Starting phenix.real_space_refine on Fri Jul 19 05:58:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/07_2024/8uns_42415.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/07_2024/8uns_42415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/07_2024/8uns_42415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/07_2024/8uns_42415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/07_2024/8uns_42415.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/07_2024/8uns_42415.cif" } resolution = 3.4 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= 0.022 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 42 5.16 5 C 4291 2.51 5 N 1154 2.21 5 O 1193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "R GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6683 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 171 Conformer: "B" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 171 bond proxies already assigned to first conformer: 1797 Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2364 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 373 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 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': 59} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 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: 5.77, per 1000 atoms: 0.86 Number of scatterers: 6683 At special positions: 0 Unit cell: (83.2992, 137.097, 98.9178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 3 15.00 O 1193 8.00 N 1154 7.00 C 4291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 47.2% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.050A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.646A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.005A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.555A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.537A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.154A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.671A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.673A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.627A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.552A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.586A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.546A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.356A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'R' and resid 121 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.624A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.623A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.568A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.742A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.909A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.846A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.514A 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 removed outlier: 3.510A pdb=" N CYS R 327 " --> pdb=" O PRO R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.201A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.058A 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: 6.670A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.010A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.566A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.376A 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: 7.013A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.842A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.897A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.853A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1047 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: 1.82 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1596 1.33 - 1.45: 1497 1.45 - 1.58: 3674 1.58 - 1.70: 5 1.70 - 1.82: 57 Bond restraints: 6829 Sorted by residual: bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.14e-02 7.69e+03 1.61e+01 bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.32e-02 5.74e+03 1.03e+01 bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.521 1.485 0.037 1.19e-02 7.06e+03 9.50e+00 bond pdb=" N ARG A 61 " pdb=" CA ARG A 61 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.61e+00 bond pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.46e+00 ... (remaining 6824 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 203 107.28 - 113.96: 3889 113.96 - 120.65: 2776 120.65 - 127.33: 2405 127.33 - 134.01: 76 Bond angle restraints: 9349 Sorted by residual: angle pdb=" C GLN A 262 " pdb=" CA GLN A 262 " pdb=" CB GLN A 262 " ideal model delta sigma weight residual 116.54 108.64 7.90 1.15e+00 7.56e-01 4.72e+01 angle pdb=" N GLU A 259 " pdb=" CA GLU A 259 " pdb=" C GLU A 259 " ideal model delta sigma weight residual 113.23 105.07 8.16 1.22e+00 6.72e-01 4.47e+01 angle pdb=" N GLN A 19 " pdb=" CA GLN A 19 " pdb=" C GLN A 19 " ideal model delta sigma weight residual 111.28 104.93 6.35 1.09e+00 8.42e-01 3.39e+01 angle pdb=" N ASN A 261 " pdb=" CA ASN A 261 " pdb=" C ASN A 261 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.70e+01 angle pdb=" CA LEU A 63 " pdb=" C LEU A 63 " pdb=" O LEU A 63 " ideal model delta sigma weight residual 120.55 115.23 5.32 1.06e+00 8.90e-01 2.52e+01 ... (remaining 9344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.23: 3818 28.23 - 56.46: 112 56.46 - 84.69: 7 84.69 - 112.92: 4 112.92 - 141.15: 4 Dihedral angle restraints: 3945 sinusoidal: 1267 harmonic: 2678 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 93.00 153.31 -60.31 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -149.58 -141.15 1 2.00e+01 2.50e-03 4.27e+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 -28.04 132.64 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 3942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 886 0.054 - 0.107: 165 0.107 - 0.161: 53 0.161 - 0.214: 8 0.214 - 0.268: 7 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CA ASP A 260 " pdb=" N ASP A 260 " pdb=" C ASP A 260 " pdb=" CB ASP A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN A 19 " pdb=" N GLN A 19 " pdb=" C GLN A 19 " pdb=" CB GLN A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1116 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO R 211 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.013 2.00e-02 2.50e+03 9.94e-03 1.98e+00 pdb=" CG TYR B 59 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 15 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLU A 15 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU A 15 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 16 " 0.008 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2367 2.85 - 3.36: 6024 3.36 - 3.87: 10280 3.87 - 4.39: 10938 4.39 - 4.90: 20361 Nonbonded interactions: 49970 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.332 2.440 nonbonded pdb=" OD2 ASP B 258 " pdb=" NH2 ARG G 27 " model vdw 2.368 2.520 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.372 2.520 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.397 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.407 2.440 ... (remaining 49965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.040 Set scattering table: 0.070 Process input model: 23.520 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.004 0.054 6829 Z= 0.304 Angle : 0.771 10.404 9349 Z= 0.494 Chirality : 0.051 0.268 1119 Planarity : 0.003 0.043 1173 Dihedral : 14.481 141.151 2201 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 1.05 (0.29), residues: 905 helix: 2.33 (0.27), residues: 393 sheet: 0.02 (0.41), residues: 173 loop : -0.92 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 158 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE A 222 TYR 0.024 0.001 TYR B 59 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.746 Fit side-chains REVERT: G 15 LEU cc_start: 0.8931 (tp) cc_final: 0.8649 (tp) REVERT: R 171 MET cc_start: 0.7983 (mmm) cc_final: 0.7769 (mmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1614 time to fit residues: 21.4555 Evaluate side-chains 74 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.0020 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6829 Z= 0.129 Angle : 0.457 5.983 9349 Z= 0.244 Chirality : 0.039 0.146 1119 Planarity : 0.003 0.041 1173 Dihedral : 9.811 159.366 1006 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.65 % Allowed : 7.11 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 905 helix: 2.59 (0.27), residues: 400 sheet: 0.43 (0.41), residues: 170 loop : -0.95 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.019 0.001 TYR B 59 ARG 0.002 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.989 Fit side-chains REVERT: A 211 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8213 (mmtt) REVERT: A 267 GLN cc_start: 0.8565 (tp40) cc_final: 0.8182 (tm-30) REVERT: A 368 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: R 61 PHE cc_start: 0.8721 (m-80) cc_final: 0.8474 (m-10) REVERT: R 171 MET cc_start: 0.7993 (mmm) cc_final: 0.7729 (mmm) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 0.1949 time to fit residues: 24.0237 Evaluate side-chains 85 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6829 Z= 0.273 Angle : 0.503 5.891 9349 Z= 0.269 Chirality : 0.041 0.146 1119 Planarity : 0.003 0.044 1173 Dihedral : 8.489 110.135 1006 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.82 % Allowed : 9.42 % Favored : 88.76 % 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: 1.36 (0.29), residues: 905 helix: 2.64 (0.27), residues: 403 sheet: 0.16 (0.40), residues: 172 loop : -0.93 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.008 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.027 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8684 (tp40) cc_final: 0.8268 (tm-30) REVERT: A 368 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: R 171 MET cc_start: 0.7885 (mmm) cc_final: 0.7603 (mmm) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.1577 time to fit residues: 19.2542 Evaluate side-chains 82 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 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: 0.8367 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6829 Z= 0.136 Angle : 0.440 6.003 9349 Z= 0.232 Chirality : 0.039 0.139 1119 Planarity : 0.003 0.042 1173 Dihedral : 7.654 102.298 1006 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.49 % Allowed : 11.40 % Favored : 87.11 % 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: 1.48 (0.29), residues: 905 helix: 2.81 (0.27), residues: 400 sheet: 0.16 (0.40), residues: 172 loop : -0.90 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8370 (mmtt) REVERT: A 236 GLN cc_start: 0.8918 (mt0) cc_final: 0.8664 (pt0) REVERT: A 267 GLN cc_start: 0.8641 (tp40) cc_final: 0.8201 (tm-30) REVERT: A 368 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: R 61 PHE cc_start: 0.8561 (m-10) cc_final: 0.8177 (m-10) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 0.1697 time to fit residues: 21.4715 Evaluate side-chains 85 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 8.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.8344 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6829 Z= 0.120 Angle : 0.428 6.388 9349 Z= 0.225 Chirality : 0.039 0.141 1119 Planarity : 0.003 0.040 1173 Dihedral : 7.314 96.097 1006 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.82 % Allowed : 13.06 % Favored : 85.12 % 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: 1.63 (0.30), residues: 905 helix: 2.94 (0.27), residues: 400 sheet: 0.25 (0.41), residues: 172 loop : -0.84 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.001 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8942 (mt0) cc_final: 0.8710 (pt0) REVERT: A 267 GLN cc_start: 0.8663 (tp40) cc_final: 0.8183 (tm-30) REVERT: A 368 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7255 (m-30) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.1531 time to fit residues: 20.1914 Evaluate side-chains 93 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8371 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6829 Z= 0.165 Angle : 0.452 6.401 9349 Z= 0.236 Chirality : 0.040 0.138 1119 Planarity : 0.003 0.040 1173 Dihedral : 7.163 92.822 1006 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.48 % Allowed : 13.39 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.30), residues: 905 helix: 2.93 (0.27), residues: 400 sheet: 0.22 (0.41), residues: 172 loop : -0.87 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8919 (mt0) cc_final: 0.8681 (pt0) REVERT: A 267 GLN cc_start: 0.8697 (tp40) cc_final: 0.8170 (tm-30) REVERT: A 368 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7275 (m-30) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.1699 time to fit residues: 22.4617 Evaluate side-chains 96 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.8424 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6829 Z= 0.257 Angle : 0.497 6.286 9349 Z= 0.264 Chirality : 0.041 0.144 1119 Planarity : 0.003 0.043 1173 Dihedral : 7.180 92.258 1006 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.98 % Allowed : 13.88 % Favored : 83.14 % 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: 1.49 (0.29), residues: 905 helix: 2.79 (0.27), residues: 403 sheet: 0.19 (0.41), residues: 172 loop : -0.90 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.009 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.013 0.001 TYR A 339 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8380 (mmtt) REVERT: A 236 GLN cc_start: 0.8965 (mt0) cc_final: 0.8691 (pt0) REVERT: A 267 GLN cc_start: 0.8738 (tp40) cc_final: 0.8204 (tm-30) REVERT: A 368 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: B 234 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.7943 (t80) REVERT: R 82 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.7004 (ttp) outliers start: 18 outliers final: 12 residues processed: 92 average time/residue: 0.1625 time to fit residues: 21.0455 Evaluate side-chains 93 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.0170 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 48 optimal weight: 0.1980 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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: 0.8334 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6829 Z= 0.109 Angle : 0.431 6.218 9349 Z= 0.225 Chirality : 0.039 0.133 1119 Planarity : 0.003 0.040 1173 Dihedral : 6.842 90.595 1006 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.32 % Allowed : 15.70 % Favored : 82.98 % 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: 905 helix: 2.98 (0.27), residues: 400 sheet: 0.26 (0.42), residues: 170 loop : -0.91 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.010 0.001 HIS A 220 PHE 0.012 0.001 PHE A 222 TYR 0.013 0.001 TYR A 339 ARG 0.001 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8438 (mmtt) REVERT: A 236 GLN cc_start: 0.8940 (mt0) cc_final: 0.8689 (pt0) REVERT: A 267 GLN cc_start: 0.8658 (tp40) cc_final: 0.8150 (tm-30) REVERT: A 368 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: B 234 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.7792 (t80) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 0.1574 time to fit residues: 20.6909 Evaluate side-chains 90 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.0040 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6829 Z= 0.145 Angle : 0.435 6.208 9349 Z= 0.230 Chirality : 0.039 0.137 1119 Planarity : 0.003 0.041 1173 Dihedral : 6.770 90.365 1006 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.49 % Allowed : 16.36 % Favored : 82.15 % 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: 1.63 (0.30), residues: 905 helix: 2.99 (0.27), residues: 400 sheet: 0.22 (0.42), residues: 170 loop : -0.88 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 297 HIS 0.009 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.011 0.001 TYR A 339 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8436 (mmtt) REVERT: A 236 GLN cc_start: 0.8925 (mt0) cc_final: 0.8692 (pt0) REVERT: A 267 GLN cc_start: 0.8687 (tp40) cc_final: 0.8136 (tm-30) REVERT: A 368 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: B 234 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.7790 (t80) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.1542 time to fit residues: 19.5629 Evaluate side-chains 90 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 230 LEU 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 88 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.8426 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6829 Z= 0.277 Angle : 0.498 6.171 9349 Z= 0.266 Chirality : 0.041 0.143 1119 Planarity : 0.003 0.043 1173 Dihedral : 6.940 91.873 1006 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.82 % Allowed : 16.20 % Favored : 81.98 % 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: 1.50 (0.30), residues: 905 helix: 2.80 (0.27), residues: 403 sheet: 0.19 (0.42), residues: 172 loop : -0.89 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.009 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8476 (mmtt) REVERT: A 236 GLN cc_start: 0.8962 (mt0) cc_final: 0.8684 (pt0) REVERT: A 267 GLN cc_start: 0.8746 (tp40) cc_final: 0.8189 (tm-30) REVERT: A 368 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: B 234 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.7989 (t80) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.1515 time to fit residues: 18.8550 Evaluate side-chains 87 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER 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: 1.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.123353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099188 restraints weight = 37206.392| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 4.17 r_work: 0.3007 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6829 Z= 0.135 Angle : 0.446 6.208 9349 Z= 0.235 Chirality : 0.040 0.136 1119 Planarity : 0.003 0.040 1173 Dihedral : 6.741 91.197 1006 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.65 % Allowed : 16.20 % Favored : 82.15 % 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: 905 helix: 2.92 (0.27), residues: 400 sheet: 0.18 (0.42), residues: 170 loop : -0.93 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.009 0.001 HIS A 220 PHE 0.013 0.001 PHE A 222 TYR 0.013 0.001 TYR A 339 ARG 0.001 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.25 seconds wall clock time: 30 minutes 44.91 seconds (1844.91 seconds total)