Starting phenix.real_space_refine (version: dev) on Mon Feb 20 05:25:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/02_2023/4uis_2974_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/02_2023/4uis_2974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/02_2023/4uis_2974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/02_2023/4uis_2974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/02_2023/4uis_2974_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/02_2023/4uis_2974_neut.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2965 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4372 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 555} Chain breaks: 12 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'UNK:plan-1': 61} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1522 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 2, 'TRANS': 238} Chain breaks: 6 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 139 Planarities with less than four sites: {'UNK:plan-1': 139} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 969 Classifications: {'peptide': 196} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 185} Link IDs: {'CIS': 1, 'TRANS': 194} Chain breaks: 4 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 610 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 196} Unresolved non-hydrogen planarities: 196 Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 306 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 58} Link IDs: {'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 62} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 1349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 bond proxies already assigned to first conformer: 1250 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AGLU G 5 " occ=0.32 ... (16 atoms not shown) pdb=" OE2BGLU G 5 " occ=0.68 residue: pdb=" N AARG G 76 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG G 76 " occ=0.43 residue: pdb=" N ALYS G 135 " occ=0.29 ... (16 atoms not shown) pdb=" NZ BLYS G 135 " occ=0.71 residue: pdb=" N AARG G 137 " occ=0.41 ... (20 atoms not shown) pdb=" NH2BARG G 137 " occ=0.59 residue: pdb=" N AASN G 140 " occ=0.46 ... (14 atoms not shown) pdb=" ND2BASN G 140 " occ=0.54 residue: pdb=" N AGLN G 141 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN G 141 " occ=0.54 Time building chain proxies: 5.77, per 1000 atoms: 0.68 Number of scatterers: 8518 At special positions: 0 Unit cell: (122.76, 113.52, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1611 8.00 N 1523 7.00 C 5352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.66 Conformation dependent library (CDL) restraints added in 1.3 seconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 97.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.440A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.042A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 201 removed outlier: 4.087A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A 199 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.707A pdb=" N PHE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.652A pdb=" N VAL A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.753A pdb=" N SER A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 4.089A pdb=" N SER A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.774A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.797A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.988A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.583A pdb=" N ASP A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 542 " --> pdb=" O ARG A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 561 through 575 removed outlier: 3.584A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 665 through 687 removed outlier: 3.576A pdb=" N UNK A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 101 removed outlier: 3.723A pdb=" N UNK B 73 " --> pdb=" O UNK B 69 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.679A pdb=" N UNK B 171 " --> pdb=" O UNK B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.570A pdb=" N UNK B 198 " --> pdb=" O UNK B 194 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK B 216 " --> pdb=" O UNK B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 241 removed outlier: 3.671A pdb=" N GLN B 222 " --> pdb=" O UNK B 218 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK B 241 " --> pdb=" O UNK B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.851A pdb=" N UNK B 250 " --> pdb=" O UNK B 246 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 257 " --> pdb=" O UNK B 253 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N UNK B 265 " --> pdb=" O UNK B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.941A pdb=" N UNK B 399 " --> pdb=" O UNK B 395 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK B 400 " --> pdb=" O UNK B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.505A pdb=" N UNK B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.672A pdb=" N UNK B 438 " --> pdb=" O UNK B 434 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 444 " --> pdb=" O UNK B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.645A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 removed outlier: 4.389A pdb=" N UNK C 18 " --> pdb=" O UNK C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 56 removed outlier: 4.133A pdb=" N UNK C 40 " --> pdb=" O UNK C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 102 removed outlier: 3.851A pdb=" N UNK C 86 " --> pdb=" O UNK C 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK C 87 " --> pdb=" O UNK C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 152 through 178 removed outlier: 4.032A pdb=" N UNK C 156 " --> pdb=" O UNK C 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK C 177 " --> pdb=" O UNK C 173 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N UNK C 178 " --> pdb=" O UNK C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.744A pdb=" N UNK C 183 " --> pdb=" O UNK C 179 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK C 184 " --> pdb=" O UNK C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 184' Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.643A pdb=" N UNK C 188 " --> pdb=" O UNK C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 220 removed outlier: 4.123A pdb=" N UNK C 208 " --> pdb=" O UNK C 204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N UNK C 213 " --> pdb=" O UNK C 209 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK C 214 " --> pdb=" O UNK C 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK C 215 " --> pdb=" O UNK C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 4.057A pdb=" N UNK D 13 " --> pdb=" O UNK D 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK D 16 " --> pdb=" O UNK D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.753A pdb=" N UNK D 25 " --> pdb=" O UNK D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 72 removed outlier: 4.028A pdb=" N UNK D 47 " --> pdb=" O UNK D 43 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK D 49 " --> pdb=" O UNK D 45 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N UNK D 50 " --> pdb=" O UNK D 46 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N UNK D 51 " --> pdb=" O UNK D 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N UNK D 55 " --> pdb=" O UNK D 51 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N UNK D 56 " --> pdb=" O UNK D 52 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK D 65 " --> pdb=" O UNK D 61 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N UNK D 66 " --> pdb=" O UNK D 62 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N UNK D 67 " --> pdb=" O UNK D 63 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N UNK D 68 " --> pdb=" O UNK D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 38 through 51 removed outlier: 3.888A pdb=" N ALA G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 75 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 83 through 91 removed outlier: 3.924A pdb=" N VAL G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 removed outlier: 3.969A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 142 through 156 Processing helix chain 'G' and resid 158 through 162 Processing sheet with id= AA, first strand: chain 'A' and resid 47 through 48 Processing sheet with id= AB, first strand: chain 'A' and resid 53 through 54 Processing sheet with id= AC, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.378A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= AE, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.813A pdb=" N ASP A 253 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.735A pdb=" N VAL A 276 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 280 through 281 Processing sheet with id= AH, first strand: chain 'A' and resid 365 through 366 Processing sheet with id= AI, first strand: chain 'A' and resid 605 through 606 Processing sheet with id= GA, first strand: chain 'G' and resid 17 through 19 removed outlier: 7.694A pdb=" N TYR G 25 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1554 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: 2.38 Time building geometry restraints manager: 3.90 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: 2893 1.34 - 1.46: 1592 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 8625 Sorted by residual: bond pdb=" CA PHE A 302 " pdb=" C PHE A 302 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.27e-02 6.20e+03 1.10e+01 bond pdb=" CA VAL A 256 " pdb=" CB VAL A 256 " ideal model delta sigma weight residual 1.540 1.503 0.037 1.36e-02 5.41e+03 7.32e+00 bond pdb=" N VAL A 303 " pdb=" CA VAL A 303 " ideal model delta sigma weight residual 1.459 1.427 0.032 1.25e-02 6.40e+03 6.39e+00 bond pdb=" CA ALA A 119 " pdb=" CB ALA A 119 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.51e-02 4.39e+03 5.94e+00 bond pdb=" C ALA A 556 " pdb=" O ALA A 556 " ideal model delta sigma weight residual 1.239 1.215 0.023 9.60e-03 1.09e+04 5.94e+00 ... (remaining 8620 not shown) Histogram of bond angle deviations from ideal: 99.49 - 107.11: 232 107.11 - 114.74: 5095 114.74 - 122.37: 4811 122.37 - 129.99: 1571 129.99 - 137.62: 55 Bond angle restraints: 11764 Sorted by residual: angle pdb=" C GLY A 89 " pdb=" N PRO A 90 " pdb=" CA PRO A 90 " ideal model delta sigma weight residual 119.84 109.60 10.24 1.25e+00 6.40e-01 6.70e+01 angle pdb=" N VAL A 85 " pdb=" CA VAL A 85 " pdb=" C VAL A 85 " ideal model delta sigma weight residual 111.67 104.39 7.28 9.50e-01 1.11e+00 5.87e+01 angle pdb=" N LEU A 542 " pdb=" CA LEU A 542 " pdb=" C LEU A 542 " ideal model delta sigma weight residual 108.23 117.36 -9.13 1.38e+00 5.25e-01 4.38e+01 angle pdb=" C ALA A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.78 126.51 -6.73 1.03e+00 9.43e-01 4.26e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 118.35 -7.65 1.22e+00 6.72e-01 3.93e+01 ... (remaining 11759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4968 17.72 - 35.44: 120 35.44 - 53.16: 26 53.16 - 70.88: 3 70.88 - 88.60: 5 Dihedral angle restraints: 5122 sinusoidal: 1481 harmonic: 3641 Sorted by residual: dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N LEU B 452 " pdb=" CA LEU B 452 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLN A 552 " pdb=" C GLN A 552 " pdb=" N HIS A 553 " pdb=" CA HIS A 553 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N GLN A 454 " pdb=" CA GLN A 454 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 5119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.118: 365 0.118 - 0.177: 41 0.177 - 0.236: 7 0.236 - 0.295: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CB ILE A 338 " pdb=" CA ILE A 338 " pdb=" CG1 ILE A 338 " pdb=" CG2 ILE A 338 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA CYS A 159 " pdb=" N CYS A 159 " pdb=" C CYS A 159 " pdb=" CB CYS A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA UNK A 626 " pdb=" N UNK A 626 " pdb=" C UNK A 626 " pdb=" CB UNK A 626 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1435 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 164 " 0.018 2.00e-02 2.50e+03 1.64e-02 6.69e+00 pdb=" CG TRP A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 164 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 164 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO A 473 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 138 " -0.018 2.00e-02 2.50e+03 1.33e-02 4.39e+00 pdb=" CG TRP G 138 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP G 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 138 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 138 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 138 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 138 " -0.001 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 17 2.22 - 2.89: 3660 2.89 - 3.56: 13504 3.56 - 4.23: 18838 4.23 - 4.90: 29789 Nonbonded interactions: 65808 Sorted by model distance: nonbonded pdb=" O UNK D 42 " pdb=" N UNK D 44 " model vdw 1.546 2.520 nonbonded pdb=" OE2 GLU G 11 " pdb=" NH1 ARG G 145 " model vdw 1.835 2.520 nonbonded pdb=" O GLN A 516 " pdb=" CD ARG A 520 " model vdw 1.874 3.440 nonbonded pdb=" CB SER A 219 " pdb=" CG2 ILE A 656 " model vdw 1.909 3.860 nonbonded pdb=" OD2 ASP G 10 " pdb=" ND2 ASN G 101 " model vdw 2.006 2.520 ... (remaining 65803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5352 2.51 5 N 1523 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.29 max=1.00 mean=0.99 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 2.720 Check model and map are aligned: 0.110 Process input model: 25.580 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 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 : 0.009 0.068 8625 Z= 0.539 Angle : 1.293 12.617 11764 Z= 0.833 Chirality : 0.057 0.295 1438 Planarity : 0.005 0.055 1537 Dihedral : 9.916 88.595 2721 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 4.97 % Allowed : 7.65 % Favored : 87.38 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.00 (0.30), residues: 750 helix: -1.94 (0.21), residues: 332 sheet: -2.97 (0.56), residues: 68 loop : -0.04 (0.38), residues: 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 229 average time/residue: 0.2185 time to fit residues: 67.0214 Evaluate side-chains 141 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1845 time to fit residues: 1.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 216 GLN A 290 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8625 Z= 0.282 Angle : 0.860 17.982 11764 Z= 0.428 Chirality : 0.042 0.198 1438 Planarity : 0.005 0.053 1537 Dihedral : 6.281 31.716 1291 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 1.61 % Allowed : 9.13 % Favored : 89.26 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.78 (0.29), residues: 750 helix: -0.55 (0.26), residues: 331 sheet: -3.36 (0.44), residues: 84 loop : -1.07 (0.35), residues: 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 195 average time/residue: 0.1817 time to fit residues: 49.8297 Evaluate side-chains 138 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 255 ASN A 313 GLN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 8625 Z= 0.451 Angle : 0.988 18.435 11764 Z= 0.488 Chirality : 0.045 0.187 1438 Planarity : 0.006 0.051 1537 Dihedral : 6.498 29.958 1291 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 1.48 % Allowed : 10.87 % Favored : 87.65 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.23 (0.29), residues: 750 helix: -0.71 (0.27), residues: 330 sheet: -3.35 (0.46), residues: 75 loop : -1.72 (0.33), residues: 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 151 average time/residue: 0.1840 time to fit residues: 39.5656 Evaluate side-chains 124 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0970 time to fit residues: 1.4435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.067 8625 Z= 0.448 Angle : 0.947 18.535 11764 Z= 0.468 Chirality : 0.043 0.165 1438 Planarity : 0.005 0.054 1537 Dihedral : 6.416 29.714 1291 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 1.61 % Allowed : 10.60 % Favored : 87.79 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.35 (0.29), residues: 750 helix: -0.68 (0.27), residues: 332 sheet: -3.31 (0.44), residues: 80 loop : -1.93 (0.32), residues: 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 148 average time/residue: 0.1922 time to fit residues: 40.2466 Evaluate side-chains 109 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1150 time to fit residues: 1.7020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8625 Z= 0.216 Angle : 0.765 18.293 11764 Z= 0.374 Chirality : 0.038 0.172 1438 Planarity : 0.004 0.058 1537 Dihedral : 5.648 27.379 1291 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 1.34 % Allowed : 8.99 % Favored : 89.66 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.68 (0.30), residues: 750 helix: 0.06 (0.28), residues: 331 sheet: -3.17 (0.47), residues: 79 loop : -1.74 (0.34), residues: 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.1875 time to fit residues: 41.8174 Evaluate side-chains 128 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0961 time to fit residues: 1.1878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 8625 Z= 0.294 Angle : 0.787 18.262 11764 Z= 0.392 Chirality : 0.040 0.202 1438 Planarity : 0.005 0.053 1537 Dihedral : 5.577 27.455 1291 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.20 % Favored : 88.46 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.70 (0.30), residues: 750 helix: 0.13 (0.28), residues: 331 sheet: -3.21 (0.46), residues: 79 loop : -1.85 (0.33), residues: 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1863 time to fit residues: 39.3450 Evaluate side-chains 125 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 8625 Z= 0.384 Angle : 0.867 18.276 11764 Z= 0.431 Chirality : 0.042 0.166 1438 Planarity : 0.005 0.052 1537 Dihedral : 5.820 27.335 1291 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 1.48 % Allowed : 10.60 % Favored : 87.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.94 (0.30), residues: 750 helix: -0.13 (0.28), residues: 336 sheet: -3.57 (0.51), residues: 67 loop : -1.95 (0.32), residues: 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1969 time to fit residues: 41.9757 Evaluate side-chains 124 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 75 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 91 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 216 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 8625 Z= 0.337 Angle : 0.826 18.429 11764 Z= 0.413 Chirality : 0.041 0.258 1438 Planarity : 0.004 0.052 1537 Dihedral : 5.776 26.950 1291 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.60 % Favored : 88.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.90 (0.30), residues: 750 helix: -0.08 (0.28), residues: 334 sheet: -3.43 (0.53), residues: 67 loop : -1.97 (0.32), residues: 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1902 time to fit residues: 41.9265 Evaluate side-chains 125 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 8625 Z= 0.326 Angle : 0.838 18.455 11764 Z= 0.417 Chirality : 0.042 0.235 1438 Planarity : 0.005 0.052 1537 Dihedral : 5.905 27.269 1291 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.74 % Favored : 87.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.96 (0.30), residues: 750 helix: -0.07 (0.28), residues: 333 sheet: -3.64 (0.50), residues: 69 loop : -2.01 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1976 time to fit residues: 42.0259 Evaluate side-chains 121 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 8 optimal weight: 0.0970 chunk 60 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 8625 Z= 0.259 Angle : 0.782 18.421 11764 Z= 0.389 Chirality : 0.040 0.179 1438 Planarity : 0.004 0.053 1537 Dihedral : 5.627 25.836 1291 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.26 % Favored : 89.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.75 (0.30), residues: 750 helix: 0.08 (0.28), residues: 336 sheet: -2.94 (0.53), residues: 72 loop : -2.00 (0.32), residues: 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1854 time to fit residues: 41.2075 Evaluate side-chains 123 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 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 = 0.3773 r_free = 0.3773 target = 0.106466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079596 restraints weight = 148269.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.079487 restraints weight = 73327.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080369 restraints weight = 41365.282| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 8625 Z= 0.259 Angle : 0.777 18.383 11764 Z= 0.385 Chirality : 0.040 0.199 1438 Planarity : 0.004 0.052 1537 Dihedral : 5.653 25.913 1291 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.20 % Favored : 88.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.76 (0.30), residues: 750 helix: 0.12 (0.28), residues: 334 sheet: -3.07 (0.50), residues: 77 loop : -2.02 (0.32), residues: 339 =============================================================================== Job complete usr+sys time: 1469.30 seconds wall clock time: 27 minutes 59.31 seconds (1679.31 seconds total)