Starting phenix.real_space_refine on Mon Mar 11 11:54:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8q_37356/03_2024/8w8q_37356_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8q_37356/03_2024/8w8q_37356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8q_37356/03_2024/8w8q_37356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8q_37356/03_2024/8w8q_37356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8q_37356/03_2024/8w8q_37356_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8q_37356/03_2024/8w8q_37356_neut.pdb" } resolution = 2.89 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5209 2.51 5 N 1417 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 128": "OD1" <-> "OD2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8168 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2283 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2579 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.72, per 1000 atoms: 0.58 Number of scatterers: 8168 At special positions: 0 Unit cell: (77.848, 124.136, 92.576, 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 49 16.00 O 1493 8.00 N 1417 7.00 C 5209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 42.9% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 27 through 59 removed outlier: 3.591A pdb=" N LYS C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 93 removed outlier: 3.732A pdb=" N PHE C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 100 through 135 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 168 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 201 through 228 Processing helix chain 'C' and resid 394 through 425 Proline residue: C 414 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.904A pdb=" N GLN C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 445 removed outlier: 3.637A pdb=" N ILE C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 455 Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 458 through 473 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.573A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.540A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.538A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.615A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.194A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.645A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 174 through 176 removed outlier: 3.585A pdb=" N SER C 183 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 176 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 181 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.404A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.425A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.512A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.526A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.614A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.600A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.163A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.324A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1269 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: 2.43 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2098 1.33 - 1.45: 1585 1.45 - 1.57: 4592 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8342 Sorted by residual: bond pdb=" C CYS B 233 " pdb=" N PHE B 234 " ideal model delta sigma weight residual 1.331 1.231 0.099 1.41e-02 5.03e+03 4.94e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.32e-02 5.74e+03 1.01e+01 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.26e+00 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 8.96e+00 bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.59e+00 ... (remaining 8337 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.49: 194 106.49 - 113.42: 4566 113.42 - 120.35: 3146 120.35 - 127.28: 3322 127.28 - 134.21: 93 Bond angle restraints: 11321 Sorted by residual: angle pdb=" CA THR B 274 " pdb=" CB THR B 274 " pdb=" OG1 THR B 274 " ideal model delta sigma weight residual 109.60 99.74 9.86 1.50e+00 4.44e-01 4.32e+01 angle pdb=" C CYS B 233 " pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 121.50 129.91 -8.41 1.43e+00 4.89e-01 3.46e+01 angle pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" C ASP A 284 " ideal model delta sigma weight residual 113.30 106.71 6.59 1.34e+00 5.57e-01 2.42e+01 angle pdb=" O ASP B 247 " pdb=" C ASP B 247 " pdb=" N ALA B 248 " ideal model delta sigma weight residual 122.39 127.12 -4.73 1.29e+00 6.01e-01 1.34e+01 angle pdb=" C ASP B 298 " pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " ideal model delta sigma weight residual 109.89 115.50 -5.61 1.60e+00 3.91e-01 1.23e+01 ... (remaining 11316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 4364 17.17 - 34.34: 445 34.34 - 51.51: 122 51.51 - 68.67: 27 68.67 - 85.84: 4 Dihedral angle restraints: 4962 sinusoidal: 1918 harmonic: 3044 Sorted by residual: dihedral pdb=" CA ILE C 201 " pdb=" C ILE C 201 " pdb=" N VAL C 202 " pdb=" CA VAL C 202 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 65.31 27.69 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 4959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1007 0.052 - 0.103: 204 0.103 - 0.155: 57 0.155 - 0.207: 17 0.207 - 0.258: 7 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU B 146 " pdb=" N LEU B 146 " pdb=" C LEU B 146 " pdb=" CB LEU B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1289 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 29 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ALA C 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 29 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS C 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 40 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ILE C 40 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 40 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 41 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 413 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 414 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.023 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1068 2.75 - 3.29: 7912 3.29 - 3.83: 14110 3.83 - 4.36: 16957 4.36 - 4.90: 29011 Nonbonded interactions: 69058 Sorted by model distance: nonbonded pdb=" O PHE C 200 " pdb=" OH TYR C 408 " model vdw 2.216 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.255 2.520 nonbonded pdb=" N GLU G 58 " pdb=" OE1 GLU G 58 " model vdw 2.259 2.520 nonbonded pdb=" O MET C 143 " pdb=" NH2 ARG A 38 " model vdw 2.281 2.520 nonbonded pdb=" O VAL C 88 " pdb=" OG1 THR C 91 " model vdw 2.290 2.440 ... (remaining 69053 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.950 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.340 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.005 0.099 8342 Z= 0.330 Angle : 0.741 9.863 11321 Z= 0.492 Chirality : 0.051 0.258 1292 Planarity : 0.004 0.041 1435 Dihedral : 15.287 85.843 2981 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 21.53 % Favored : 76.77 % 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: 1.04 (0.25), residues: 1028 helix: 1.98 (0.25), residues: 407 sheet: 0.61 (0.33), residues: 219 loop : -0.60 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.006 0.001 HIS C 223 PHE 0.011 0.001 PHE A 376 TYR 0.015 0.001 TYR C 454 ARG 0.003 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.936 Fit side-chains REVERT: C 61 GLN cc_start: 0.7222 (mt0) cc_final: 0.6987 (tp40) REVERT: C 96 PHE cc_start: 0.6225 (m-80) cc_final: 0.5766 (t80) REVERT: C 183 SER cc_start: 0.8282 (t) cc_final: 0.7815 (p) REVERT: C 464 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 53 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: A 221 MET cc_start: 0.8966 (ttp) cc_final: 0.8424 (ttp) REVERT: B 59 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8429 (t80) outliers start: 15 outliers final: 5 residues processed: 138 average time/residue: 1.2436 time to fit residues: 181.8913 Evaluate side-chains 121 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 222 GLN C 223 HIS A 357 HIS A 371 ASN B 9 GLN B 32 GLN N 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8342 Z= 0.193 Angle : 0.529 7.555 11321 Z= 0.284 Chirality : 0.042 0.159 1292 Planarity : 0.004 0.042 1435 Dihedral : 4.865 54.635 1147 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.99 % Allowed : 20.39 % Favored : 75.63 % 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: 1.23 (0.25), residues: 1028 helix: 2.23 (0.25), residues: 411 sheet: 0.52 (0.33), residues: 223 loop : -0.52 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.013 0.001 PHE A 376 TYR 0.013 0.001 TYR C 454 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 0.949 Fit side-chains REVERT: C 61 GLN cc_start: 0.7241 (mt0) cc_final: 0.7023 (tp40) REVERT: C 96 PHE cc_start: 0.6225 (m-80) cc_final: 0.5687 (t80) REVERT: A 221 MET cc_start: 0.8937 (ttp) cc_final: 0.8363 (ttp) REVERT: B 59 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8565 (t80) REVERT: B 198 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8416 (pp) REVERT: B 262 MET cc_start: 0.9238 (mtp) cc_final: 0.8765 (mmm) outliers start: 35 outliers final: 12 residues processed: 149 average time/residue: 1.1649 time to fit residues: 184.6604 Evaluate side-chains 128 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN C 223 HIS A 29 GLN B 9 GLN B 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8342 Z= 0.245 Angle : 0.535 7.555 11321 Z= 0.288 Chirality : 0.042 0.161 1292 Planarity : 0.004 0.046 1435 Dihedral : 4.747 56.428 1139 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.67 % Allowed : 21.30 % Favored : 74.03 % 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: 1.18 (0.25), residues: 1028 helix: 2.29 (0.24), residues: 411 sheet: 0.36 (0.33), residues: 225 loop : -0.57 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS C 112 PHE 0.023 0.001 PHE C 41 TYR 0.014 0.002 TYR A 339 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 119 time to evaluate : 0.926 Fit side-chains REVERT: C 96 PHE cc_start: 0.6213 (m-80) cc_final: 0.5637 (t80) REVERT: C 440 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7321 (mp) REVERT: A 221 MET cc_start: 0.9068 (ttp) cc_final: 0.8523 (ttp) REVERT: B 59 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8571 (t80) REVERT: B 198 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8415 (pp) REVERT: B 217 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8176 (pmm) REVERT: B 262 MET cc_start: 0.9158 (mtp) cc_final: 0.8873 (mmm) REVERT: G 42 GLU cc_start: 0.8028 (pp20) cc_final: 0.7805 (tm-30) outliers start: 41 outliers final: 21 residues processed: 150 average time/residue: 1.2339 time to fit residues: 196.9239 Evaluate side-chains 143 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8342 Z= 0.209 Angle : 0.516 7.320 11321 Z= 0.278 Chirality : 0.041 0.158 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.690 56.412 1139 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.90 % Allowed : 21.41 % Favored : 73.69 % 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: 1.22 (0.25), residues: 1028 helix: 2.33 (0.24), residues: 411 sheet: 0.36 (0.33), residues: 226 loop : -0.54 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.020 0.001 PHE C 41 TYR 0.013 0.001 TYR N 95 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.203 Fit side-chains REVERT: C 61 GLN cc_start: 0.7194 (tp40) cc_final: 0.6968 (tp-100) REVERT: C 96 PHE cc_start: 0.6244 (m-80) cc_final: 0.5597 (t80) REVERT: C 147 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7669 (tpp80) REVERT: C 440 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7319 (mp) REVERT: C 473 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.5701 (t80) REVERT: A 221 MET cc_start: 0.8899 (ttp) cc_final: 0.8601 (ttp) REVERT: B 31 SER cc_start: 0.8233 (m) cc_final: 0.7959 (t) REVERT: B 59 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8558 (t80) REVERT: B 198 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8413 (pp) REVERT: B 217 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8143 (pmm) REVERT: B 262 MET cc_start: 0.9145 (mtp) cc_final: 0.8908 (mtp) REVERT: G 42 GLU cc_start: 0.8022 (pp20) cc_final: 0.7802 (tm-30) REVERT: N 43 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7842 (mttt) outliers start: 43 outliers final: 22 residues processed: 158 average time/residue: 1.2576 time to fit residues: 211.5681 Evaluate side-chains 148 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.0060 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 223 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 9 GLN B 237 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8342 Z= 0.159 Angle : 0.495 7.186 11321 Z= 0.266 Chirality : 0.041 0.152 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.523 55.551 1139 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.01 % Allowed : 21.41 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.25), residues: 1028 helix: 2.42 (0.24), residues: 411 sheet: 0.33 (0.33), residues: 226 loop : -0.49 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 118 time to evaluate : 1.056 Fit side-chains REVERT: C 61 GLN cc_start: 0.7197 (tp-100) cc_final: 0.6981 (tp-100) REVERT: C 96 PHE cc_start: 0.6275 (m-80) cc_final: 0.5552 (t80) REVERT: C 440 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7362 (mp) REVERT: C 473 PHE cc_start: 0.5926 (OUTLIER) cc_final: 0.5696 (t80) REVERT: A 216 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8398 (mttp) REVERT: A 221 MET cc_start: 0.9047 (ttp) cc_final: 0.8592 (ttp) REVERT: B 31 SER cc_start: 0.8143 (m) cc_final: 0.7917 (t) REVERT: B 59 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8555 (t80) REVERT: B 198 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8401 (pp) REVERT: B 217 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8031 (pmm) REVERT: B 262 MET cc_start: 0.9140 (mtp) cc_final: 0.8885 (mtp) REVERT: N 43 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7800 (mttt) outliers start: 44 outliers final: 20 residues processed: 150 average time/residue: 1.2056 time to fit residues: 191.9518 Evaluate side-chains 144 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 294 GLN B 9 GLN B 32 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8342 Z= 0.171 Angle : 0.497 7.211 11321 Z= 0.266 Chirality : 0.041 0.150 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.403 56.083 1137 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.13 % Allowed : 21.30 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.25), residues: 1028 helix: 2.41 (0.24), residues: 411 sheet: 0.27 (0.33), residues: 228 loop : -0.44 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 123 time to evaluate : 0.948 Fit side-chains REVERT: C 96 PHE cc_start: 0.6327 (m-80) cc_final: 0.5571 (t80) REVERT: C 440 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7348 (mp) REVERT: C 473 PHE cc_start: 0.5926 (OUTLIER) cc_final: 0.5681 (t80) REVERT: A 216 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: A 221 MET cc_start: 0.8969 (ttp) cc_final: 0.8595 (ttp) REVERT: B 31 SER cc_start: 0.8158 (m) cc_final: 0.7942 (t) REVERT: B 59 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8561 (t80) REVERT: B 198 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8390 (pp) REVERT: B 217 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (pmm) REVERT: B 262 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8810 (mtp) REVERT: N 43 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7806 (mttt) outliers start: 45 outliers final: 23 residues processed: 154 average time/residue: 1.2256 time to fit residues: 200.0979 Evaluate side-chains 150 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 0.0070 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 31 GLN A 294 GLN B 9 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8342 Z= 0.176 Angle : 0.501 7.070 11321 Z= 0.267 Chirality : 0.041 0.141 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.411 56.567 1137 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.01 % Allowed : 21.98 % Favored : 73.01 % 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: 1.28 (0.25), residues: 1028 helix: 2.39 (0.24), residues: 411 sheet: 0.24 (0.33), residues: 228 loop : -0.42 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.012 0.001 TYR N 95 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 1.044 Fit side-chains REVERT: C 96 PHE cc_start: 0.6310 (m-80) cc_final: 0.5546 (t80) REVERT: C 440 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7357 (mp) REVERT: C 473 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5678 (t80) REVERT: A 216 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8458 (mttp) REVERT: A 221 MET cc_start: 0.8907 (ttp) cc_final: 0.8624 (ttp) REVERT: B 31 SER cc_start: 0.8162 (m) cc_final: 0.7951 (t) REVERT: B 59 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8595 (t80) REVERT: B 198 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 217 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7912 (pmm) REVERT: B 262 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8803 (mtp) REVERT: G 42 GLU cc_start: 0.7956 (pp20) cc_final: 0.7739 (pp20) REVERT: N 43 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7799 (mttt) outliers start: 44 outliers final: 21 residues processed: 153 average time/residue: 1.2160 time to fit residues: 197.4450 Evaluate side-chains 146 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS C 458 HIS A 31 GLN A 294 GLN B 9 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8342 Z= 0.187 Angle : 0.505 7.253 11321 Z= 0.271 Chirality : 0.041 0.139 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.430 57.115 1137 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.44 % Allowed : 23.12 % Favored : 72.44 % 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: 1.29 (0.25), residues: 1028 helix: 2.38 (0.24), residues: 411 sheet: 0.32 (0.33), residues: 220 loop : -0.44 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.012 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 0.966 Fit side-chains REVERT: C 96 PHE cc_start: 0.6338 (m-80) cc_final: 0.5560 (t80) REVERT: C 440 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7377 (mp) REVERT: C 473 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5676 (t80) REVERT: B 31 SER cc_start: 0.8187 (m) cc_final: 0.7975 (t) REVERT: B 59 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8607 (t80) REVERT: B 198 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8361 (pp) REVERT: B 217 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7915 (pmm) REVERT: B 262 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8814 (mtp) REVERT: G 42 GLU cc_start: 0.7980 (pp20) cc_final: 0.7770 (pp20) REVERT: N 43 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7805 (mttt) outliers start: 39 outliers final: 23 residues processed: 148 average time/residue: 1.2249 time to fit residues: 192.3552 Evaluate side-chains 147 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 31 GLN B 9 GLN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8342 Z= 0.276 Angle : 0.553 7.405 11321 Z= 0.297 Chirality : 0.043 0.142 1292 Planarity : 0.004 0.045 1435 Dihedral : 4.680 58.959 1137 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.21 % Allowed : 23.58 % Favored : 72.21 % 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: 1.18 (0.25), residues: 1028 helix: 2.23 (0.24), residues: 411 sheet: 0.31 (0.33), residues: 226 loop : -0.46 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 441 HIS 0.004 0.001 HIS C 223 PHE 0.023 0.002 PHE C 41 TYR 0.016 0.002 TYR A 339 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 0.965 Fit side-chains REVERT: C 96 PHE cc_start: 0.6387 (m-80) cc_final: 0.5577 (t80) REVERT: C 473 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5674 (t80) REVERT: B 31 SER cc_start: 0.8255 (m) cc_final: 0.8015 (t) REVERT: B 59 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8558 (t80) REVERT: B 198 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8356 (pp) REVERT: B 217 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7960 (pmm) REVERT: B 262 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8837 (mtp) REVERT: N 43 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7850 (mttt) outliers start: 37 outliers final: 23 residues processed: 146 average time/residue: 1.2458 time to fit residues: 192.9784 Evaluate side-chains 148 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS B 9 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8342 Z= 0.167 Angle : 0.517 7.155 11321 Z= 0.277 Chirality : 0.041 0.139 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.467 57.373 1137 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.76 % Allowed : 24.26 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.25), residues: 1028 helix: 2.34 (0.24), residues: 411 sheet: 0.30 (0.33), residues: 226 loop : -0.43 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.011 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 0.934 Fit side-chains REVERT: C 96 PHE cc_start: 0.6338 (m-80) cc_final: 0.5856 (t80) REVERT: C 473 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.5672 (t80) REVERT: B 31 SER cc_start: 0.8178 (m) cc_final: 0.7968 (t) REVERT: B 59 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8578 (t80) REVERT: B 198 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8343 (pp) REVERT: B 217 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7739 (pmm) REVERT: B 262 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8791 (mtp) REVERT: G 42 GLU cc_start: 0.7965 (pp20) cc_final: 0.7703 (pp20) REVERT: N 43 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7807 (mttt) outliers start: 33 outliers final: 21 residues processed: 148 average time/residue: 1.1982 time to fit residues: 188.8534 Evaluate side-chains 144 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS B 9 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094068 restraints weight = 11266.327| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.10 r_work: 0.2981 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8342 Z= 0.158 Angle : 0.524 9.554 11321 Z= 0.274 Chirality : 0.041 0.194 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.382 56.810 1137 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.30 % Allowed : 25.17 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.32 (0.25), residues: 1028 helix: 2.41 (0.24), residues: 411 sheet: 0.27 (0.33), residues: 220 loop : -0.38 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.011 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3541.44 seconds wall clock time: 63 minutes 32.44 seconds (3812.44 seconds total)