Starting phenix.real_space_refine on Fri Dec 8 03:19:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/12_2023/7xk8_33247_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/12_2023/7xk8_33247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/12_2023/7xk8_33247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/12_2023/7xk8_33247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/12_2023/7xk8_33247_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/12_2023/7xk8_33247_updated.pdb" } resolution = 3.3 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= 0.003 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 46 5.16 5 C 4352 2.51 5 N 1151 2.21 5 O 1247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R GLU 127": "OE1" <-> "OE2" Residue "R PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 333": "NH1" <-> "NH2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6796 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 203 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 22} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2115 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 99 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1673 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2432 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 373 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.30, per 1000 atoms: 0.63 Number of scatterers: 6796 At special positions: 0 Unit cell: (111.815, 127.49, 85.69, 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 46 16.00 O 1247 8.00 N 1151 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 204 " 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: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 8 sheets defined 39.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'R' and resid 46 through 71 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 79 through 107 Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 116 through 149 Processing helix chain 'R' and resid 151 through 158 removed outlier: 5.574A pdb=" N GLN R 157 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 183 Proline residue: R 180 - end of helix Processing helix chain 'R' and resid 210 through 246 removed outlier: 4.502A pdb=" N LEU R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) Proline residue: R 228 - end of helix Processing helix chain 'R' and resid 259 through 290 Proline residue: R 283 - end of helix removed outlier: 3.987A pdb=" N ARG R 288 " --> pdb=" O PHE R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 327 Proline residue: R 324 - end of helix Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.733A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.172A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'C' and resid 12 through 22 removed outlier: 3.963A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.952A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 197 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 36 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.584A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.863A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.801A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.618A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.745A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.626A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 335 through 339 removed outlier: 4.251A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 969 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: 1.80 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1099 1.31 - 1.44: 1926 1.44 - 1.56: 3856 1.56 - 1.69: 0 1.69 - 1.82: 62 Bond restraints: 6943 Sorted by residual: bond pdb=" C ASN P 25 " pdb=" N NH2 P 26 " ideal model delta sigma weight residual 2.329 1.452 0.877 1.40e-02 5.10e+03 3.92e+03 bond pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.10e-02 2.27e+03 3.46e+01 bond pdb=" CG ASN P 25 " pdb=" OD1 ASN P 25 " ideal model delta sigma weight residual 1.231 1.185 0.046 1.90e-02 2.77e+03 5.92e+00 bond pdb=" C ASN P 25 " pdb=" O ASN P 25 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C SER P 9 " pdb=" N PRO P 10 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.12e+00 ... (remaining 6938 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 162 107.08 - 113.80: 3935 113.80 - 120.53: 2784 120.53 - 127.25: 2521 127.25 - 133.97: 75 Bond angle restraints: 9477 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 112.96 109.56 3.40 1.00e+00 1.00e+00 1.16e+01 angle pdb=" N GLY R 186 " pdb=" CA GLY R 186 " pdb=" C GLY R 186 " ideal model delta sigma weight residual 110.80 115.68 -4.88 1.71e+00 3.42e-01 8.15e+00 angle pdb=" OD1 ASN P 25 " pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 122.60 119.99 2.61 1.00e+00 1.00e+00 6.82e+00 angle pdb=" N THR B 196 " pdb=" CA THR B 196 " pdb=" CB THR B 196 " ideal model delta sigma weight residual 113.65 110.02 3.63 1.47e+00 4.63e-01 6.11e+00 angle pdb=" CB ASN P 25 " pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 116.40 120.02 -3.62 1.50e+00 4.44e-01 5.81e+00 ... (remaining 9472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 3698 15.57 - 31.14: 291 31.14 - 46.70: 57 46.70 - 62.27: 7 62.27 - 77.84: 1 Dihedral angle restraints: 4054 sinusoidal: 1361 harmonic: 2693 Sorted by residual: dihedral pdb=" CA PHE R 189 " pdb=" C PHE R 189 " pdb=" N HIS R 190 " pdb=" CA HIS R 190 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 204 " pdb=" CB CYS R 204 " ideal model delta sinusoidal sigma weight residual 93.00 65.34 27.66 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ASP B 38 " pdb=" CB ASP B 38 " pdb=" CG ASP B 38 " pdb=" OD1 ASP B 38 " ideal model delta sinusoidal sigma weight residual -30.00 -83.44 53.44 1 2.00e+01 2.50e-03 9.71e+00 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 756 0.030 - 0.059: 243 0.059 - 0.089: 79 0.089 - 0.119: 44 0.119 - 0.149: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE R 187 " pdb=" N ILE R 187 " pdb=" C ILE R 187 " pdb=" CB ILE R 187 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CB ILE R 184 " pdb=" CA ILE R 184 " pdb=" CG1 ILE R 184 " pdb=" CG2 ILE R 184 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1122 not shown) Planarity restraints: 1204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 78 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO R 79 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 79 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 79 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 282 " 0.018 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO R 283 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.20e-01 pdb=" N PRO B 236 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.013 5.00e-02 4.00e+02 ... (remaining 1201 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1400 2.78 - 3.31: 6630 3.31 - 3.84: 11544 3.84 - 4.37: 12499 4.37 - 4.90: 22116 Nonbonded interactions: 54189 Sorted by model distance: nonbonded pdb=" O LEU R 289 " pdb=" OG SER R 292 " model vdw 2.248 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR R 78 " pdb=" OD1 ASP A 350 " model vdw 2.270 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.278 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.306 2.440 ... (remaining 54184 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.960 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.310 Find NCS groups from input model: 0.190 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 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 : 0.011 0.877 6943 Z= 0.764 Angle : 0.481 6.142 9477 Z= 0.272 Chirality : 0.038 0.149 1125 Planarity : 0.003 0.029 1204 Dihedral : 11.624 77.838 2301 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: -1.25 (0.25), residues: 907 helix: 0.38 (0.24), residues: 371 sheet: -0.45 (0.38), residues: 154 loop : -2.23 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 99 HIS 0.003 0.000 HIS R 285 PHE 0.010 0.001 PHE R 291 TYR 0.004 0.001 TYR B 289 ARG 0.001 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2225 time to fit residues: 46.0090 Evaluate side-chains 97 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 43 HIS R 285 HIS A 57 HIS A 294 ASN A 304 GLN A 347 ASN C 18 GLN C 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6943 Z= 0.193 Angle : 0.553 7.339 9477 Z= 0.278 Chirality : 0.041 0.231 1125 Planarity : 0.003 0.027 1204 Dihedral : 3.473 26.172 978 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.24 % Allowed : 15.97 % Favored : 81.79 % 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: -0.04 (0.27), residues: 907 helix: 1.60 (0.26), residues: 372 sheet: 0.22 (0.42), residues: 136 loop : -1.77 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.022 0.001 PHE R 316 TYR 0.017 0.001 TYR R 213 ARG 0.005 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 0.1810 time to fit residues: 30.1338 Evaluate side-chains 107 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0713 time to fit residues: 2.3063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6943 Z= 0.196 Angle : 0.532 6.325 9477 Z= 0.270 Chirality : 0.040 0.150 1125 Planarity : 0.003 0.032 1204 Dihedral : 3.627 32.838 978 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.84 % Allowed : 19.85 % Favored : 77.31 % 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: 0.33 (0.28), residues: 907 helix: 1.96 (0.27), residues: 374 sheet: -0.01 (0.40), residues: 156 loop : -1.53 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.012 0.001 HIS R 285 PHE 0.018 0.001 PHE R 316 TYR 0.011 0.001 TYR R 225 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.735 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 0.1843 time to fit residues: 30.6937 Evaluate side-chains 112 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1509 time to fit residues: 4.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6943 Z= 0.184 Angle : 0.529 6.251 9477 Z= 0.266 Chirality : 0.041 0.238 1125 Planarity : 0.003 0.031 1204 Dihedral : 3.663 34.296 978 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.54 % Allowed : 20.90 % Favored : 76.57 % 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: 0.52 (0.28), residues: 907 helix: 2.08 (0.27), residues: 375 sheet: -0.02 (0.42), residues: 157 loop : -1.34 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.003 0.001 HIS R 285 PHE 0.018 0.001 PHE R 316 TYR 0.015 0.001 TYR B 111 ARG 0.008 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.735 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 119 average time/residue: 0.1465 time to fit residues: 24.8009 Evaluate side-chains 106 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1216 time to fit residues: 2.3562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 17 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6943 Z= 0.172 Angle : 0.528 7.190 9477 Z= 0.266 Chirality : 0.039 0.145 1125 Planarity : 0.003 0.031 1204 Dihedral : 3.688 34.288 978 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.99 % Allowed : 22.09 % Favored : 74.93 % 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: 0.60 (0.28), residues: 907 helix: 2.18 (0.27), residues: 374 sheet: 0.01 (0.44), residues: 140 loop : -1.28 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.013 0.001 HIS R 285 PHE 0.018 0.001 PHE R 316 TYR 0.010 0.001 TYR R 225 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.728 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 117 average time/residue: 0.1533 time to fit residues: 25.5276 Evaluate side-chains 108 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0641 time to fit residues: 2.3002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.0040 chunk 83 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6943 Z= 0.176 Angle : 0.537 8.106 9477 Z= 0.269 Chirality : 0.041 0.256 1125 Planarity : 0.003 0.031 1204 Dihedral : 3.705 34.150 978 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.69 % Allowed : 22.84 % Favored : 74.48 % 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: 0.63 (0.28), residues: 907 helix: 2.24 (0.27), residues: 375 sheet: -0.03 (0.44), residues: 139 loop : -1.27 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS R 285 PHE 0.019 0.001 PHE R 316 TYR 0.017 0.001 TYR B 59 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.792 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 114 average time/residue: 0.1595 time to fit residues: 25.6347 Evaluate side-chains 105 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0681 time to fit residues: 2.4039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6943 Z= 0.300 Angle : 0.609 9.397 9477 Z= 0.309 Chirality : 0.042 0.176 1125 Planarity : 0.003 0.032 1204 Dihedral : 4.155 39.092 978 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.54 % Allowed : 23.88 % 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: 0.43 (0.28), residues: 907 helix: 2.05 (0.26), residues: 376 sheet: -0.34 (0.42), residues: 149 loop : -1.29 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.011 0.002 HIS R 285 PHE 0.021 0.002 PHE R 316 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.774 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 110 average time/residue: 0.1730 time to fit residues: 26.8715 Evaluate side-chains 104 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0698 time to fit residues: 2.0527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 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 285 HIS A 294 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6943 Z= 0.204 Angle : 0.589 9.510 9477 Z= 0.293 Chirality : 0.042 0.262 1125 Planarity : 0.003 0.032 1204 Dihedral : 4.019 37.235 978 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.04 % Allowed : 26.57 % Favored : 72.39 % 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: 0.49 (0.28), residues: 907 helix: 2.13 (0.26), residues: 376 sheet: -0.20 (0.43), residues: 144 loop : -1.34 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS R 285 PHE 0.020 0.001 PHE R 316 TYR 0.009 0.001 TYR R 225 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.806 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 0.1603 time to fit residues: 23.9260 Evaluate side-chains 102 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0649 time to fit residues: 1.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6943 Z= 0.375 Angle : 0.684 9.371 9477 Z= 0.346 Chirality : 0.044 0.219 1125 Planarity : 0.004 0.068 1204 Dihedral : 4.429 36.102 978 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.94 % Allowed : 25.82 % Favored : 72.24 % 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: 0.22 (0.28), residues: 907 helix: 1.91 (0.26), residues: 376 sheet: -0.52 (0.39), residues: 165 loop : -1.44 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 339 HIS 0.006 0.002 HIS B 311 PHE 0.023 0.002 PHE R 316 TYR 0.016 0.002 TYR B 59 ARG 0.008 0.001 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.821 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 0.1689 time to fit residues: 25.0935 Evaluate side-chains 99 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0710 time to fit residues: 1.9759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6943 Z= 0.217 Angle : 0.627 9.101 9477 Z= 0.314 Chirality : 0.042 0.189 1125 Planarity : 0.003 0.035 1204 Dihedral : 4.200 35.981 978 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.60 % Allowed : 27.16 % Favored : 72.24 % 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: 0.33 (0.28), residues: 907 helix: 2.00 (0.26), residues: 377 sheet: -0.35 (0.43), residues: 145 loop : -1.41 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 285 PHE 0.030 0.001 PHE R 316 TYR 0.008 0.001 TYR R 225 ARG 0.005 0.000 ARG R 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.802 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 102 average time/residue: 0.1629 time to fit residues: 23.4794 Evaluate side-chains 94 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0700 time to fit residues: 1.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.197653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.154289 restraints weight = 7761.556| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 3.32 r_work: 0.3765 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6943 Z= 0.411 Angle : 0.734 10.101 9477 Z= 0.377 Chirality : 0.046 0.287 1125 Planarity : 0.004 0.038 1204 Dihedral : 4.598 34.179 978 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.75 % Allowed : 27.76 % Favored : 71.49 % 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: 0.05 (0.27), residues: 907 helix: 1.74 (0.26), residues: 377 sheet: -0.73 (0.41), residues: 146 loop : -1.43 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.007 0.002 HIS B 183 PHE 0.035 0.002 PHE R 316 TYR 0.013 0.002 TYR B 59 ARG 0.010 0.001 ARG R 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.68 seconds wall clock time: 35 minutes 30.98 seconds (2130.98 seconds total)