Starting phenix.real_space_refine on Fri Nov 15 01:04:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itl_35706/11_2024/8itl_35706.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itl_35706/11_2024/8itl_35706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itl_35706/11_2024/8itl_35706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itl_35706/11_2024/8itl_35706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itl_35706/11_2024/8itl_35706.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itl_35706/11_2024/8itl_35706.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5024 2.51 5 N 1421 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7954 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2139 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1875 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2567 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 417 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 956 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.60, per 1000 atoms: 0.58 Number of scatterers: 7954 At special positions: 0 Unit cell: (76.041, 102.816, 125.307, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1466 8.00 N 1421 7.00 C 5024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 180 " - pdb=" SG CYS R 250 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.2 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 43.4% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'R' and resid 88 through 126 Processing helix chain 'R' and resid 131 through 158 removed outlier: 3.890A pdb=" N LEU R 152 " --> pdb=" O ALA R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 211 removed outlier: 3.854A pdb=" N TYR R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 245 Proline residue: R 231 - end of helix Proline residue: R 237 - end of helix Processing helix chain 'R' and resid 256 through 293 removed outlier: 3.987A pdb=" N ILE R 262 " --> pdb=" O ALA R 258 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE R 263 " --> pdb=" O ILE R 259 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.597A pdb=" N ARG R 292 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 321 removed outlier: 3.525A pdb=" N ARG R 302 " --> pdb=" O ASP R 298 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU R 303 " --> pdb=" O TYR R 299 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 332 through 356 removed outlier: 3.792A pdb=" N ILE R 342 " --> pdb=" O LEU R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 379 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.767A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.678A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.647A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.284A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.528A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.430A 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 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.788A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.867A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 7.219A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.639A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.046A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.621A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.008A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.775A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.510A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.097A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2652 1.34 - 1.46: 1957 1.46 - 1.58: 3446 1.58 - 1.70: 0 1.70 - 1.83: 56 Bond restraints: 8111 Sorted by residual: bond pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 1.528 1.490 0.037 1.35e-02 5.49e+03 7.71e+00 bond pdb=" CA MET A 221 " pdb=" C MET A 221 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.21e-02 6.83e+03 4.15e+00 bond pdb=" CA GLU B 260 " pdb=" C GLU B 260 " ideal model delta sigma weight residual 1.526 1.504 0.023 1.37e-02 5.33e+03 2.76e+00 bond pdb=" C VAL R 311 " pdb=" N PRO R 312 " ideal model delta sigma weight residual 1.333 1.357 -0.023 1.44e-02 4.82e+03 2.64e+00 bond pdb=" CA ASN B 293 " pdb=" C ASN B 293 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.08e-02 8.57e+03 2.57e+00 ... (remaining 8106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 10759 1.65 - 3.30: 201 3.30 - 4.95: 35 4.95 - 6.59: 11 6.59 - 8.24: 3 Bond angle restraints: 11009 Sorted by residual: angle pdb=" C PHE A 312 " pdb=" N PRO A 313 " pdb=" CA PRO A 313 " ideal model delta sigma weight residual 119.28 115.02 4.26 1.10e+00 8.26e-01 1.50e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 113.15 108.61 4.54 1.19e+00 7.06e-01 1.46e+01 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 112.47 116.75 -4.28 1.24e+00 6.50e-01 1.19e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 126.51 -4.97 1.91e+00 2.74e-01 6.78e+00 angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 113.65 109.88 3.77 1.47e+00 4.63e-01 6.58e+00 ... (remaining 11004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4343 17.85 - 35.69: 370 35.69 - 53.54: 76 53.54 - 71.39: 3 71.39 - 89.23: 17 Dihedral angle restraints: 4809 sinusoidal: 1805 harmonic: 3004 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -9.28 -76.72 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS R 180 " pdb=" SG CYS R 180 " pdb=" SG CYS R 250 " pdb=" CB CYS R 250 " ideal model delta sinusoidal sigma weight residual 93.00 164.32 -71.32 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " pdb=" CD GLU B 215 " pdb=" OE1 GLU B 215 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 4806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 794 0.034 - 0.068: 323 0.068 - 0.102: 92 0.102 - 0.135: 40 0.135 - 0.169: 1 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1247 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 220 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C HIS A 220 " -0.047 2.00e-02 2.50e+03 pdb=" O HIS A 220 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A 221 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 352 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C VAL R 352 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL R 352 " -0.012 2.00e-02 2.50e+03 pdb=" N SER R 353 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 311 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO R 312 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO R 312 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 312 " -0.026 5.00e-02 4.00e+02 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 5 2.06 - 2.77: 1571 2.77 - 3.48: 11187 3.48 - 4.19: 17869 4.19 - 4.90: 33508 Nonbonded interactions: 64140 Sorted by model distance: nonbonded pdb=" CE1 PHE B 292 " pdb=" N ARG B 314 " model vdw 1.351 3.420 nonbonded pdb=" CZ PHE B 292 " pdb=" OD1 ASN B 313 " model vdw 1.862 3.340 nonbonded pdb=" CE1 PHE B 292 " pdb=" C ASN B 313 " model vdw 1.955 3.570 nonbonded pdb=" CD1 PHE B 292 " pdb=" C ASN B 313 " model vdw 2.018 3.570 nonbonded pdb=" CD1 PHE B 292 " pdb=" N ARG B 314 " model vdw 2.035 3.420 ... (remaining 64135 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 0.038 8111 Z= 0.264 Angle : 0.608 8.243 11009 Z= 0.350 Chirality : 0.042 0.169 1250 Planarity : 0.003 0.044 1416 Dihedral : 14.366 89.234 2858 Min Nonbonded Distance : 1.351 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 1019 helix: 1.82 (0.26), residues: 410 sheet: -1.08 (0.36), residues: 228 loop : -1.55 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 197 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.002 PHE B 241 TYR 0.025 0.002 TYR N 115 ARG 0.002 0.000 ARG R 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.841 Fit side-chains REVERT: R 99 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7881 (mt-10) REVERT: A 209 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6818 (mm-30) REVERT: B 246 ASP cc_start: 0.7715 (m-30) cc_final: 0.7459 (m-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2075 time to fit residues: 36.4115 Evaluate side-chains 102 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.0010 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 373 HIS A 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8111 Z= 0.194 Angle : 0.535 9.638 11009 Z= 0.283 Chirality : 0.041 0.157 1250 Planarity : 0.004 0.060 1416 Dihedral : 4.075 18.506 1132 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.74 % Allowed : 8.50 % Favored : 90.76 % 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: 0.37 (0.28), residues: 1019 helix: 2.36 (0.26), residues: 408 sheet: -0.97 (0.35), residues: 226 loop : -1.31 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE N 108 TYR 0.013 0.001 TYR R 195 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.913 Fit side-chains REVERT: R 99 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 118 ASP cc_start: 0.7399 (t0) cc_final: 0.7161 (t0) REVERT: B 246 ASP cc_start: 0.7847 (m-30) cc_final: 0.7632 (m-30) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.2247 time to fit residues: 32.6183 Evaluate side-chains 98 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7301 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8111 Z= 0.209 Angle : 0.518 10.196 11009 Z= 0.272 Chirality : 0.041 0.160 1250 Planarity : 0.004 0.059 1416 Dihedral : 3.997 19.007 1132 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.48 % Allowed : 11.82 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.27), residues: 1019 helix: 2.24 (0.26), residues: 420 sheet: -0.87 (0.36), residues: 216 loop : -1.54 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 197 HIS 0.003 0.001 HIS A 357 PHE 0.022 0.001 PHE R 335 TYR 0.018 0.001 TYR B 59 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.935 Fit side-chains REVERT: R 99 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7879 (mt-10) REVERT: R 113 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6768 (mp) REVERT: R 335 PHE cc_start: 0.6084 (p90) cc_final: 0.5618 (p90) REVERT: R 341 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 221 MET cc_start: 0.7262 (tpp) cc_final: 0.7032 (mmm) REVERT: B 175 GLN cc_start: 0.7720 (pm20) cc_final: 0.7503 (pm20) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.1950 time to fit residues: 28.2249 Evaluate side-chains 100 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7280 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8111 Z= 0.168 Angle : 0.491 10.825 11009 Z= 0.256 Chirality : 0.040 0.154 1250 Planarity : 0.004 0.057 1416 Dihedral : 3.833 18.839 1132 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.85 % Allowed : 14.04 % Favored : 84.11 % 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: 0.48 (0.27), residues: 1019 helix: 2.48 (0.26), residues: 414 sheet: -0.79 (0.36), residues: 216 loop : -1.45 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 197 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE R 335 TYR 0.012 0.001 TYR R 195 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.869 Fit side-chains REVERT: R 99 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7873 (mt-10) REVERT: R 335 PHE cc_start: 0.5857 (p90) cc_final: 0.5400 (p90) REVERT: R 341 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7314 (mt-10) REVERT: R 358 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.6002 (m-10) REVERT: A 60 MET cc_start: 0.6624 (ptt) cc_final: 0.6240 (ptt) REVERT: B 175 GLN cc_start: 0.7666 (pm20) cc_final: 0.7400 (pm20) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.2113 time to fit residues: 31.0394 Evaluate side-chains 102 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8111 Z= 0.368 Angle : 0.629 14.475 11009 Z= 0.319 Chirality : 0.044 0.161 1250 Planarity : 0.004 0.063 1416 Dihedral : 4.240 20.762 1132 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.08 % Allowed : 15.39 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.27), residues: 1019 helix: 2.23 (0.26), residues: 411 sheet: -1.03 (0.35), residues: 218 loop : -1.48 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 197 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.002 PHE R 335 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.980 Fit side-chains REVERT: R 99 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7905 (mt-10) REVERT: R 117 LEU cc_start: 0.7540 (mm) cc_final: 0.7328 (mm) REVERT: R 341 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7419 (mt-10) REVERT: R 358 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.6009 (m-10) REVERT: B 59 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: B 175 GLN cc_start: 0.7818 (pm20) cc_final: 0.7524 (pm20) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 0.2010 time to fit residues: 28.9597 Evaluate side-chains 102 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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: 0.7308 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8111 Z= 0.189 Angle : 0.525 11.295 11009 Z= 0.269 Chirality : 0.041 0.154 1250 Planarity : 0.004 0.056 1416 Dihedral : 3.936 18.787 1132 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.59 % Allowed : 16.26 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1019 helix: 2.38 (0.26), residues: 413 sheet: -0.98 (0.35), residues: 221 loop : -1.43 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.002 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.016 0.001 TYR R 105 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.912 Fit side-chains REVERT: R 99 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7905 (mt-10) REVERT: R 341 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7447 (mt-10) REVERT: R 358 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5895 (m-10) REVERT: A 21 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6602 (mt-10) REVERT: B 59 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: B 90 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8210 (m) REVERT: B 175 GLN cc_start: 0.7649 (pm20) cc_final: 0.7397 (pm20) REVERT: B 234 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7830 (m-80) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.2020 time to fit residues: 31.0754 Evaluate side-chains 108 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8111 Z= 0.234 Angle : 0.549 11.571 11009 Z= 0.280 Chirality : 0.042 0.157 1250 Planarity : 0.004 0.058 1416 Dihedral : 4.008 19.996 1132 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.46 % Allowed : 17.12 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 1019 helix: 2.31 (0.26), residues: 412 sheet: -0.97 (0.35), residues: 221 loop : -1.43 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 197 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE R 335 TYR 0.012 0.001 TYR R 195 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.940 Fit side-chains REVERT: R 99 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7913 (mt-10) REVERT: R 335 PHE cc_start: 0.5826 (p90) cc_final: 0.5301 (p90) REVERT: R 341 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7451 (mt-10) REVERT: R 358 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6026 (m-10) REVERT: A 21 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6589 (mt-10) REVERT: A 60 MET cc_start: 0.6871 (ptt) cc_final: 0.6581 (ptt) REVERT: B 59 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 90 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8245 (m) REVERT: B 175 GLN cc_start: 0.7686 (pm20) cc_final: 0.7437 (pm20) REVERT: B 234 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7842 (m-80) outliers start: 20 outliers final: 14 residues processed: 106 average time/residue: 0.2036 time to fit residues: 29.6284 Evaluate side-chains 109 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 85 optimal weight: 4.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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: 0.7304 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8111 Z= 0.192 Angle : 0.540 12.008 11009 Z= 0.272 Chirality : 0.041 0.241 1250 Planarity : 0.003 0.056 1416 Dihedral : 3.895 19.253 1132 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.71 % Allowed : 16.75 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1019 helix: 2.38 (0.26), residues: 413 sheet: -0.92 (0.35), residues: 221 loop : -1.38 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.002 0.001 HIS A 357 PHE 0.018 0.001 PHE R 335 TYR 0.013 0.001 TYR R 195 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: R 99 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7870 (mt-10) REVERT: R 335 PHE cc_start: 0.5740 (p90) cc_final: 0.5234 (p90) REVERT: R 341 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7468 (mt-10) REVERT: R 358 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.5932 (m-10) REVERT: A 21 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: A 60 MET cc_start: 0.6689 (ptt) cc_final: 0.6383 (ptt) REVERT: A 311 TYR cc_start: 0.6938 (m-80) cc_final: 0.6697 (m-80) REVERT: B 59 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: B 90 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8224 (m) REVERT: B 175 GLN cc_start: 0.7647 (pm20) cc_final: 0.7388 (pm20) REVERT: B 234 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7820 (m-80) outliers start: 22 outliers final: 14 residues processed: 111 average time/residue: 0.2132 time to fit residues: 32.6640 Evaluate side-chains 112 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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: 0.7270 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 8111 Z= 0.155 Angle : 0.516 12.470 11009 Z= 0.260 Chirality : 0.041 0.235 1250 Planarity : 0.003 0.054 1416 Dihedral : 3.762 18.397 1132 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.34 % Allowed : 17.24 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1019 helix: 2.42 (0.26), residues: 415 sheet: -0.81 (0.35), residues: 220 loop : -1.33 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.000 HIS A 357 PHE 0.017 0.001 PHE R 335 TYR 0.013 0.001 TYR R 195 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: R 99 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7885 (mt-10) REVERT: R 145 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6160 (mpp) REVERT: R 335 PHE cc_start: 0.5549 (p90) cc_final: 0.5089 (p90) REVERT: R 341 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7443 (mt-10) REVERT: R 358 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6086 (m-10) REVERT: A 21 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: A 60 MET cc_start: 0.6666 (ptt) cc_final: 0.6441 (ptt) REVERT: A 221 MET cc_start: 0.7395 (tpp) cc_final: 0.7140 (mmm) REVERT: A 311 TYR cc_start: 0.6873 (m-80) cc_final: 0.6666 (m-80) REVERT: B 59 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 175 GLN cc_start: 0.7560 (pm20) cc_final: 0.7288 (pm20) REVERT: B 234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7882 (m-80) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 0.1947 time to fit residues: 29.7591 Evaluate side-chains 110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 MET Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8111 Z= 0.198 Angle : 0.528 12.558 11009 Z= 0.269 Chirality : 0.041 0.154 1250 Planarity : 0.004 0.056 1416 Dihedral : 3.817 19.155 1132 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.09 % Allowed : 17.61 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1019 helix: 2.41 (0.26), residues: 415 sheet: -0.77 (0.35), residues: 220 loop : -1.34 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 197 HIS 0.004 0.001 HIS A 387 PHE 0.017 0.001 PHE R 335 TYR 0.011 0.001 TYR R 195 ARG 0.006 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: R 99 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7899 (mt-10) REVERT: R 335 PHE cc_start: 0.5516 (p90) cc_final: 0.5075 (p90) REVERT: R 341 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7454 (mt-10) REVERT: R 358 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6155 (m-80) REVERT: A 21 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6580 (mt-10) REVERT: A 60 MET cc_start: 0.6697 (ptt) cc_final: 0.6474 (ptt) REVERT: A 221 MET cc_start: 0.7414 (tpp) cc_final: 0.7171 (mmm) REVERT: A 311 TYR cc_start: 0.6901 (m-80) cc_final: 0.6673 (m-80) REVERT: B 59 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: B 175 GLN cc_start: 0.7579 (pm20) cc_final: 0.7324 (pm20) REVERT: B 234 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7813 (m-80) outliers start: 17 outliers final: 12 residues processed: 106 average time/residue: 0.2048 time to fit residues: 29.9967 Evaluate side-chains 106 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 245 TYR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 358 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.196892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154719 restraints weight = 9153.191| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.18 r_work: 0.3534 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8111 Z= 0.213 Angle : 0.550 12.440 11009 Z= 0.277 Chirality : 0.041 0.212 1250 Planarity : 0.003 0.054 1416 Dihedral : 3.844 19.291 1132 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.22 % Allowed : 17.73 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1019 helix: 2.37 (0.26), residues: 412 sheet: -0.76 (0.34), residues: 220 loop : -1.38 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 197 HIS 0.003 0.001 HIS A 387 PHE 0.017 0.001 PHE R 335 TYR 0.012 0.001 TYR R 195 ARG 0.004 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.96 seconds wall clock time: 34 minutes 51.76 seconds (2091.76 seconds total)