Starting phenix.real_space_refine on Wed Feb 12 01:37:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gdc_29946/02_2025/8gdc_29946_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gdc_29946/02_2025/8gdc_29946.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/cci-nas-00/data/ceres_data/8gdc_29946/02_2025/8gdc_29946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gdc_29946/02_2025/8gdc_29946.map" model { file = "/net/cci-nas-00/data/ceres_data/8gdc_29946/02_2025/8gdc_29946_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gdc_29946/02_2025/8gdc_29946_neut.cif" } 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1646 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 3631 2.51 5 N 966 2.21 5 O 1020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1457 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 2, 'TRANS': 204} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2174 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 304} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 14, 'ASN:plan1': 5, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 213 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 258, 1781 Classifications: {'peptide': 258} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 65} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Conformer: "B" Number of residues, atoms: 258, 1781 Classifications: {'peptide': 258} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 65} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 bond proxies already assigned to first conformer: 1808 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.01, per 1000 atoms: 1.06 Number of scatterers: 5657 At special positions: 0 Unit cell: (84.15, 93.5, 108.8, 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 40 16.00 O 1020 8.00 N 966 7.00 C 3631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 130 " - pdb=" SG CYS R 208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.80 Conformation dependent library (CDL) restraints added in 1.8 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 41.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.702A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.420A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 216 removed outlier: 4.026A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 341 through 351 removed outlier: 3.651A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 4.128A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'R' and resid 53 through 76 removed outlier: 4.227A pdb=" N LEU R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG R 75 " --> pdb=" O LEU R 71 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 105 removed outlier: 4.101A pdb=" N LEU R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR R 98 " --> pdb=" O TRP R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 117 removed outlier: 4.054A pdb=" N VAL R 110 " --> pdb=" O THR R 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU R 115 " --> pdb=" O ILE R 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS R 117 " --> pdb=" O VAL R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 Processing helix chain 'R' and resid 128 through 161 removed outlier: 3.599A pdb=" N LEU R 135 " --> pdb=" O THR R 131 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR R 138 " --> pdb=" O GLY R 134 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER R 144 " --> pdb=" O PHE R 140 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU R 145 " --> pdb=" O GLY R 141 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA R 150 " --> pdb=" O PHE R 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE R 159 " --> pdb=" O ARG R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 169 removed outlier: 3.525A pdb=" N SER R 167 " --> pdb=" O HIS R 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS R 168 " --> pdb=" O TRP R 164 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET R 169 " --> pdb=" O TYR R 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 163 through 169' Processing helix chain 'R' and resid 180 through 190 removed outlier: 4.378A pdb=" N PHE R 188 " --> pdb=" O ALA R 184 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 262 removed outlier: 4.136A pdb=" N ALA R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 242 " --> pdb=" O GLY R 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 284 removed outlier: 3.949A pdb=" N ILE R 276 " --> pdb=" O GLN R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 294 removed outlier: 4.057A pdb=" N SER R 292 " --> pdb=" O MET R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 307 removed outlier: 3.586A pdb=" N MET R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS R 304 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 348 removed outlier: 3.530A pdb=" N ILE R 330 " --> pdb=" O ASN R 326 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 332 " --> pdb=" O PHE R 328 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN R 338 " --> pdb=" O LEU R 334 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 3.796A pdb=" N TYR R 346 " --> pdb=" O ASP R 342 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU R 347 " --> pdb=" O PRO R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 3.605A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.600A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.550A pdb=" N LEU A 266 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 52 removed outlier: 4.341A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.700A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.999A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 202 removed outlier: 3.648A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.994A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AB2, first strand: chain 'R' and resid 199 through 201 239 hydrogen bonds defined for protein. 699 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: 2.29 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 919 1.28 - 1.42: 1528 1.42 - 1.55: 3253 1.55 - 1.68: 13 1.68 - 1.82: 54 Bond restraints: 5767 Sorted by residual: bond pdb=" CA ILE R 159 " pdb=" CB ILE R 159 " ideal model delta sigma weight residual 1.540 1.435 0.104 1.29e-02 6.01e+03 6.54e+01 bond pdb=" C PRO R 162 " pdb=" O PRO R 162 " ideal model delta sigma weight residual 1.237 1.152 0.086 1.29e-02 6.01e+03 4.41e+01 bond pdb=" C VAL R 112 " pdb=" O VAL R 112 " ideal model delta sigma weight residual 1.237 1.162 0.074 1.12e-02 7.97e+03 4.41e+01 bond pdb=" C LEU R 347 " pdb=" O LEU R 347 " ideal model delta sigma weight residual 1.236 1.180 0.056 8.80e-03 1.29e+04 4.00e+01 bond pdb=" CA ALA R 150 " pdb=" C ALA R 150 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.29e-02 6.01e+03 3.99e+01 ... (remaining 5762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 7360 2.65 - 5.29: 405 5.29 - 7.94: 81 7.94 - 10.58: 28 10.58 - 13.23: 7 Bond angle restraints: 7881 Sorted by residual: angle pdb=" C ALA R 161 " pdb=" N PRO R 162 " pdb=" CA PRO R 162 " ideal model delta sigma weight residual 119.32 130.23 -10.91 1.14e+00 7.69e-01 9.15e+01 angle pdb=" N ILE R 147 " pdb=" CA ILE R 147 " pdb=" C ILE R 147 " ideal model delta sigma weight residual 112.96 103.95 9.01 1.00e+00 1.00e+00 8.12e+01 angle pdb=" N SER R 116 " pdb=" CA SER R 116 " pdb=" C SER R 116 " ideal model delta sigma weight residual 111.28 121.04 -9.76 1.09e+00 8.42e-01 8.01e+01 angle pdb=" N HIS R 168 " pdb=" CA HIS R 168 " pdb=" C HIS R 168 " ideal model delta sigma weight residual 112.92 123.81 -10.89 1.23e+00 6.61e-01 7.84e+01 angle pdb=" N ALA R 187 " pdb=" CA ALA R 187 " pdb=" C ALA R 187 " ideal model delta sigma weight residual 112.97 103.65 9.32 1.06e+00 8.90e-01 7.74e+01 ... (remaining 7876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 3028 16.68 - 33.37: 239 33.37 - 50.05: 49 50.05 - 66.74: 5 66.74 - 83.42: 3 Dihedral angle restraints: 3324 sinusoidal: 994 harmonic: 2330 Sorted by residual: dihedral pdb=" C TYR R 114 " pdb=" N TYR R 114 " pdb=" CA TYR R 114 " pdb=" CB TYR R 114 " ideal model delta harmonic sigma weight residual -122.60 -162.91 40.31 0 2.50e+00 1.60e-01 2.60e+02 dihedral pdb=" N TYR R 114 " pdb=" C TYR R 114 " pdb=" CA TYR R 114 " pdb=" CB TYR R 114 " ideal model delta harmonic sigma weight residual 122.80 163.01 -40.21 0 2.50e+00 1.60e-01 2.59e+02 dihedral pdb=" C TYR R 165 " pdb=" N TYR R 165 " pdb=" CA TYR R 165 " pdb=" CB TYR R 165 " ideal model delta harmonic sigma weight residual -122.60 -144.10 21.50 0 2.50e+00 1.60e-01 7.39e+01 ... (remaining 3321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.360: 942 0.360 - 0.719: 12 0.719 - 1.079: 2 1.079 - 1.438: 0 1.438 - 1.798: 1 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA TYR R 114 " pdb=" N TYR R 114 " pdb=" C TYR R 114 " pdb=" CB TYR R 114 " both_signs ideal model delta sigma weight residual False 2.51 0.71 1.80 2.00e-01 2.50e+01 8.08e+01 chirality pdb=" CA ASN R 249 " pdb=" N ASN R 249 " pdb=" C ASN R 249 " pdb=" CB ASN R 249 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA TYR R 165 " pdb=" N TYR R 165 " pdb=" C TYR R 165 " pdb=" CB TYR R 165 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 954 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.085 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C5 P2E R 401 " 0.251 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " -0.274 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " 0.168 2.00e-02 2.50e+03 1.76e-01 3.11e+02 pdb=" C13 P2E R 401 " -0.149 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " -0.202 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 238 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C GLY R 238 " 0.085 2.00e-02 2.50e+03 pdb=" O GLY R 238 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU R 239 " -0.029 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1707 2.81 - 3.33: 4952 3.33 - 3.86: 8581 3.86 - 4.38: 9420 4.38 - 4.90: 16948 Nonbonded interactions: 41608 Sorted by model distance: nonbonded pdb=" OG SER B 122 " pdb=" OE1 GLU B 138 " model vdw 2.289 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.319 3.040 nonbonded pdb=" O ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.325 3.040 nonbonded pdb=" N LEU R 284 " pdb=" N MET R 285 " model vdw 2.373 2.560 ... (remaining 41603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.290 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.012 0.104 5767 Z= 0.765 Angle : 1.459 13.227 7881 Z= 0.943 Chirality : 0.122 1.798 957 Planarity : 0.012 0.198 999 Dihedral : 13.132 83.419 1807 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.62 % Allowed : 4.34 % Favored : 95.04 % Cbeta Deviations : 1.32 % 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: -3.62 (0.27), residues: 787 helix: -1.68 (0.27), residues: 300 sheet: -2.44 (0.39), residues: 161 loop : -2.97 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 164 HIS 0.011 0.003 HIS R 168 PHE 0.027 0.003 PHE B 234 TYR 0.040 0.004 TYR R 114 ARG 0.006 0.001 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.692 Fit side-chains REVERT: B 246 ASP cc_start: 0.8607 (t0) cc_final: 0.8346 (t70) REVERT: B 300 LEU cc_start: 0.7936 (tp) cc_final: 0.7720 (tt) outliers start: 3 outliers final: 3 residues processed: 89 average time/residue: 0.1975 time to fit residues: 23.1244 Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 GLN Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 155 ASN R 103 GLN R 163 HIS A R 168 HIS ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.171324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145643 restraints weight = 13989.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151829 restraints weight = 6700.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154721 restraints weight = 3882.444| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5767 Z= 0.214 Angle : 0.641 9.637 7881 Z= 0.332 Chirality : 0.044 0.250 957 Planarity : 0.004 0.046 999 Dihedral : 6.457 44.005 876 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.65 % Allowed : 10.33 % Favored : 88.02 % 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: -2.27 (0.29), residues: 787 helix: -0.03 (0.29), residues: 323 sheet: -1.92 (0.41), residues: 149 loop : -2.87 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 207 HIS 0.005 0.001 HIS B 225 PHE 0.014 0.002 PHE B 234 TYR 0.023 0.002 TYR B 105 ARG 0.001 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.561 Fit side-chains REVERT: A 196 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6522 (p90) REVERT: A 337 ASP cc_start: 0.7633 (t70) cc_final: 0.7351 (m-30) REVERT: B 95 LEU cc_start: 0.6630 (mt) cc_final: 0.6225 (mt) REVERT: B 103 CYS cc_start: 0.6813 (p) cc_final: 0.6510 (m) REVERT: B 246 ASP cc_start: 0.8384 (t0) cc_final: 0.8167 (t0) REVERT: B 300 LEU cc_start: 0.7749 (tp) cc_final: 0.7490 (tt) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.1660 time to fit residues: 18.6237 Evaluate side-chains 78 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.173375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150971 restraints weight = 7065.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.155200 restraints weight = 4184.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.158117 restraints weight = 2859.866| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5767 Z= 0.139 Angle : 0.533 9.430 7881 Z= 0.276 Chirality : 0.041 0.184 957 Planarity : 0.003 0.042 999 Dihedral : 5.157 39.044 869 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.03 % Allowed : 13.22 % Favored : 85.74 % 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: -1.62 (0.30), residues: 787 helix: 0.64 (0.31), residues: 322 sheet: -1.63 (0.42), residues: 150 loop : -2.64 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.002 0.001 HIS B 225 PHE 0.010 0.001 PHE B 278 TYR 0.011 0.001 TYR B 105 ARG 0.002 0.000 ARG R 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.566 Fit side-chains REVERT: A 34 VAL cc_start: 0.8120 (t) cc_final: 0.7854 (m) REVERT: B 95 LEU cc_start: 0.6602 (mt) cc_final: 0.6170 (mt) REVERT: B 103 CYS cc_start: 0.6705 (p) cc_final: 0.6499 (m) REVERT: B 188 MET cc_start: 0.6704 (tpp) cc_final: 0.5928 (mmt) outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 0.1468 time to fit residues: 15.1140 Evaluate side-chains 75 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 3.9990 chunk 15 optimal weight: 0.0060 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.175133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.154130 restraints weight = 9172.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.157126 restraints weight = 5816.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160694 restraints weight = 3851.811| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5767 Z= 0.138 Angle : 0.508 8.632 7881 Z= 0.263 Chirality : 0.041 0.142 957 Planarity : 0.003 0.039 999 Dihedral : 4.896 37.028 869 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.48 % Allowed : 14.26 % Favored : 83.26 % 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: -1.14 (0.31), residues: 787 helix: 1.02 (0.31), residues: 325 sheet: -1.39 (0.41), residues: 154 loop : -2.38 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS B 225 PHE 0.009 0.001 PHE B 278 TYR 0.011 0.001 TYR B 105 ARG 0.001 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.629 Fit side-chains REVERT: B 155 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.6328 (t0) REVERT: B 188 MET cc_start: 0.6564 (tpp) cc_final: 0.5961 (mmt) REVERT: R 295 TRP cc_start: 0.7912 (m100) cc_final: 0.7619 (m100) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.1316 time to fit residues: 14.2227 Evaluate side-chains 75 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN R 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145401 restraints weight = 11137.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150552 restraints weight = 6567.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155553 restraints weight = 3719.554| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5767 Z= 0.293 Angle : 0.597 8.250 7881 Z= 0.312 Chirality : 0.044 0.158 957 Planarity : 0.003 0.039 999 Dihedral : 5.450 39.628 869 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.10 % Allowed : 15.50 % Favored : 81.40 % 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: -1.26 (0.30), residues: 787 helix: 0.66 (0.30), residues: 336 sheet: -1.26 (0.43), residues: 152 loop : -2.33 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 273 HIS 0.004 0.001 HIS B 225 PHE 0.020 0.002 PHE B 199 TYR 0.013 0.002 TYR B 105 ARG 0.002 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.567 Fit side-chains REVERT: A 196 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6946 (p90) REVERT: B 188 MET cc_start: 0.6773 (tpp) cc_final: 0.6063 (mmt) REVERT: R 295 TRP cc_start: 0.8008 (m100) cc_final: 0.7660 (m100) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.1484 time to fit residues: 19.0558 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.171328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144951 restraints weight = 15258.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.151391 restraints weight = 7135.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.154256 restraints weight = 3952.854| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5767 Z= 0.154 Angle : 0.531 9.166 7881 Z= 0.268 Chirality : 0.041 0.143 957 Planarity : 0.003 0.039 999 Dihedral : 4.892 38.339 869 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 17.77 % Favored : 79.75 % 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: -0.94 (0.31), residues: 787 helix: 1.19 (0.31), residues: 326 sheet: -1.37 (0.41), residues: 161 loop : -2.25 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 273 HIS 0.002 0.001 HIS A 213 PHE 0.010 0.001 PHE B 278 TYR 0.010 0.001 TYR B 105 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.582 Fit side-chains REVERT: A 20 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6512 (t0) REVERT: A 196 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7386 (p90) REVERT: A 337 ASP cc_start: 0.7463 (m-30) cc_final: 0.7179 (m-30) REVERT: B 61 MET cc_start: 0.5846 (ppp) cc_final: 0.5587 (ppp) REVERT: B 188 MET cc_start: 0.6734 (tpp) cc_final: 0.6384 (mmm) REVERT: R 295 TRP cc_start: 0.7907 (m100) cc_final: 0.7591 (m100) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.1257 time to fit residues: 14.9499 Evaluate side-chains 82 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.172500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.146242 restraints weight = 15058.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153306 restraints weight = 7058.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.154397 restraints weight = 3720.347| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5767 Z= 0.137 Angle : 0.513 8.291 7881 Z= 0.258 Chirality : 0.041 0.133 957 Planarity : 0.003 0.038 999 Dihedral : 4.653 35.813 869 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.27 % Allowed : 19.01 % Favored : 78.72 % 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: -0.75 (0.31), residues: 787 helix: 1.40 (0.31), residues: 326 sheet: -1.27 (0.41), residues: 161 loop : -2.22 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 273 HIS 0.002 0.001 HIS A 213 PHE 0.009 0.001 PHE A 189 TYR 0.008 0.001 TYR B 105 ARG 0.001 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.602 Fit side-chains REVERT: A 20 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6561 (t70) REVERT: A 196 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7319 (p90) REVERT: A 337 ASP cc_start: 0.7446 (m-30) cc_final: 0.7214 (m-30) REVERT: B 188 MET cc_start: 0.6703 (tpp) cc_final: 0.6363 (mmm) REVERT: R 295 TRP cc_start: 0.7895 (m100) cc_final: 0.7623 (m100) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.1216 time to fit residues: 13.6837 Evaluate side-chains 78 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.172453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147421 restraints weight = 9437.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152333 restraints weight = 5153.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.155882 restraints weight = 3324.137| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5767 Z= 0.145 Angle : 0.521 7.846 7881 Z= 0.260 Chirality : 0.041 0.136 957 Planarity : 0.003 0.039 999 Dihedral : 4.547 34.080 869 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.69 % Allowed : 19.21 % Favored : 78.10 % 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: -0.64 (0.31), residues: 787 helix: 1.53 (0.31), residues: 325 sheet: -1.22 (0.41), residues: 160 loop : -2.19 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 273 HIS 0.002 0.001 HIS A 213 PHE 0.011 0.001 PHE B 278 TYR 0.009 0.001 TYR B 105 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.549 Fit side-chains REVERT: A 20 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6576 (t70) REVERT: A 53 MET cc_start: 0.6074 (ptp) cc_final: 0.5335 (ptp) REVERT: A 196 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7398 (p90) REVERT: A 337 ASP cc_start: 0.7342 (m-30) cc_final: 0.7123 (m-30) REVERT: B 188 MET cc_start: 0.6391 (tpp) cc_final: 0.5908 (mmt) REVERT: R 295 TRP cc_start: 0.7894 (m100) cc_final: 0.7542 (m100) outliers start: 13 outliers final: 8 residues processed: 86 average time/residue: 0.1498 time to fit residues: 17.7631 Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.173142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147543 restraints weight = 13887.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.151849 restraints weight = 7104.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.156302 restraints weight = 4189.873| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5767 Z= 0.141 Angle : 0.507 7.584 7881 Z= 0.257 Chirality : 0.041 0.132 957 Planarity : 0.003 0.037 999 Dihedral : 4.461 32.562 869 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 20.04 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.31), residues: 787 helix: 1.74 (0.31), residues: 322 sheet: -1.10 (0.41), residues: 160 loop : -2.18 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 273 HIS 0.002 0.001 HIS A 213 PHE 0.012 0.001 PHE B 234 TYR 0.009 0.001 TYR B 105 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.627 Fit side-chains REVERT: A 20 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6536 (t70) REVERT: A 196 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7288 (p90) REVERT: A 337 ASP cc_start: 0.7402 (m-30) cc_final: 0.7183 (m-30) REVERT: B 188 MET cc_start: 0.6077 (tpp) cc_final: 0.5705 (mmm) REVERT: R 295 TRP cc_start: 0.7893 (m100) cc_final: 0.7516 (m100) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 0.1591 time to fit residues: 17.8752 Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.172233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.150760 restraints weight = 7123.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.154473 restraints weight = 4386.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157043 restraints weight = 3086.047| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5767 Z= 0.178 Angle : 0.535 7.605 7881 Z= 0.271 Chirality : 0.041 0.144 957 Planarity : 0.003 0.037 999 Dihedral : 4.519 32.812 869 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.27 % Allowed : 20.45 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.31), residues: 787 helix: 1.66 (0.31), residues: 326 sheet: -0.83 (0.42), residues: 153 loop : -2.21 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR B 105 ARG 0.002 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.516 Fit side-chains REVERT: A 20 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6562 (t70) REVERT: A 196 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.6841 (p90) REVERT: A 337 ASP cc_start: 0.7256 (m-30) cc_final: 0.7033 (m-30) REVERT: B 188 MET cc_start: 0.6088 (tpp) cc_final: 0.5720 (mmm) REVERT: R 295 TRP cc_start: 0.7902 (m100) cc_final: 0.7571 (m100) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1357 time to fit residues: 16.0185 Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.173502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147366 restraints weight = 14003.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153717 restraints weight = 6703.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156794 restraints weight = 3839.944| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5767 Z= 0.127 Angle : 0.500 7.707 7881 Z= 0.254 Chirality : 0.040 0.131 957 Planarity : 0.003 0.035 999 Dihedral : 4.371 32.391 869 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.27 % Allowed : 20.25 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.31), residues: 787 helix: 1.92 (0.31), residues: 322 sheet: -1.05 (0.41), residues: 163 loop : -2.07 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.002 0.001 HIS A 213 PHE 0.009 0.001 PHE A 189 TYR 0.008 0.001 TYR B 105 ARG 0.002 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2045.65 seconds wall clock time: 37 minutes 22.63 seconds (2242.63 seconds total)