Starting phenix.real_space_refine on Tue Feb 13 15:53:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/02_2024/7xk8_33247_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/02_2024/7xk8_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_33247/02_2024/7xk8_33247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/02_2024/7xk8_33247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/02_2024/7xk8_33247_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk8_33247/02_2024/7xk8_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.16, per 1000 atoms: 0.61 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: 2.42 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: 1.46 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: 1.69 Time building geometry restraints manager: 2.67 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 1.329 1.452 -0.123 1.40e-02 5.10e+03 7.75e+01 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: 0.800 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: 3.970 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.000 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- 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 : 0.003 0.124 6943 Z= 0.174 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 : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 127 GLU cc_start: 0.6422 (tp30) cc_final: 0.6077 (tp30) REVERT: R 333 ARG cc_start: 0.4321 (pmt170) cc_final: 0.3932 (tpp-160) REVERT: A 9 ASP cc_start: 0.7360 (t70) cc_final: 0.6993 (t0) REVERT: B 188 MET cc_start: 0.7046 (mmm) cc_final: 0.6843 (mmm) REVERT: C 62 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6392 (mtm110) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2115 time to fit residues: 43.3130 Evaluate side-chains 99 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.1198 ------------------------------------------------------------------------------- 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 ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN C 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6943 Z= 0.251 Angle : 0.575 7.449 9477 Z= 0.292 Chirality : 0.042 0.222 1125 Planarity : 0.003 0.027 1204 Dihedral : 3.695 31.126 978 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.69 % Allowed : 15.37 % Favored : 81.94 % 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: -0.13 (0.27), residues: 907 helix: 1.57 (0.26), residues: 372 sheet: -0.18 (0.39), residues: 154 loop : -1.79 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.005 0.001 HIS B 142 PHE 0.024 0.002 PHE R 316 TYR 0.016 0.001 TYR B 59 ARG 0.003 0.000 ARG R 288 *********************** 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 125 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 333 ARG cc_start: 0.4470 (pmt170) cc_final: 0.3806 (tpp-160) REVERT: A 9 ASP cc_start: 0.7480 (t70) cc_final: 0.7143 (t0) REVERT: C 62 ARG cc_start: 0.6725 (mtm-85) cc_final: 0.6508 (mtm110) outliers start: 18 outliers final: 11 residues processed: 118 average time/residue: 0.1930 time to fit residues: 30.2011 Evaluate side-chains 106 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 322 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 0.0030 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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: 0.6542 moved from start: 0.2178 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= 0.171 Angle : 0.519 6.201 9477 Z= 0.261 Chirality : 0.040 0.175 1125 Planarity : 0.003 0.029 1204 Dihedral : 3.613 33.241 978 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.99 % Allowed : 19.55 % Favored : 77.46 % 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: 0.30 (0.27), residues: 907 helix: 1.97 (0.27), residues: 374 sheet: -0.04 (0.42), residues: 148 loop : -1.56 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS R 285 PHE 0.016 0.001 PHE R 316 TYR 0.012 0.001 TYR R 225 ARG 0.003 0.000 ARG A 15 *********************** 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 133 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: R 281 TRP cc_start: 0.5045 (m100) cc_final: 0.4433 (m100) REVERT: R 333 ARG cc_start: 0.4250 (pmt170) cc_final: 0.3792 (tpp-160) REVERT: A 9 ASP cc_start: 0.7451 (t70) cc_final: 0.7108 (t0) REVERT: B 82 TRP cc_start: 0.7733 (m100) cc_final: 0.7437 (m100) REVERT: C 62 ARG cc_start: 0.6724 (mtm-85) cc_final: 0.6431 (mtm110) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.1919 time to fit residues: 31.6138 Evaluate side-chains 119 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 322 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 25 ASN R 285 HIS A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6943 Z= 0.316 Angle : 0.599 6.886 9477 Z= 0.305 Chirality : 0.042 0.153 1125 Planarity : 0.003 0.034 1204 Dihedral : 4.104 37.603 978 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.07 % Allowed : 20.75 % Favored : 74.18 % 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 (0.28), residues: 907 helix: 1.90 (0.26), residues: 374 sheet: -0.21 (0.39), residues: 163 loop : -1.38 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.009 0.002 HIS R 285 PHE 0.019 0.002 PHE R 316 TYR 0.013 0.002 TYR B 59 ARG 0.003 0.000 ARG A 15 *********************** 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 139 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 0.716 Fit side-chains REVERT: R 169 ILE cc_start: 0.4803 (OUTLIER) cc_final: 0.4410 (tp) REVERT: R 239 MET cc_start: 0.5621 (mtp) cc_final: 0.5283 (ttm) REVERT: R 333 ARG cc_start: 0.4201 (pmt170) cc_final: 0.3591 (tpp-160) REVERT: A 9 ASP cc_start: 0.7524 (t70) cc_final: 0.7171 (t0) REVERT: A 197 LYS cc_start: 0.8221 (ptpt) cc_final: 0.7945 (ptmt) REVERT: A 287 TYR cc_start: 0.5890 (m-80) cc_final: 0.5675 (m-10) outliers start: 34 outliers final: 22 residues processed: 129 average time/residue: 0.1641 time to fit residues: 28.9264 Evaluate side-chains 120 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 25 ASN ** 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: 0.6693 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6943 Z= 0.255 Angle : 0.571 6.438 9477 Z= 0.289 Chirality : 0.041 0.148 1125 Planarity : 0.003 0.034 1204 Dihedral : 4.051 34.990 978 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.07 % Allowed : 22.84 % Favored : 72.09 % 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: 0.36 (0.28), residues: 907 helix: 1.97 (0.27), residues: 374 sheet: -0.21 (0.39), residues: 167 loop : -1.42 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.019 0.001 PHE R 316 TYR 0.020 0.001 TYR B 111 ARG 0.006 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 142 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.758 Fit side-chains REVERT: R 84 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5966 (mp) REVERT: R 239 MET cc_start: 0.5741 (mtp) cc_final: 0.5390 (ttm) REVERT: R 333 ARG cc_start: 0.4261 (pmt170) cc_final: 0.3620 (tmt170) REVERT: A 9 ASP cc_start: 0.7552 (t70) cc_final: 0.7199 (t0) REVERT: A 197 LYS cc_start: 0.8272 (ptpt) cc_final: 0.7927 (ptmt) REVERT: B 82 TRP cc_start: 0.7803 (m100) cc_final: 0.7311 (m100) REVERT: B 228 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8158 (p0) outliers start: 34 outliers final: 20 residues processed: 133 average time/residue: 0.1707 time to fit residues: 31.4414 Evaluate side-chains 126 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.0070 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 25 ASN ** 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: 0.6684 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6943 Z= 0.227 Angle : 0.573 8.787 9477 Z= 0.288 Chirality : 0.042 0.291 1125 Planarity : 0.003 0.033 1204 Dihedral : 4.007 34.301 978 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.82 % Allowed : 22.99 % Favored : 71.19 % 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: 1.97 (0.26), residues: 376 sheet: -0.26 (0.39), residues: 160 loop : -1.45 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE R 316 TYR 0.011 0.001 TYR R 120 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 141 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 102 time to evaluate : 0.772 Fit side-chains REVERT: R 84 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5938 (mp) REVERT: R 169 ILE cc_start: 0.5035 (OUTLIER) cc_final: 0.4657 (tp) REVERT: R 239 MET cc_start: 0.5766 (mtp) cc_final: 0.5424 (ttm) REVERT: R 333 ARG cc_start: 0.4286 (pmt170) cc_final: 0.3613 (tmt170) REVERT: A 197 LYS cc_start: 0.8286 (ptpt) cc_final: 0.7959 (ptmt) REVERT: B 82 TRP cc_start: 0.7808 (m100) cc_final: 0.7301 (m100) REVERT: B 228 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8310 (p0) REVERT: B 338 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6270 (mm) outliers start: 39 outliers final: 30 residues processed: 130 average time/residue: 0.1637 time to fit residues: 29.4011 Evaluate side-chains 132 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 6943 Z= 0.447 Angle : 0.711 10.276 9477 Z= 0.362 Chirality : 0.046 0.270 1125 Planarity : 0.004 0.039 1204 Dihedral : 4.695 32.227 978 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 7.01 % Allowed : 24.03 % Favored : 68.96 % 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: -0.09 (0.27), residues: 907 helix: 1.60 (0.26), residues: 376 sheet: -0.77 (0.39), residues: 152 loop : -1.48 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.007 0.002 HIS B 54 PHE 0.022 0.002 PHE R 316 TYR 0.016 0.002 TYR B 59 ARG 0.003 0.001 ARG P 22 *********************** 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 138 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 91 time to evaluate : 0.782 Fit side-chains REVERT: R 169 ILE cc_start: 0.4816 (OUTLIER) cc_final: 0.4498 (tp) REVERT: R 239 MET cc_start: 0.5873 (mtp) cc_final: 0.5523 (ttm) REVERT: R 333 ARG cc_start: 0.4553 (pmt170) cc_final: 0.3641 (tmt170) REVERT: B 228 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8212 (p0) REVERT: B 338 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6562 (mm) outliers start: 47 outliers final: 37 residues processed: 130 average time/residue: 0.1614 time to fit residues: 29.3346 Evaluate side-chains 126 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 86 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3815 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= 0.203 Angle : 0.591 9.485 9477 Z= 0.296 Chirality : 0.042 0.267 1125 Planarity : 0.004 0.044 1204 Dihedral : 4.273 35.956 978 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.82 % Allowed : 25.97 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 907 helix: 1.85 (0.26), residues: 377 sheet: -0.37 (0.40), residues: 162 loop : -1.43 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.020 0.001 PHE R 316 TYR 0.013 0.001 TYR R 120 ARG 0.004 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 139 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 0.767 Fit side-chains REVERT: R 333 ARG cc_start: 0.4480 (pmt170) cc_final: 0.3616 (tmt170) REVERT: A 197 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8072 (ptmt) REVERT: B 82 TRP cc_start: 0.7804 (m100) cc_final: 0.7304 (m100) REVERT: B 228 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8164 (p0) REVERT: B 338 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6299 (mm) outliers start: 39 outliers final: 28 residues processed: 129 average time/residue: 0.1684 time to fit residues: 29.7983 Evaluate side-chains 122 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 53 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6943 Z= 0.262 Angle : 0.634 9.268 9477 Z= 0.322 Chirality : 0.043 0.267 1125 Planarity : 0.004 0.035 1204 Dihedral : 4.300 33.955 978 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.37 % Allowed : 27.16 % Favored : 67.46 % 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: 0.18 (0.28), residues: 907 helix: 1.84 (0.26), residues: 376 sheet: -0.61 (0.39), residues: 169 loop : -1.38 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS B 142 PHE 0.032 0.001 PHE R 316 TYR 0.015 0.001 TYR R 120 ARG 0.004 0.000 ARG A 15 *********************** 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 132 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 0.758 Fit side-chains REVERT: R 120 TYR cc_start: 0.4469 (m-10) cc_final: 0.4228 (m-80) REVERT: R 333 ARG cc_start: 0.4528 (pmt170) cc_final: 0.3630 (tmt170) REVERT: A 243 MET cc_start: 0.8575 (tpp) cc_final: 0.8186 (tpp) REVERT: B 82 TRP cc_start: 0.7859 (m100) cc_final: 0.7240 (m100) REVERT: B 228 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8136 (p0) REVERT: B 338 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6384 (mm) outliers start: 36 outliers final: 32 residues processed: 120 average time/residue: 0.1732 time to fit residues: 28.6241 Evaluate side-chains 127 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6943 Z= 0.203 Angle : 0.619 11.295 9477 Z= 0.314 Chirality : 0.042 0.265 1125 Planarity : 0.003 0.033 1204 Dihedral : 4.220 33.849 978 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.52 % Allowed : 27.46 % Favored : 67.01 % 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: 0.27 (0.28), residues: 907 helix: 1.91 (0.26), residues: 376 sheet: -0.54 (0.39), residues: 169 loop : -1.35 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.031 0.001 PHE R 316 TYR 0.013 0.001 TYR R 120 ARG 0.004 0.000 ARG A 15 ********************** 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 132 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 0.760 Fit side-chains REVERT: R 263 ARG cc_start: 0.5120 (tmm160) cc_final: 0.4286 (tmm160) REVERT: R 333 ARG cc_start: 0.4478 (pmt170) cc_final: 0.3626 (tmt170) REVERT: A 9 ASP cc_start: 0.7619 (t70) cc_final: 0.7277 (t0) REVERT: B 82 TRP cc_start: 0.7781 (m100) cc_final: 0.7269 (m100) REVERT: B 228 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8094 (p0) REVERT: B 338 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6327 (mm) outliers start: 37 outliers final: 31 residues processed: 122 average time/residue: 0.1538 time to fit residues: 26.4337 Evaluate side-chains 124 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 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 ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.203143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.159997 restraints weight = 7651.431| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 3.11 r_work: 0.3847 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6943 Z= 0.210 Angle : 0.621 10.784 9477 Z= 0.314 Chirality : 0.042 0.264 1125 Planarity : 0.003 0.033 1204 Dihedral : 4.183 33.201 978 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.52 % Allowed : 27.61 % Favored : 66.87 % 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 (0.28), residues: 907 helix: 1.97 (0.26), residues: 376 sheet: -0.41 (0.40), residues: 159 loop : -1.35 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.003 0.001 HIS R 285 PHE 0.030 0.001 PHE R 316 TYR 0.015 0.001 TYR R 120 ARG 0.004 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.47 seconds wall clock time: 34 minutes 20.40 seconds (2060.40 seconds total)