Starting phenix.real_space_refine on Sat Apr 6 00:48:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unu_42417/04_2024/8unu_42417_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unu_42417/04_2024/8unu_42417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unu_42417/04_2024/8unu_42417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unu_42417/04_2024/8unu_42417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unu_42417/04_2024/8unu_42417_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unu_42417/04_2024/8unu_42417_updated.pdb" } resolution = 3.5 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= 0.023 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 39 5.16 5 C 4192 2.51 5 N 1117 2.21 5 O 1163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6514 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1697 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1685 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 124 Conformer: "B" Number of residues, atoms: 225, 1685 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 124 bond proxies already assigned to first conformer: 1702 Chain: "B" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2401 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 132 Chain: "G" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 325 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2044 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 7, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 4.72, per 1000 atoms: 0.72 Number of scatterers: 6514 At special positions: 0 Unit cell: (83.2992, 133.626, 98.9178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 3 15.00 O 1163 8.00 N 1117 7.00 C 4192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 2.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 8 sheets defined 43.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.975A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.606A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.576A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.550A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.655A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.535A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 36 through 60 removed outlier: 3.548A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.472A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.974A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 163 removed outlier: 3.847A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.734A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 237 removed outlier: 4.094A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.879A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.389A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 4.151A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.020A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.784A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.872A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.823A 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 151 removed outlier: 7.155A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.945A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.957A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.785A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.625A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1172 1.33 - 1.45: 1782 1.45 - 1.57: 3642 1.57 - 1.70: 6 1.70 - 1.82: 52 Bond restraints: 6654 Sorted by residual: bond pdb=" N VAL A 57 " pdb=" CA VAL A 57 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.20e-02 6.94e+03 1.28e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.37e+00 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.59e+00 bond pdb=" N ILE A 372 " pdb=" CA ILE A 372 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.19e+00 bond pdb=" N ILE R 58 " pdb=" CA ILE R 58 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00 ... (remaining 6649 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.91: 144 106.91 - 113.69: 3738 113.69 - 120.47: 2579 120.47 - 127.25: 2570 127.25 - 134.04: 73 Bond angle restraints: 9104 Sorted by residual: angle pdb=" N GLN A 59 " pdb=" CA GLN A 59 " pdb=" C GLN A 59 " ideal model delta sigma weight residual 111.28 104.89 6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" N PRO G 60 " pdb=" CA PRO G 60 " pdb=" C PRO G 60 " ideal model delta sigma weight residual 113.53 105.84 7.69 1.39e+00 5.18e-01 3.06e+01 angle pdb=" N LYS A 233 " pdb=" CA LYS A 233 " pdb=" C LYS A 233 " ideal model delta sigma weight residual 113.72 106.74 6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" CA PHE A 212 " pdb=" CB PHE A 212 " pdb=" CG PHE A 212 " ideal model delta sigma weight residual 113.80 118.67 -4.87 1.00e+00 1.00e+00 2.38e+01 angle pdb=" N THR A 350 " pdb=" CA THR A 350 " pdb=" C THR A 350 " ideal model delta sigma weight residual 111.40 117.32 -5.92 1.22e+00 6.72e-01 2.35e+01 ... (remaining 9099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 3767 34.96 - 69.92: 59 69.92 - 104.88: 7 104.88 - 139.83: 0 139.83 - 174.79: 2 Dihedral angle restraints: 3835 sinusoidal: 1235 harmonic: 2600 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 172.56 -79.56 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -162.99 76.99 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -105.52 174.79 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 3832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 913 0.068 - 0.135: 152 0.135 - 0.203: 28 0.203 - 0.271: 1 0.271 - 0.339: 1 Chirality restraints: 1095 Sorted by residual: chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE R 233 " pdb=" N ILE R 233 " pdb=" C ILE R 233 " pdb=" CB ILE R 233 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 1092 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.56e+00 pdb=" C ASP A 223 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP A 223 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 224 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 368 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ASP A 368 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 368 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 320 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C THR A 320 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A 320 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 321 " -0.011 2.00e-02 2.50e+03 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 998 2.76 - 3.30: 6102 3.30 - 3.83: 10158 3.83 - 4.37: 11142 4.37 - 4.90: 20459 Nonbonded interactions: 48859 Sorted by model distance: nonbonded pdb=" CD LYS A 233 " pdb=" CE MET B 188 " model vdw 2.227 3.860 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.243 2.440 nonbonded pdb=" OE2 GLU A 209 " pdb=" CE1 PHE A 222 " model vdw 2.256 3.340 nonbonded pdb=" OD2 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.332 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.333 2.440 ... (remaining 48854 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 7.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 23.340 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6654 Z= 0.364 Angle : 0.832 10.201 9104 Z= 0.553 Chirality : 0.053 0.339 1095 Planarity : 0.004 0.078 1135 Dihedral : 14.141 174.793 2137 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.50 % Allowed : 1.85 % Favored : 97.65 % 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: 1.67 (0.30), residues: 869 helix: 2.61 (0.28), residues: 382 sheet: 0.94 (0.43), residues: 166 loop : -0.70 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 173 HIS 0.004 0.001 HIS B 183 PHE 0.021 0.001 PHE A 212 TYR 0.008 0.001 TYR A 318 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.744 Fit side-chains REVERT: A 53 LYS cc_start: 0.8067 (ptpt) cc_final: 0.7698 (ptpt) REVERT: A 211 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7314 (mmtt) outliers start: 3 outliers final: 2 residues processed: 109 average time/residue: 0.1570 time to fit residues: 23.6216 Evaluate side-chains 80 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 GLN R 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6654 Z= 0.213 Angle : 0.489 6.469 9104 Z= 0.263 Chirality : 0.041 0.142 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.557 171.536 974 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.51 % Allowed : 8.72 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.29), residues: 869 helix: 2.78 (0.27), residues: 386 sheet: 0.66 (0.42), residues: 165 loop : -0.72 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.001 PHE B 241 TYR 0.014 0.001 TYR B 289 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8203 (ptpt) cc_final: 0.7790 (ptpt) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.1422 time to fit residues: 18.3126 Evaluate side-chains 81 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 0.0370 chunk 63 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6654 Z= 0.147 Angle : 0.430 6.440 9104 Z= 0.231 Chirality : 0.039 0.138 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.435 173.568 972 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.17 % Allowed : 10.74 % Favored : 88.09 % 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: 1.79 (0.29), residues: 869 helix: 2.86 (0.27), residues: 382 sheet: 0.56 (0.40), residues: 176 loop : -0.61 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.009 0.001 PHE B 241 TYR 0.007 0.001 TYR R 308 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 390 GLN cc_start: 0.8122 (tp40) cc_final: 0.7781 (tp-100) REVERT: B 291 ASP cc_start: 0.8465 (t70) cc_final: 0.8086 (t0) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.1746 time to fit residues: 21.4649 Evaluate side-chains 78 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 75 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6654 Z= 0.126 Angle : 0.421 6.514 9104 Z= 0.223 Chirality : 0.039 0.135 1095 Planarity : 0.003 0.038 1135 Dihedral : 8.389 175.536 971 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.34 % Allowed : 12.58 % Favored : 86.07 % 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: 1.85 (0.29), residues: 869 helix: 2.88 (0.27), residues: 383 sheet: 0.64 (0.41), residues: 170 loop : -0.54 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.732 Fit side-chains REVERT: B 291 ASP cc_start: 0.8572 (t70) cc_final: 0.8207 (t0) REVERT: R 82 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6655 (ttm) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.1474 time to fit residues: 19.1790 Evaluate side-chains 84 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6654 Z= 0.162 Angle : 0.441 6.569 9104 Z= 0.234 Chirality : 0.039 0.140 1095 Planarity : 0.003 0.038 1135 Dihedral : 8.402 175.372 971 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.51 % Allowed : 13.93 % Favored : 84.56 % 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: 1.73 (0.29), residues: 869 helix: 2.71 (0.27), residues: 389 sheet: 0.58 (0.40), residues: 175 loop : -0.60 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.749 Fit side-chains REVERT: B 291 ASP cc_start: 0.8601 (t70) cc_final: 0.8164 (t0) REVERT: R 82 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6664 (ttm) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.1411 time to fit residues: 18.6742 Evaluate side-chains 86 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.0270 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6654 Z= 0.174 Angle : 0.449 6.698 9104 Z= 0.237 Chirality : 0.040 0.137 1095 Planarity : 0.003 0.039 1135 Dihedral : 8.522 179.904 971 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.18 % Allowed : 14.77 % Favored : 83.05 % 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: 1.65 (0.29), residues: 869 helix: 2.66 (0.27), residues: 389 sheet: 0.39 (0.38), residues: 182 loop : -0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.007 0.001 TYR R 308 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.749 Fit side-chains REVERT: B 291 ASP cc_start: 0.8603 (t70) cc_final: 0.8210 (t0) REVERT: R 82 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6707 (ttm) outliers start: 13 outliers final: 11 residues processed: 90 average time/residue: 0.1433 time to fit residues: 18.7153 Evaluate side-chains 90 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6654 Z= 0.163 Angle : 0.440 6.703 9104 Z= 0.233 Chirality : 0.039 0.138 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.479 178.880 971 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.35 % Allowed : 15.10 % Favored : 82.55 % 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: 1.60 (0.29), residues: 869 helix: 2.66 (0.27), residues: 389 sheet: 0.32 (0.39), residues: 176 loop : -0.62 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: B 291 ASP cc_start: 0.8514 (t70) cc_final: 0.8144 (t0) REVERT: R 82 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6726 (ttm) outliers start: 14 outliers final: 11 residues processed: 95 average time/residue: 0.1499 time to fit residues: 20.4677 Evaluate side-chains 91 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6654 Z= 0.183 Angle : 0.460 9.642 9104 Z= 0.240 Chirality : 0.040 0.137 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.448 176.735 971 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.52 % Allowed : 15.27 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 869 helix: 2.66 (0.27), residues: 388 sheet: 0.26 (0.39), residues: 170 loop : -0.65 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: B 291 ASP cc_start: 0.8513 (t70) cc_final: 0.8149 (t0) REVERT: R 82 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6732 (ttm) outliers start: 15 outliers final: 13 residues processed: 92 average time/residue: 0.1496 time to fit residues: 20.0817 Evaluate side-chains 92 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6654 Z= 0.187 Angle : 0.464 6.852 9104 Z= 0.242 Chirality : 0.040 0.143 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.438 174.897 971 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.52 % Allowed : 15.27 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 869 helix: 2.66 (0.27), residues: 388 sheet: 0.19 (0.39), residues: 170 loop : -0.66 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.020 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: B 291 ASP cc_start: 0.8504 (t70) cc_final: 0.8139 (t0) REVERT: R 82 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6770 (ttm) outliers start: 15 outliers final: 14 residues processed: 93 average time/residue: 0.1579 time to fit residues: 20.9228 Evaluate side-chains 95 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.0010 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6654 Z= 0.136 Angle : 0.449 7.120 9104 Z= 0.233 Chirality : 0.039 0.136 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.365 174.005 971 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.01 % Allowed : 16.44 % Favored : 81.54 % 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: 1.57 (0.30), residues: 869 helix: 2.65 (0.27), residues: 388 sheet: 0.20 (0.38), residues: 176 loop : -0.58 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.006 0.001 HIS R 296 PHE 0.010 0.001 PHE B 241 TYR 0.020 0.001 TYR R 308 ARG 0.002 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: B 291 ASP cc_start: 0.8472 (t70) cc_final: 0.8181 (t0) REVERT: R 82 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6747 (ttm) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.1458 time to fit residues: 19.3825 Evaluate side-chains 95 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.127856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101217 restraints weight = 39461.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105980 restraints weight = 13609.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109514 restraints weight = 6373.710| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6654 Z= 0.165 Angle : 0.452 6.820 9104 Z= 0.235 Chirality : 0.039 0.137 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.353 173.118 971 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 15.94 % Favored : 81.71 % 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: 1.51 (0.29), residues: 869 helix: 2.54 (0.27), residues: 394 sheet: 0.18 (0.38), residues: 176 loop : -0.58 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 169 HIS 0.007 0.001 HIS R 296 PHE 0.011 0.001 PHE B 241 TYR 0.022 0.001 TYR R 308 ARG 0.002 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.70 seconds wall clock time: 29 minutes 43.95 seconds (1783.95 seconds total)