Starting phenix.real_space_refine on Sat Aug 3 01:55:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/08_2024/8uny_42421.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/08_2024/8uny_42421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/08_2024/8uny_42421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/08_2024/8uny_42421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/08_2024/8uny_42421.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/08_2024/8uny_42421.cif" } resolution = 3.6 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= 0.018 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 36 5.16 5 C 4217 2.51 5 N 1131 2.21 5 O 1159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 219": "NH1" <-> "NH2" Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6546 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 211 Conformer: "B" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 211 bond proxies already assigned to first conformer: 1693 Chain: "B" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2386 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 5, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 149 Chain: "G" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 316 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2110 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} 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: 5.18, per 1000 atoms: 0.79 Number of scatterers: 6546 At special positions: 0 Unit cell: (85.0346, 137.097, 99.7855, 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 36 16.00 P 3 15.00 O 1159 8.00 N 1131 7.00 C 4217 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=2.04 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: 2.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.6% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.564A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.580A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.055A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.870A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.901A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.663A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.780A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 13 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.527A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 86 removed outlier: 3.847A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.057A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.948A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.617A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.980A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 4.038A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.541A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.611A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 4.022A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.581A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.236A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.169A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.100A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.995A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 3.548A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1019 1.32 - 1.44: 1908 1.44 - 1.57: 3709 1.57 - 1.69: 6 1.69 - 1.82: 47 Bond restraints: 6689 Sorted by residual: bond pdb=" C SER R 74 " pdb=" N LEU R 75 " ideal model delta sigma weight residual 1.335 1.398 -0.063 1.30e-02 5.92e+03 2.35e+01 bond pdb=" C LYS A 17 " pdb=" O LYS A 17 " ideal model delta sigma weight residual 1.237 1.291 -0.054 1.17e-02 7.31e+03 2.17e+01 bond pdb=" C GLU A 21 " pdb=" O GLU A 21 " ideal model delta sigma weight residual 1.237 1.289 -0.053 1.17e-02 7.31e+03 2.01e+01 bond pdb=" C PRO R 168 " pdb=" O PRO R 168 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.20e-02 6.94e+03 1.50e+01 bond pdb=" N ILE R 43 " pdb=" CA ILE R 43 " ideal model delta sigma weight residual 1.458 1.504 -0.047 1.41e-02 5.03e+03 1.09e+01 ... (remaining 6684 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.86: 161 106.86 - 113.70: 3766 113.70 - 120.53: 2719 120.53 - 127.37: 2449 127.37 - 134.21: 78 Bond angle restraints: 9173 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 103.32 7.96 1.09e+00 8.42e-01 5.34e+01 angle pdb=" C LYS A 24 " pdb=" N LYS A 25 " pdb=" CA LYS A 25 " ideal model delta sigma weight residual 120.44 111.59 8.85 1.36e+00 5.41e-01 4.24e+01 angle pdb=" N SER R 165 " pdb=" CA SER R 165 " pdb=" C SER R 165 " ideal model delta sigma weight residual 111.14 118.08 -6.94 1.08e+00 8.57e-01 4.13e+01 angle pdb=" C TYR A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta sigma weight residual 121.14 111.68 9.46 1.75e+00 3.27e-01 2.92e+01 angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 105.49 5.79 1.09e+00 8.42e-01 2.82e+01 ... (remaining 9168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 3760 31.95 - 63.89: 76 63.89 - 95.84: 5 95.84 - 127.79: 3 127.79 - 159.73: 3 Dihedral angle restraints: 3847 sinusoidal: 1182 harmonic: 2665 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 93.00 168.43 -75.43 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 101.14 159.73 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -44.75 149.34 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 775 0.047 - 0.093: 214 0.093 - 0.140: 84 0.140 - 0.187: 36 0.187 - 0.233: 6 Chirality restraints: 1115 Sorted by residual: chirality pdb=" CA GLN A 12 " pdb=" N GLN A 12 " pdb=" C GLN A 12 " pdb=" CB GLN A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA MET R 171 " pdb=" N MET R 171 " pdb=" C MET R 171 " pdb=" CB MET R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1112 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 215 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C GLU B 215 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU B 215 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 216 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 173 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR B 173 " 0.049 2.00e-02 2.50e+03 pdb=" O THR B 173 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 174 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 11 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C ASP A 11 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP A 11 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN A 12 " -0.016 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1459 2.78 - 3.31: 6203 3.31 - 3.84: 10050 3.84 - 4.37: 10841 4.37 - 4.90: 19726 Nonbonded interactions: 48279 Sorted by model distance: nonbonded pdb=" SG CYS B 271 " pdb=" OD1 ASP B 291 " model vdw 2.255 3.400 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.262 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.331 3.040 nonbonded pdb=" O HIS A 64 " pdb=" C VAL A 65 " model vdw 2.354 3.270 ... (remaining 48274 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=0.49 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: 2.110 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.250 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.006 0.063 6689 Z= 0.405 Angle : 0.966 9.998 9173 Z= 0.668 Chirality : 0.057 0.233 1115 Planarity : 0.006 0.092 1145 Dihedral : 14.644 159.734 2111 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.32 (0.29), residues: 899 helix: 2.35 (0.27), residues: 386 sheet: 0.70 (0.44), residues: 168 loop : -0.76 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 105 HIS 0.009 0.001 HIS R 296 PHE 0.010 0.001 PHE B 234 TYR 0.043 0.001 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.696 Fit side-chains REVERT: A 51 SER cc_start: 0.9275 (p) cc_final: 0.9043 (p) REVERT: A 311 TYR cc_start: 0.9266 (m-80) cc_final: 0.8978 (m-80) REVERT: B 89 LYS cc_start: 0.8742 (mttp) cc_final: 0.8375 (mtmt) REVERT: B 111 TYR cc_start: 0.8649 (m-80) cc_final: 0.8411 (m-80) REVERT: B 254 ASP cc_start: 0.8490 (t70) cc_final: 0.8235 (t0) REVERT: R 232 LYS cc_start: 0.8145 (tppp) cc_final: 0.7942 (ttmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1677 time to fit residues: 23.6514 Evaluate side-chains 70 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 278 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6689 Z= 0.185 Angle : 0.537 6.413 9173 Z= 0.291 Chirality : 0.041 0.149 1115 Planarity : 0.004 0.039 1145 Dihedral : 9.815 152.428 998 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.17 % Allowed : 10.28 % Favored : 89.55 % 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: 1.33 (0.29), residues: 899 helix: 2.25 (0.27), residues: 395 sheet: 0.77 (0.42), residues: 180 loop : -0.79 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.007 0.001 HIS A 220 PHE 0.009 0.001 PHE A 363 TYR 0.032 0.002 TYR R 185 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.727 Fit side-chains REVERT: A 51 SER cc_start: 0.9224 (p) cc_final: 0.8973 (p) REVERT: B 45 MET cc_start: 0.8968 (mtt) cc_final: 0.8765 (mtt) REVERT: B 59 TYR cc_start: 0.8726 (m-10) cc_final: 0.8338 (m-10) REVERT: B 89 LYS cc_start: 0.8792 (mttp) cc_final: 0.8375 (mtpt) REVERT: B 111 TYR cc_start: 0.8672 (m-80) cc_final: 0.7954 (m-80) outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.1607 time to fit residues: 18.8037 Evaluate side-chains 76 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 183 HIS R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6689 Z= 0.233 Angle : 0.526 5.947 9173 Z= 0.286 Chirality : 0.041 0.148 1115 Planarity : 0.003 0.041 1145 Dihedral : 8.313 140.045 998 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.39 % Allowed : 12.02 % Favored : 86.59 % 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: 1.30 (0.29), residues: 899 helix: 2.26 (0.27), residues: 400 sheet: 0.49 (0.41), residues: 180 loop : -0.73 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.045 0.002 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.757 Fit side-chains REVERT: A 51 SER cc_start: 0.9166 (p) cc_final: 0.8915 (p) REVERT: B 89 LYS cc_start: 0.8855 (mttp) cc_final: 0.8333 (mtpt) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.1760 time to fit residues: 20.0621 Evaluate side-chains 79 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6689 Z= 0.184 Angle : 0.490 5.949 9173 Z= 0.264 Chirality : 0.040 0.149 1115 Planarity : 0.003 0.037 1145 Dihedral : 7.529 133.282 998 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.74 % Allowed : 12.89 % Favored : 85.37 % 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: 1.40 (0.30), residues: 899 helix: 2.50 (0.27), residues: 393 sheet: 0.41 (0.41), residues: 180 loop : -0.75 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.007 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.033 0.002 TYR R 185 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.716 Fit side-chains REVERT: A 51 SER cc_start: 0.9131 (p) cc_final: 0.8866 (p) REVERT: A 293 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7927 (mmtp) REVERT: B 89 LYS cc_start: 0.8855 (mttp) cc_final: 0.8320 (mtpt) outliers start: 10 outliers final: 9 residues processed: 91 average time/residue: 0.1590 time to fit residues: 20.1585 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6689 Z= 0.255 Angle : 0.531 5.965 9173 Z= 0.288 Chirality : 0.041 0.140 1115 Planarity : 0.003 0.037 1145 Dihedral : 7.116 128.744 998 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.14 % Allowed : 13.41 % Favored : 83.45 % 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: 1.28 (0.29), residues: 899 helix: 2.56 (0.27), residues: 387 sheet: 0.28 (0.42), residues: 175 loop : -0.91 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.007 0.001 HIS A 362 PHE 0.014 0.001 PHE B 235 TYR 0.029 0.002 TYR R 185 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.736 Fit side-chains REVERT: A 51 SER cc_start: 0.9063 (p) cc_final: 0.8808 (p) REVERT: A 293 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8083 (mmtp) REVERT: B 89 LYS cc_start: 0.8857 (mttp) cc_final: 0.8313 (mtpt) outliers start: 18 outliers final: 14 residues processed: 90 average time/residue: 0.1648 time to fit residues: 20.5227 Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7809 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6689 Z= 0.198 Angle : 0.487 6.049 9173 Z= 0.265 Chirality : 0.040 0.145 1115 Planarity : 0.003 0.033 1145 Dihedral : 6.851 126.242 998 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.61 % Allowed : 14.63 % Favored : 82.75 % 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: 1.32 (0.30), residues: 899 helix: 2.65 (0.27), residues: 387 sheet: 0.20 (0.42), residues: 175 loop : -0.91 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.006 0.001 HIS A 362 PHE 0.010 0.001 PHE B 241 TYR 0.025 0.001 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.735 Fit side-chains REVERT: A 51 SER cc_start: 0.9118 (p) cc_final: 0.8874 (p) REVERT: A 293 LYS cc_start: 0.8237 (mmtp) cc_final: 0.8006 (mmtp) REVERT: B 89 LYS cc_start: 0.8855 (mttp) cc_final: 0.8321 (mtpt) REVERT: R 82 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7855 (ttm) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.1558 time to fit residues: 19.6161 Evaluate side-chains 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7781 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6689 Z= 0.156 Angle : 0.479 6.141 9173 Z= 0.258 Chirality : 0.040 0.138 1115 Planarity : 0.003 0.034 1145 Dihedral : 6.584 123.648 998 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.61 % Allowed : 15.68 % 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: 1.40 (0.30), residues: 899 helix: 2.76 (0.27), residues: 387 sheet: 0.03 (0.41), residues: 185 loop : -0.81 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.024 0.001 TYR R 185 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.802 Fit side-chains REVERT: A 51 SER cc_start: 0.9105 (p) cc_final: 0.8870 (p) REVERT: A 293 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7905 (mmtp) REVERT: B 89 LYS cc_start: 0.8866 (mttp) cc_final: 0.8349 (mtpt) REVERT: R 185 TYR cc_start: 0.8322 (m-80) cc_final: 0.7985 (m-80) outliers start: 15 outliers final: 13 residues processed: 94 average time/residue: 0.1597 time to fit residues: 20.9035 Evaluate side-chains 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6689 Z= 0.151 Angle : 0.478 6.159 9173 Z= 0.256 Chirality : 0.039 0.143 1115 Planarity : 0.003 0.031 1145 Dihedral : 6.396 121.483 998 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.79 % Allowed : 15.33 % Favored : 81.88 % 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: 1.45 (0.30), residues: 899 helix: 2.80 (0.27), residues: 387 sheet: 0.04 (0.41), residues: 184 loop : -0.76 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.006 0.001 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.022 0.001 TYR R 185 ARG 0.005 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.808 Fit side-chains REVERT: A 51 SER cc_start: 0.9098 (p) cc_final: 0.8855 (p) REVERT: A 293 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7850 (mmtp) REVERT: B 89 LYS cc_start: 0.8862 (mttp) cc_final: 0.8345 (mtpt) REVERT: R 178 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7794 (p-80) REVERT: R 185 TYR cc_start: 0.8336 (m-80) cc_final: 0.8011 (m-80) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.1839 time to fit residues: 25.0523 Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4852 ------------------------------------------------------------------------------- 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: 0.7746 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6689 Z= 0.138 Angle : 0.466 6.180 9173 Z= 0.249 Chirality : 0.039 0.141 1115 Planarity : 0.003 0.031 1145 Dihedral : 6.240 119.340 998 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.26 % Allowed : 15.16 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.30), residues: 899 helix: 2.88 (0.27), residues: 387 sheet: 0.13 (0.40), residues: 184 loop : -0.70 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.006 0.001 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.021 0.001 TYR R 185 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.761 Fit side-chains REVERT: A 51 SER cc_start: 0.9058 (p) cc_final: 0.8815 (p) REVERT: B 89 LYS cc_start: 0.8847 (mttp) cc_final: 0.8305 (mtpt) REVERT: R 178 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7800 (p-80) REVERT: R 185 TYR cc_start: 0.8339 (m-80) cc_final: 0.8032 (m-80) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.1728 time to fit residues: 23.5676 Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN R 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6689 Z= 0.174 Angle : 0.504 9.347 9173 Z= 0.268 Chirality : 0.040 0.150 1115 Planarity : 0.003 0.031 1145 Dihedral : 6.280 121.264 998 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.44 % Allowed : 16.55 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.30), residues: 899 helix: 2.90 (0.27), residues: 387 sheet: 0.03 (0.40), residues: 186 loop : -0.72 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.007 0.001 HIS R 93 PHE 0.010 0.001 PHE B 241 TYR 0.021 0.001 TYR R 185 ARG 0.006 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.764 Fit side-chains REVERT: A 51 SER cc_start: 0.9033 (p) cc_final: 0.8806 (p) REVERT: B 89 LYS cc_start: 0.8866 (mttp) cc_final: 0.8344 (mtpt) REVERT: R 178 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7790 (p-80) REVERT: R 185 TYR cc_start: 0.8357 (m-80) cc_final: 0.8065 (m-80) outliers start: 14 outliers final: 13 residues processed: 94 average time/residue: 0.1675 time to fit residues: 21.9523 Evaluate side-chains 101 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 51 ASN R 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094388 restraints weight = 50534.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098369 restraints weight = 16090.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101178 restraints weight = 8607.885| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6689 Z= 0.164 Angle : 0.500 8.962 9173 Z= 0.266 Chirality : 0.040 0.162 1115 Planarity : 0.003 0.031 1145 Dihedral : 6.328 123.465 998 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.79 % Allowed : 16.20 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.30), residues: 899 helix: 2.88 (0.27), residues: 387 sheet: 0.02 (0.40), residues: 186 loop : -0.69 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.013 0.002 HIS R 93 PHE 0.009 0.001 PHE B 241 TYR 0.020 0.001 TYR R 185 ARG 0.005 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.11 seconds wall clock time: 29 minutes 10.06 seconds (1750.06 seconds total)