t80) cc_final: 0.8674 (t80) REVERT: E 315 SER cc_start: 0.8921 (m) cc_final: 0.8641 (p) REVERT: E 339 LEU cc_start: 0.9261 (tp) cc_final: 0.9059 (tp) REVERT: E 414 LEU cc_start: 0.8541 (mt) cc_final: 0.8272 (mt) REVERT: F 105 TYR cc_start: 0.9382 (t80) cc_final: 0.9042 (t80) REVERT: F 242 MET cc_start: 0.9076 (ptm) cc_final: 0.8659 (ppp) outliers start: 2 outliers final: 0 residues processed: 253 average time/residue: 0.3725 time to fit residues: 141.3708 Evaluate side-chains 191 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 0.0770 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 229 optimal weight: 0.0870 chunk 64 optimal weight: 7.9990 overall best weight: 3.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN F 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21423 Z= 0.185 Angle : 0.546 10.912 29035 Z= 0.283 Chirality : 0.040 0.320 3290 Planarity : 0.004 0.099 3812 Dihedral : 7.040 142.922 3150 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 0.22 % Allowed : 1.55 % Favored : 98.23 % 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: 1.70 (0.13), residues: 1514 sheet: -1.30 (0.27), residues: 320 loop : -0.46 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 457 HIS 0.004 0.001 HIS A 67 PHE 0.027 0.002 PHE C 259 TYR 0.019 0.001 TYR A 344 ARG 0.020 0.000 ARG E 93 *********************** 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 261 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 256 time to evaluate : 2.415 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 341 MET cc_start: 0.5242 (ttt) cc_final: 0.4826 (ppp) REVERT: B 235 MET cc_start: 0.4743 (mmt) cc_final: 0.4297 (mmm) REVERT: B 348 MET cc_start: 0.9134 (tpt) cc_final: 0.8699 (tpt) REVERT: C 126 VAL cc_start: 0.9676 (t) cc_final: 0.9442 (p) REVERT: C 155 GLU cc_start: 0.9428 (mp0) cc_final: 0.9220 (mp0) REVERT: C 415 ILE cc_start: 0.9452 (mt) cc_final: 0.9181 (mp) REVERT: D 105 TYR cc_start: 0.8759 (t80) cc_final: 0.8377 (t80) REVERT: D 235 MET cc_start: 0.8146 (mmt) cc_final: 0.7585 (mmm) REVERT: D 263 MET cc_start: 0.8766 (mtp) cc_final: 0.8563 (mtm) REVERT: D 323 VAL cc_start: 0.9455 (t) cc_final: 0.9112 (p) REVERT: D 348 MET cc_start: 0.9269 (tpt) cc_final: 0.8809 (tpp) REVERT: D 376 ASN cc_start: 0.9382 (t0) cc_final: 0.9113 (m-40) REVERT: D 416 MET cc_start: 0.8811 (mmm) cc_final: 0.8441 (mmm) REVERT: E 240 PHE cc_start: 0.8984 (t80) cc_final: 0.8753 (t80) REVERT: E 291 ASP cc_start: 0.9261 (t0) cc_final: 0.8742 (p0) REVERT: E 315 SER cc_start: 0.8938 (m) cc_final: 0.8666 (p) REVERT: E 339 LEU cc_start: 0.9198 (tp) cc_final: 0.8995 (tp) REVERT: E 414 LEU cc_start: 0.8511 (mt) cc_final: 0.8298 (mt) REVERT: F 105 TYR cc_start: 0.9345 (t80) cc_final: 0.8987 (t80) outliers start: 5 outliers final: 2 residues processed: 261 average time/residue: 0.3605 time to fit residues: 142.1933 Evaluate side-chains 191 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 4.9990 chunk 230 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 256 optimal weight: 40.0000 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 84 optimal weight: 0.1980 chunk 134 optimal weight: 8.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4178 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= 0.190 Angle : 0.550 11.811 29035 Z= 0.287 Chirality : 0.040 0.266 3290 Planarity : 0.004 0.055 3812 Dihedral : 6.664 142.474 3150 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 0.04 % Allowed : 1.33 % Favored : 98.63 % 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: 0.99 (0.17), residues: 2649 helix: 1.67 (0.13), residues: 1516 sheet: -1.11 (0.28), residues: 326 loop : -0.42 (0.24), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 457 HIS 0.003 0.001 HIS E 29 PHE 0.025 0.002 PHE A 147 TYR 0.013 0.001 TYR A 344 ARG 0.012 0.000 ARG C 366 *********************** 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 247 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 2.342 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: B 235 MET cc_start: 0.4852 (mmt) cc_final: 0.4402 (mmm) REVERT: B 242 MET cc_start: 0.8101 (ptt) cc_final: 0.7772 (ppp) REVERT: B 348 MET cc_start: 0.9161 (tpt) cc_final: 0.8791 (tpt) REVERT: C 126 VAL cc_start: 0.9672 (t) cc_final: 0.9450 (p) REVERT: C 155 GLU cc_start: 0.9439 (mp0) cc_final: 0.9232 (mp0) REVERT: C 257 LEU cc_start: 0.9268 (tt) cc_final: 0.9063 (tt) REVERT: C 263 MET cc_start: 0.6759 (mmt) cc_final: 0.6370 (mmt) REVERT: D 105 TYR cc_start: 0.8755 (t80) cc_final: 0.8529 (t80) REVERT: D 235 MET cc_start: 0.8177 (mmt) cc_final: 0.7555 (mmm) REVERT: D 263 MET cc_start: 0.8794 (mtp) cc_final: 0.8535 (mtm) REVERT: D 269 MET cc_start: 0.9266 (ttm) cc_final: 0.9036 (ttm) REVERT: D 291 ASP cc_start: 0.9266 (t0) cc_final: 0.8858 (p0) REVERT: D 323 VAL cc_start: 0.9477 (t) cc_final: 0.9159 (p) REVERT: D 348 MET cc_start: 0.9207 (tpt) cc_final: 0.8982 (tpp) REVERT: D 376 ASN cc_start: 0.9383 (t0) cc_final: 0.9105 (m-40) REVERT: D 415 ILE cc_start: 0.9581 (mp) cc_final: 0.9363 (pt) REVERT: D 416 MET cc_start: 0.8850 (mmm) cc_final: 0.8618 (mmm) REVERT: E 240 PHE cc_start: 0.8961 (t80) cc_final: 0.8648 (t80) REVERT: E 263 MET cc_start: 0.8110 (mmp) cc_final: 0.7808 (mmm) REVERT: E 268 ILE cc_start: 0.9373 (mm) cc_final: 0.9062 (mt) REVERT: E 291 ASP cc_start: 0.9250 (t0) cc_final: 0.8733 (p0) REVERT: E 315 SER cc_start: 0.9000 (m) cc_final: 0.8744 (p) REVERT: E 339 LEU cc_start: 0.9177 (tp) cc_final: 0.8870 (tp) REVERT: E 414 LEU cc_start: 0.8517 (mt) cc_final: 0.8300 (mt) REVERT: F 105 TYR cc_start: 0.9362 (t80) cc_final: 0.9022 (t80) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.3448 time to fit residues: 129.9812 Evaluate side-chains 189 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 255 optimal weight: 40.0000 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 40.0000 chunk 117 optimal weight: 0.4980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21423 Z= 0.166 Angle : 0.546 12.541 29035 Z= 0.282 Chirality : 0.040 0.254 3290 Planarity : 0.004 0.048 3812 Dihedral : 6.591 142.622 3150 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.85 % 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: 1.01 (0.17), residues: 2649 helix: 1.65 (0.13), residues: 1515 sheet: -0.91 (0.29), residues: 321 loop : -0.44 (0.24), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 457 HIS 0.003 0.001 HIS A 29 PHE 0.035 0.002 PHE C 259 TYR 0.012 0.001 TYR B 105 ARG 0.013 0.000 ARG E 164 *********************** 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 242 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 2.379 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 339 LEU cc_start: 0.8422 (mm) cc_final: 0.8141 (pp) REVERT: B 87 LEU cc_start: 0.9043 (mt) cc_final: 0.8733 (pp) REVERT: B 235 MET cc_start: 0.4279 (mmt) cc_final: 0.3938 (mmm) REVERT: B 242 MET cc_start: 0.8222 (ptt) cc_final: 0.7863 (ppp) REVERT: B 348 MET cc_start: 0.9166 (tpt) cc_final: 0.8838 (tpt) REVERT: C 126 VAL cc_start: 0.9668 (t) cc_final: 0.9433 (p) REVERT: C 155 GLU cc_start: 0.9449 (mp0) cc_final: 0.9216 (mp0) REVERT: C 226 LEU cc_start: 0.9345 (tp) cc_final: 0.9114 (mt) REVERT: D 235 MET cc_start: 0.8071 (mmt) cc_final: 0.7498 (mmm) REVERT: D 240 PHE cc_start: 0.9319 (t80) cc_final: 0.8933 (t80) REVERT: D 263 MET cc_start: 0.8714 (mtp) cc_final: 0.8483 (mtm) REVERT: D 269 MET cc_start: 0.9290 (ttm) cc_final: 0.9028 (ttm) REVERT: D 291 ASP cc_start: 0.9272 (t0) cc_final: 0.8853 (p0) REVERT: D 323 VAL cc_start: 0.9466 (t) cc_final: 0.9157 (p) REVERT: D 376 ASN cc_start: 0.9385 (t0) cc_final: 0.9099 (m-40) REVERT: D 416 MET cc_start: 0.8818 (mmm) cc_final: 0.8602 (mmm) REVERT: E 166 PHE cc_start: 0.9412 (m-80) cc_final: 0.9194 (m-80) REVERT: E 240 PHE cc_start: 0.8960 (t80) cc_final: 0.8683 (t80) REVERT: E 268 ILE cc_start: 0.9352 (mm) cc_final: 0.9087 (mm) REVERT: E 291 ASP cc_start: 0.9307 (t0) cc_final: 0.8806 (p0) REVERT: E 315 SER cc_start: 0.8988 (m) cc_final: 0.8709 (p) REVERT: E 339 LEU cc_start: 0.9112 (tp) cc_final: 0.8856 (tp) REVERT: E 414 LEU cc_start: 0.8528 (mt) cc_final: 0.8307 (mt) REVERT: F 105 TYR cc_start: 0.9348 (t80) cc_final: 0.9020 (t80) REVERT: F 235 MET cc_start: 0.7824 (ttt) cc_final: 0.7304 (tpt) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.3413 time to fit residues: 127.8017 Evaluate side-chains 188 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 174 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN F 462 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 21423 Z= 0.156 Angle : 0.545 10.580 29035 Z= 0.280 Chirality : 0.040 0.173 3290 Planarity : 0.004 0.074 3812 Dihedral : 6.503 142.671 3150 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 1.08 (0.17), residues: 2649 helix: 1.70 (0.13), residues: 1511 sheet: -0.73 (0.29), residues: 319 loop : -0.45 (0.24), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 457 HIS 0.006 0.001 HIS D 65 PHE 0.018 0.001 PHE F 147 TYR 0.013 0.001 TYR B 105 ARG 0.016 0.000 ARG A 164 *********************** 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 240 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.499 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: A 339 LEU cc_start: 0.8321 (mm) cc_final: 0.8041 (pp) REVERT: B 87 LEU cc_start: 0.9034 (mt) cc_final: 0.8732 (pp) REVERT: B 172 ARG cc_start: 0.6849 (mmt180) cc_final: 0.6643 (mmt180) REVERT: B 235 MET cc_start: 0.4432 (mmt) cc_final: 0.3989 (mmm) REVERT: B 242 MET cc_start: 0.8067 (ptt) cc_final: 0.7714 (ppp) REVERT: B 348 MET cc_start: 0.9120 (tpt) cc_final: 0.8850 (tpt) REVERT: C 126 VAL cc_start: 0.9630 (t) cc_final: 0.9401 (p) REVERT: C 226 LEU cc_start: 0.9358 (tp) cc_final: 0.9132 (mt) REVERT: D 235 MET cc_start: 0.7988 (mmt) cc_final: 0.7375 (mmm) REVERT: D 240 PHE cc_start: 0.9305 (t80) cc_final: 0.8912 (t80) REVERT: D 263 MET cc_start: 0.8716 (mtp) cc_final: 0.8471 (mtm) REVERT: D 269 MET cc_start: 0.9294 (ttm) cc_final: 0.9025 (ttm) REVERT: D 291 ASP cc_start: 0.9224 (t0) cc_final: 0.8791 (p0) REVERT: D 348 MET cc_start: 0.9184 (tpt) cc_final: 0.8878 (tpp) REVERT: D 376 ASN cc_start: 0.9354 (t0) cc_final: 0.9107 (m-40) REVERT: D 416 MET cc_start: 0.8817 (mmm) cc_final: 0.8534 (mmm) REVERT: E 166 PHE cc_start: 0.9453 (m-80) cc_final: 0.9218 (m-80) REVERT: E 240 PHE cc_start: 0.8980 (t80) cc_final: 0.8690 (t80) REVERT: E 291 ASP cc_start: 0.9300 (t0) cc_final: 0.8828 (p0) REVERT: E 315 SER cc_start: 0.8971 (m) cc_final: 0.8710 (p) REVERT: E 339 LEU cc_start: 0.9052 (tp) cc_final: 0.8766 (tp) REVERT: E 414 LEU cc_start: 0.8551 (mt) cc_final: 0.8318 (mt) REVERT: F 105 TYR cc_start: 0.9343 (t80) cc_final: 0.9041 (t80) REVERT: F 235 MET cc_start: 0.7843 (ttt) cc_final: 0.7348 (tpt) REVERT: F 270 MET cc_start: 0.9490 (ttt) cc_final: 0.8443 (tmm) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3368 time to fit residues: 124.8665 Evaluate side-chains 187 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 0.0270 chunk 244 optimal weight: 8.9990 chunk 223 optimal weight: 0.8980 chunk 238 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 215 optimal weight: 0.0870 chunk 225 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 443 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 21423 Z= 0.154 Angle : 0.542 11.962 29035 Z= 0.278 Chirality : 0.041 0.202 3290 Planarity : 0.003 0.054 3812 Dihedral : 6.429 141.268 3150 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.16 (0.17), residues: 2649 helix: 1.79 (0.13), residues: 1511 sheet: -0.66 (0.29), residues: 317 loop : -0.47 (0.24), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 48 HIS 0.003 0.001 HIS C 65 PHE 0.027 0.001 PHE C 259 TYR 0.013 0.001 TYR B 105 ARG 0.010 0.000 ARG C 366 *********************** 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 241 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.449 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 339 LEU cc_start: 0.8350 (mm) cc_final: 0.8069 (pp) REVERT: B 87 LEU cc_start: 0.9027 (mt) cc_final: 0.8731 (pp) REVERT: B 235 MET cc_start: 0.4524 (mmt) cc_final: 0.4106 (mmm) REVERT: B 242 MET cc_start: 0.8104 (ptt) cc_final: 0.7792 (ppp) REVERT: B 348 MET cc_start: 0.9029 (tpt) cc_final: 0.8821 (tpt) REVERT: C 126 VAL cc_start: 0.9641 (t) cc_final: 0.9398 (p) REVERT: C 226 LEU cc_start: 0.9377 (tp) cc_final: 0.8964 (mt) REVERT: C 228 ILE cc_start: 0.9645 (mm) cc_final: 0.9346 (tp) REVERT: C 257 LEU cc_start: 0.9252 (tt) cc_final: 0.8999 (mm) REVERT: C 415 ILE cc_start: 0.9381 (mp) cc_final: 0.9054 (pt) REVERT: D 235 MET cc_start: 0.7987 (mmt) cc_final: 0.7377 (mmm) REVERT: D 240 PHE cc_start: 0.9287 (t80) cc_final: 0.8904 (t80) REVERT: D 268 ILE cc_start: 0.9687 (mm) cc_final: 0.9161 (mm) REVERT: D 269 MET cc_start: 0.9299 (ttm) cc_final: 0.9079 (ttm) REVERT: D 270 MET cc_start: 0.9460 (ptm) cc_final: 0.9248 (ptp) REVERT: D 291 ASP cc_start: 0.9238 (t0) cc_final: 0.8784 (p0) REVERT: D 339 LEU cc_start: 0.9574 (tp) cc_final: 0.9351 (pp) REVERT: D 376 ASN cc_start: 0.9362 (t0) cc_final: 0.9129 (m-40) REVERT: E 166 PHE cc_start: 0.9467 (m-80) cc_final: 0.9231 (m-80) REVERT: E 240 PHE cc_start: 0.8966 (t80) cc_final: 0.8698 (t80) REVERT: E 257 LEU cc_start: 0.8768 (tp) cc_final: 0.8491 (tp) REVERT: E 269 MET cc_start: 0.9029 (tpt) cc_final: 0.8817 (tpp) REVERT: E 291 ASP cc_start: 0.9281 (t0) cc_final: 0.8858 (p0) REVERT: E 414 LEU cc_start: 0.8599 (mt) cc_final: 0.8373 (mt) REVERT: F 105 TYR cc_start: 0.9372 (t80) cc_final: 0.9086 (t80) REVERT: F 270 MET cc_start: 0.9480 (ttt) cc_final: 0.8359 (tmm) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3374 time to fit residues: 125.4569 Evaluate side-chains 189 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 174 optimal weight: 40.0000 chunk 264 optimal weight: 40.0000 chunk 242 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 21 optimal weight: 0.2980 chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21423 Z= 0.175 Angle : 0.553 12.436 29035 Z= 0.286 Chirality : 0.040 0.175 3290 Planarity : 0.004 0.048 3812 Dihedral : 6.423 137.796 3150 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.14 (0.17), residues: 2649 helix: 1.80 (0.13), residues: 1512 sheet: -0.73 (0.29), residues: 330 loop : -0.50 (0.24), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 48 HIS 0.004 0.001 HIS B 67 PHE 0.023 0.002 PHE C 166 TYR 0.013 0.001 TYR B 105 ARG 0.008 0.000 ARG A 164 ********************** 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 234 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.519 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: A 60 PHE cc_start: 0.7891 (m-80) cc_final: 0.7600 (m-80) REVERT: A 339 LEU cc_start: 0.8441 (mm) cc_final: 0.8190 (pp) REVERT: B 235 MET cc_start: 0.4857 (mmt) cc_final: 0.4467 (mmm) REVERT: B 242 MET cc_start: 0.8211 (ptt) cc_final: 0.7909 (ppp) REVERT: D 235 MET cc_start: 0.8125 (mmt) cc_final: 0.7524 (mmm) REVERT: D 240 PHE cc_start: 0.9301 (t80) cc_final: 0.8908 (t80) REVERT: D 268 ILE cc_start: 0.9647 (mm) cc_final: 0.9007 (mm) REVERT: D 291 ASP cc_start: 0.9239 (t0) cc_final: 0.8812 (p0) REVERT: D 339 LEU cc_start: 0.9591 (tp) cc_final: 0.9335 (pp) REVERT: D 348 MET cc_start: 0.9132 (tpt) cc_final: 0.8860 (tpt) REVERT: D 376 ASN cc_start: 0.9411 (t0) cc_final: 0.9158 (m-40) REVERT: E 166 PHE cc_start: 0.9484 (m-80) cc_final: 0.9225 (m-80) REVERT: E 240 PHE cc_start: 0.8956 (t80) cc_final: 0.8708 (t80) REVERT: E 269 MET cc_start: 0.8984 (tpt) cc_final: 0.8741 (tpp) REVERT: E 291 ASP cc_start: 0.9268 (t0) cc_final: 0.8847 (p0) REVERT: E 301 MET cc_start: 0.9453 (ptp) cc_final: 0.9248 (ptp) REVERT: E 339 LEU cc_start: 0.9132 (tp) cc_final: 0.8803 (tp) REVERT: E 414 LEU cc_start: 0.8643 (mt) cc_final: 0.8439 (mt) REVERT: F 105 TYR cc_start: 0.9386 (t80) cc_final: 0.9100 (t80) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3306 time to fit residues: 120.2367 Evaluate side-chains 181 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 31 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.061554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.047825 restraints weight = 241208.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.049290 restraints weight = 130626.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.049614 restraints weight = 77179.556| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21423 Z= 0.203 Angle : 0.579 11.380 29035 Z= 0.300 Chirality : 0.040 0.169 3290 Planarity : 0.004 0.050 3812 Dihedral : 6.499 133.868 3150 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.17), residues: 2649 helix: 1.70 (0.13), residues: 1515 sheet: -0.80 (0.30), residues: 312 loop : -0.58 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 48 HIS 0.004 0.001 HIS E 29 PHE 0.020 0.002 PHE B 240 TYR 0.015 0.002 TYR D 344 ARG 0.017 0.001 ARG A 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.69 seconds wall clock time: 70 minutes 40.22 seconds (4240.22 seconds total)