Starting phenix.real_space_refine on Thu Mar 14 14:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1q_31422/03_2024/7f1q_31422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1q_31422/03_2024/7f1q_31422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1q_31422/03_2024/7f1q_31422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1q_31422/03_2024/7f1q_31422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1q_31422/03_2024/7f1q_31422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1q_31422/03_2024/7f1q_31422.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 1938 atoms to isotropic. 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 55 5.16 5 C 4588 2.51 5 N 1198 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 236": "NH1" <-> "NH2" Residue "R ARG 264": "NH1" <-> "NH2" Residue "R ARG 319": "NH1" <-> "NH2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R ARG 328": "NH1" <-> "NH2" Residue "R ARG 331": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" 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: 7123 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1646 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'TYR:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2370 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 314} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 243 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.06, per 1000 atoms: 0.57 Number of scatterers: 7123 At special positions: 0 Unit cell: (119.13, 128.535, 76.285, 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 55 16.00 O 1282 8.00 N 1198 7.00 C 4588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 10 " - pdb=" SG CYS R 34 " distance=2.03 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 365 " distance=2.04 Simple disulfide: pdb=" SG CYS R 197 " - pdb=" SG CYS R 274 " 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 44.6% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'R' and resid 2 through 6 removed outlier: 4.547A pdb=" N THR R 6 " --> pdb=" O ALA R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 69 removed outlier: 3.912A pdb=" N LYS R 60 " --> pdb=" O GLU R 56 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU R 66 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 129 removed outlier: 3.728A pdb=" N LYS R 122 " --> pdb=" O LYS R 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 154 Processing helix chain 'R' and resid 159 through 188 Proline residue: R 180 - end of helix removed outlier: 3.766A pdb=" N ALA R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA R 188 " --> pdb=" O HIS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 228 Processing helix chain 'R' and resid 228 through 236 removed outlier: 4.252A pdb=" N LYS R 234 " --> pdb=" O VAL R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 262 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 282 through 297 removed outlier: 3.589A pdb=" N VAL R 295 " --> pdb=" O THR R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 317 removed outlier: 4.104A pdb=" N SER R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY R 312 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 322 through 356 removed outlier: 3.678A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Proline residue: R 346 - end of helix Processing helix chain 'R' and resid 364 through 394 Proline residue: R 390 - end of helix Processing helix chain 'R' and resid 397 through 409 Processing helix chain 'A' and resid 7 through 33 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.054A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.736A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.798A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.695A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'R' and resid 9 through 10 removed outlier: 3.927A pdb=" N CYS R 10 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS R 116 " --> pdb=" O CYS R 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'R' and resid 264 through 268 removed outlier: 3.505A pdb=" N HIS R 271 " --> pdb=" O GLU R 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 removed outlier: 4.081A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.705A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.682A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.202A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.813A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.900A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.785A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.715A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1101 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: 2.24 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2268 1.35 - 1.46: 1827 1.46 - 1.58: 3111 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 7279 Sorted by residual: bond pdb=" N TYR R 347 " pdb=" CA TYR R 347 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.71e+00 bond pdb=" N PHE R 360 " pdb=" CA PHE R 360 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.42e-02 4.96e+03 5.71e+00 bond pdb=" N LYS R 60 " pdb=" CA LYS R 60 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.21e-02 6.83e+03 5.16e+00 bond pdb=" N PHE R 359 " pdb=" CA PHE R 359 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.22e-02 6.72e+03 4.65e+00 bond pdb=" C PHE R 360 " pdb=" O PHE R 360 " ideal model delta sigma weight residual 1.231 1.244 -0.013 1.16e-02 7.43e+03 1.28e+00 ... (remaining 7274 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.36: 94 105.36 - 112.52: 3864 112.52 - 119.67: 2163 119.67 - 126.82: 3681 126.82 - 133.97: 101 Bond angle restraints: 9903 Sorted by residual: angle pdb=" CA PHE R 360 " pdb=" CB PHE R 360 " pdb=" CG PHE R 360 " ideal model delta sigma weight residual 113.80 118.62 -4.82 1.00e+00 1.00e+00 2.32e+01 angle pdb=" CA PHE R 359 " pdb=" C PHE R 359 " pdb=" O PHE R 359 " ideal model delta sigma weight residual 121.16 116.37 4.79 1.12e+00 7.97e-01 1.83e+01 angle pdb=" N PHE R 359 " pdb=" CA PHE R 359 " pdb=" C PHE R 359 " ideal model delta sigma weight residual 110.28 104.61 5.67 1.48e+00 4.57e-01 1.47e+01 angle pdb=" C ARG R 127 " pdb=" N LEU R 128 " pdb=" CA LEU R 128 " ideal model delta sigma weight residual 123.04 117.89 5.15 1.59e+00 3.96e-01 1.05e+01 angle pdb=" C VAL R 179 " pdb=" CA VAL R 179 " pdb=" CB VAL R 179 " ideal model delta sigma weight residual 113.70 110.70 3.00 9.50e-01 1.11e+00 9.97e+00 ... (remaining 9898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3981 17.55 - 35.10: 234 35.10 - 52.66: 40 52.66 - 70.21: 10 70.21 - 87.76: 6 Dihedral angle restraints: 4271 sinusoidal: 1533 harmonic: 2738 Sorted by residual: dihedral pdb=" CB CYS R 15 " pdb=" SG CYS R 15 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual 93.00 150.49 -57.49 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA LEU R 128 " pdb=" C LEU R 128 " pdb=" N LEU R 129 " pdb=" CA LEU R 129 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CB CYS R 116 " pdb=" SG CYS R 116 " pdb=" SG CYS R 365 " pdb=" CB CYS R 365 " ideal model delta sinusoidal sigma weight residual -86.00 -40.12 -45.88 1 1.00e+01 1.00e-02 2.92e+01 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1041 0.060 - 0.120: 118 0.120 - 0.180: 5 0.180 - 0.240: 0 0.240 - 0.300: 2 Chirality restraints: 1166 Sorted by residual: chirality pdb=" CA PHE R 359 " pdb=" N PHE R 359 " pdb=" C PHE R 359 " pdb=" CB PHE R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA PHE R 360 " pdb=" N PHE R 360 " pdb=" C PHE R 360 " pdb=" CB PHE R 360 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1163 not shown) Planarity restraints: 1241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 359 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C PHE R 359 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE R 359 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE R 360 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 290 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLN R 290 " -0.023 2.00e-02 2.50e+03 pdb=" O GLN R 290 " 0.009 2.00e-02 2.50e+03 pdb=" N THR R 291 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 257 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO R 258 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 258 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 258 " -0.019 5.00e-02 4.00e+02 ... (remaining 1238 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1719 2.79 - 3.32: 6898 3.32 - 3.85: 12255 3.85 - 4.37: 14137 4.37 - 4.90: 24602 Nonbonded interactions: 59611 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.271 2.440 nonbonded pdb=" O CYS R 386 " pdb=" ND2 ASN R 389 " model vdw 2.306 2.520 nonbonded pdb=" OG1 THR R 161 " pdb=" OD2 ASP R 221 " model vdw 2.314 2.440 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.319 2.520 ... (remaining 59606 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.520 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 : 0.002 0.034 7279 Z= 0.141 Angle : 0.549 6.692 9903 Z= 0.327 Chirality : 0.039 0.300 1166 Planarity : 0.003 0.033 1241 Dihedral : 12.031 87.760 2478 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.27 % Allowed : 2.71 % Favored : 97.01 % 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: -1.52 (0.24), residues: 924 helix: -0.33 (0.24), residues: 381 sheet: -0.72 (0.34), residues: 188 loop : -1.80 (0.27), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.002 0.000 HIS B 311 PHE 0.008 0.001 PHE A 354 TYR 0.009 0.001 TYR R 347 ARG 0.001 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 0.770 Fit side-chains REVERT: R 230 VAL cc_start: 0.8474 (m) cc_final: 0.8082 (t) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.8140 time to fit residues: 150.6712 Evaluate side-chains 114 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 18 GLN R 184 HIS R 271 HIS ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 88 ASN B 110 ASN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 7279 Z= 0.617 Angle : 0.753 9.182 9903 Z= 0.396 Chirality : 0.050 0.234 1166 Planarity : 0.004 0.037 1241 Dihedral : 4.608 24.695 995 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.16 % Allowed : 13.03 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 924 helix: 0.43 (0.25), residues: 386 sheet: -0.53 (0.33), residues: 217 loop : -0.90 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP R 182 HIS 0.014 0.002 HIS B 142 PHE 0.027 0.003 PHE R 214 TYR 0.021 0.002 TYR B 105 ARG 0.008 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 0.870 Fit side-chains REVERT: R 33 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8505 (mp-120) REVERT: R 59 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7448 (mm-40) REVERT: R 290 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7385 (tp40) REVERT: R 325 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7201 (mptm) REVERT: A 20 ASP cc_start: 0.7566 (m-30) cc_final: 0.7305 (m-30) REVERT: A 306 GLN cc_start: 0.7146 (tp40) cc_final: 0.6885 (mm-40) REVERT: A 350 ASP cc_start: 0.7141 (m-30) cc_final: 0.6896 (m-30) REVERT: B 61 MET cc_start: 0.9140 (ppp) cc_final: 0.8861 (ppp) outliers start: 38 outliers final: 21 residues processed: 161 average time/residue: 0.9529 time to fit residues: 163.9428 Evaluate side-chains 141 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 325 LYS Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 59 GLN R 271 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7279 Z= 0.216 Angle : 0.547 9.742 9903 Z= 0.283 Chirality : 0.041 0.218 1166 Planarity : 0.003 0.034 1241 Dihedral : 4.172 25.864 995 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.88 % Allowed : 17.64 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 924 helix: 1.09 (0.26), residues: 386 sheet: -0.43 (0.33), residues: 214 loop : -0.67 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 182 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 175 TYR 0.012 0.001 TYR R 61 ARG 0.006 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 0.771 Fit side-chains REVERT: R 33 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8365 (mp-120) REVERT: R 290 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7376 (tp40) REVERT: R 359 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7522 (t80) REVERT: A 306 GLN cc_start: 0.6942 (tp40) cc_final: 0.6647 (mm-40) REVERT: A 350 ASP cc_start: 0.7119 (m-30) cc_final: 0.6885 (m-30) outliers start: 36 outliers final: 14 residues processed: 151 average time/residue: 0.8429 time to fit residues: 136.8013 Evaluate side-chains 133 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 359 PHE Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 59 GLN R 271 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7279 Z= 0.220 Angle : 0.544 6.953 9903 Z= 0.282 Chirality : 0.041 0.200 1166 Planarity : 0.003 0.040 1241 Dihedral : 4.071 26.066 995 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.61 % Allowed : 19.00 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 924 helix: 1.34 (0.26), residues: 386 sheet: -0.29 (0.35), residues: 207 loop : -0.71 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE R 175 TYR 0.009 0.001 TYR R 27 ARG 0.009 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 0.723 Fit side-chains REVERT: R 33 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: R 230 VAL cc_start: 0.8659 (m) cc_final: 0.8389 (t) REVERT: R 290 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7449 (tp40) REVERT: R 359 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7602 (t80) REVERT: R 383 MET cc_start: 0.7594 (mtt) cc_final: 0.7282 (mtt) REVERT: R 384 THR cc_start: 0.8907 (m) cc_final: 0.8670 (t) REVERT: A 20 ASP cc_start: 0.7371 (m-30) cc_final: 0.7133 (m-30) REVERT: A 306 GLN cc_start: 0.7022 (tp40) cc_final: 0.6687 (mm-40) REVERT: A 350 ASP cc_start: 0.7163 (m-30) cc_final: 0.6918 (m-30) outliers start: 34 outliers final: 16 residues processed: 142 average time/residue: 0.8309 time to fit residues: 126.8208 Evaluate side-chains 135 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 359 PHE Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7279 Z= 0.289 Angle : 0.579 7.781 9903 Z= 0.300 Chirality : 0.043 0.199 1166 Planarity : 0.003 0.044 1241 Dihedral : 4.194 25.232 995 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.70 % Allowed : 18.45 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 924 helix: 1.52 (0.27), residues: 379 sheet: -0.56 (0.33), residues: 218 loop : -0.66 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.002 PHE R 175 TYR 0.014 0.001 TYR B 59 ARG 0.019 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 0.780 Fit side-chains REVERT: R 6 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7991 (p) REVERT: R 33 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: R 280 TYR cc_start: 0.8110 (p90) cc_final: 0.7879 (p90) REVERT: R 290 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7453 (tp40) REVERT: R 370 ARG cc_start: 0.6840 (mtm-85) cc_final: 0.5286 (ptt90) REVERT: R 383 MET cc_start: 0.7617 (mtt) cc_final: 0.7309 (mtt) REVERT: A 20 ASP cc_start: 0.7415 (m-30) cc_final: 0.7151 (m-30) REVERT: A 283 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 306 GLN cc_start: 0.7215 (tp40) cc_final: 0.6909 (mm-40) REVERT: A 350 ASP cc_start: 0.7138 (m-30) cc_final: 0.6875 (m-30) outliers start: 42 outliers final: 20 residues processed: 148 average time/residue: 0.8215 time to fit residues: 130.6368 Evaluate side-chains 136 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 ASN Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7279 Z= 0.284 Angle : 0.565 6.948 9903 Z= 0.294 Chirality : 0.042 0.189 1166 Planarity : 0.003 0.040 1241 Dihedral : 4.183 25.262 995 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 7.06 % Allowed : 18.32 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 924 helix: 1.62 (0.27), residues: 377 sheet: -0.46 (0.32), residues: 226 loop : -0.60 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS B 142 PHE 0.012 0.002 PHE R 175 TYR 0.014 0.001 TYR B 59 ARG 0.012 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 113 time to evaluate : 0.797 Fit side-chains REVERT: R 6 THR cc_start: 0.8207 (p) cc_final: 0.7966 (p) REVERT: R 33 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8353 (mp10) REVERT: R 52 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7008 (p0) REVERT: R 280 TYR cc_start: 0.8131 (p90) cc_final: 0.7896 (p90) REVERT: R 290 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7479 (tp40) REVERT: R 370 ARG cc_start: 0.6956 (mtm-85) cc_final: 0.5527 (ptt90) REVERT: A 20 ASP cc_start: 0.7455 (m-30) cc_final: 0.7163 (m-30) REVERT: A 283 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7890 (tt) REVERT: A 306 GLN cc_start: 0.7335 (tp40) cc_final: 0.7012 (mm-40) REVERT: A 350 ASP cc_start: 0.7136 (m-30) cc_final: 0.6878 (m-30) outliers start: 52 outliers final: 29 residues processed: 148 average time/residue: 0.8204 time to fit residues: 130.7819 Evaluate side-chains 144 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 ASN Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 384 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7279 Z= 0.196 Angle : 0.528 6.720 9903 Z= 0.274 Chirality : 0.041 0.195 1166 Planarity : 0.003 0.042 1241 Dihedral : 3.963 25.334 995 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.11 % Allowed : 19.67 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 924 helix: 1.81 (0.27), residues: 377 sheet: -0.40 (0.33), residues: 210 loop : -0.68 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.012 0.001 PHE R 175 TYR 0.010 0.001 TYR R 27 ARG 0.012 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 0.838 Fit side-chains REVERT: R 6 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7898 (p) REVERT: R 52 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.6982 (p0) REVERT: R 290 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7481 (tp40) REVERT: R 370 ARG cc_start: 0.6952 (mtm-85) cc_final: 0.5458 (ptt90) REVERT: A 20 ASP cc_start: 0.7341 (m-30) cc_final: 0.7005 (m-30) REVERT: A 306 GLN cc_start: 0.7240 (tp40) cc_final: 0.6898 (mm-40) REVERT: A 350 ASP cc_start: 0.7163 (m-30) cc_final: 0.6889 (m-30) outliers start: 45 outliers final: 30 residues processed: 147 average time/residue: 0.8836 time to fit residues: 139.2536 Evaluate side-chains 143 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 22 ASN Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 384 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7279 Z= 0.294 Angle : 0.573 7.220 9903 Z= 0.298 Chirality : 0.042 0.204 1166 Planarity : 0.004 0.045 1241 Dihedral : 4.117 24.924 995 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.97 % Allowed : 20.62 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 924 helix: 1.74 (0.27), residues: 377 sheet: -0.46 (0.33), residues: 222 loop : -0.55 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 182 HIS 0.007 0.001 HIS B 142 PHE 0.013 0.002 PHE R 175 TYR 0.011 0.001 TYR R 27 ARG 0.014 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 113 time to evaluate : 0.704 Fit side-chains REVERT: R 6 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7943 (p) REVERT: R 52 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.6968 (p0) REVERT: R 280 TYR cc_start: 0.8155 (p90) cc_final: 0.7912 (p90) REVERT: R 290 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7515 (tp40) REVERT: R 370 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.5589 (ptt90) REVERT: A 20 ASP cc_start: 0.7459 (m-30) cc_final: 0.7136 (m-30) REVERT: A 306 GLN cc_start: 0.7396 (tp40) cc_final: 0.7097 (mm-40) REVERT: A 350 ASP cc_start: 0.7192 (m-30) cc_final: 0.6878 (m-30) REVERT: B 249 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8243 (m) outliers start: 44 outliers final: 28 residues processed: 142 average time/residue: 0.9208 time to fit residues: 140.3736 Evaluate side-chains 143 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7279 Z= 0.216 Angle : 0.541 6.722 9903 Z= 0.281 Chirality : 0.041 0.197 1166 Planarity : 0.003 0.045 1241 Dihedral : 4.050 25.295 995 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.61 % Allowed : 22.12 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.28), residues: 924 helix: 1.84 (0.27), residues: 376 sheet: -0.45 (0.33), residues: 222 loop : -0.50 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE R 181 TYR 0.011 0.001 TYR R 27 ARG 0.010 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 0.834 Fit side-chains REVERT: R 6 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8114 (p) REVERT: R 52 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.6956 (p0) REVERT: R 280 TYR cc_start: 0.8134 (p90) cc_final: 0.7889 (p90) REVERT: R 290 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7509 (tp40) REVERT: R 370 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.5520 (ptt90) REVERT: A 20 ASP cc_start: 0.7412 (m-30) cc_final: 0.7059 (m-30) REVERT: A 306 GLN cc_start: 0.7315 (tp40) cc_final: 0.6944 (mm-40) REVERT: A 350 ASP cc_start: 0.7153 (m-30) cc_final: 0.6852 (m-30) outliers start: 34 outliers final: 28 residues processed: 135 average time/residue: 0.8768 time to fit residues: 127.0971 Evaluate side-chains 140 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 GLN ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7279 Z= 0.225 Angle : 0.547 7.528 9903 Z= 0.284 Chirality : 0.041 0.196 1166 Planarity : 0.004 0.074 1241 Dihedral : 4.035 25.317 995 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.34 % Allowed : 22.39 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 924 helix: 1.88 (0.27), residues: 376 sheet: -0.42 (0.33), residues: 222 loop : -0.46 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 181 TYR 0.011 0.001 TYR R 27 ARG 0.019 0.001 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 0.849 Fit side-chains REVERT: R 6 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8154 (p) REVERT: R 52 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.6994 (p0) REVERT: R 280 TYR cc_start: 0.8180 (p90) cc_final: 0.7918 (p90) REVERT: R 290 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7507 (tp40) REVERT: R 370 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.5536 (ptt90) REVERT: A 20 ASP cc_start: 0.7419 (m-30) cc_final: 0.7059 (m-30) REVERT: A 306 GLN cc_start: 0.7327 (tp40) cc_final: 0.6986 (mm-40) REVERT: A 350 ASP cc_start: 0.7027 (m-30) cc_final: 0.6776 (m-30) REVERT: B 249 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8224 (m) outliers start: 32 outliers final: 29 residues processed: 134 average time/residue: 0.9179 time to fit residues: 131.9067 Evaluate side-chains 144 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 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 = 0.3753 r_free = 0.3753 target = 0.151501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115893 restraints weight = 8154.136| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.12 r_work: 0.3192 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7279 Z= 0.226 Angle : 0.547 7.457 9903 Z= 0.284 Chirality : 0.041 0.202 1166 Planarity : 0.004 0.082 1241 Dihedral : 4.027 25.296 995 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.75 % Allowed : 22.52 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 924 helix: 1.88 (0.27), residues: 376 sheet: -0.37 (0.33), residues: 216 loop : -0.47 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE R 181 TYR 0.011 0.001 TYR R 27 ARG 0.019 0.001 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.45 seconds wall clock time: 51 minutes 43.93 seconds (3103.93 seconds total)