Starting phenix.real_space_refine on Sat Dec 28 04:55:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xji_33228/12_2024/7xji_33228.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xji_33228/12_2024/7xji_33228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xji_33228/12_2024/7xji_33228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xji_33228/12_2024/7xji_33228.map" model { file = "/net/cci-nas-00/data/ceres_data/7xji_33228/12_2024/7xji_33228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xji_33228/12_2024/7xji_33228.cif" } resolution = 3.9 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= 0.001 sd= 0.008 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 S 46 5.16 5 Cl 1 4.86 5 C 4977 2.51 5 N 1381 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7851 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2052 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'EI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.02, per 1000 atoms: 0.64 Number of scatterers: 7851 At special positions: 0 Unit cell: (101.592, 77.688, 132.667, 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) Cl 1 17.00 S 46 16.00 O 1446 8.00 N 1381 7.00 C 4977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " distance=2.04 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 40.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.513A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.702A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 57' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.886A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.375A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.547A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.553A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.899A pdb=" N ASP A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.683A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.750A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.625A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 64 removed outlier: 3.951A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 69 removed outlier: 3.560A pdb=" N GLN R 69 " --> pdb=" O PRO R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 90 removed outlier: 3.880A pdb=" N VAL R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 Processing helix chain 'R' and resid 150 through 170 Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 213 through 241 Processing helix chain 'R' and resid 289 through 318 removed outlier: 4.493A pdb=" N CYS R 304 " --> pdb=" O THR R 300 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 324 through 346 removed outlier: 3.521A pdb=" N LEU R 328 " --> pdb=" O PRO R 324 " (cutoff:3.500A) Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 349 through 360 Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.510A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.792A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.586A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.612A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.222A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 3.820A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.674A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.603A 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 234 removed outlier: 3.722A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.341A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.615A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1122 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: 2.25 Time building geometry restraints manager: 2.27 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: 2590 1.34 - 1.46: 1911 1.46 - 1.58: 3445 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 8008 Sorted by residual: bond pdb=" C6 EI5 R 401 " pdb=" O1 EI5 R 401 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" C4 EI5 R 401 " pdb=" C6 EI5 R 401 " ideal model delta sigma weight residual 1.528 1.488 0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" CB PRO R 320 " pdb=" CG PRO R 320 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.26e+00 bond pdb=" CA ASN R 192 " pdb=" CB ASN R 192 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.37e+00 bond pdb=" C16 EI5 R 401 " pdb=" O2 EI5 R 401 " ideal model delta sigma weight residual 1.401 1.423 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 8003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10638 1.64 - 3.28: 197 3.28 - 4.92: 35 4.92 - 6.56: 14 6.56 - 8.20: 3 Bond angle restraints: 10887 Sorted by residual: angle pdb=" N VAL A 357 " pdb=" CA VAL A 357 " pdb=" C VAL A 357 " ideal model delta sigma weight residual 112.43 108.30 4.13 9.20e-01 1.18e+00 2.02e+01 angle pdb=" N VAL R 37 " pdb=" CA VAL R 37 " pdb=" C VAL R 37 " ideal model delta sigma weight residual 113.71 110.07 3.64 9.50e-01 1.11e+00 1.47e+01 angle pdb=" C LEU R 221 " pdb=" N PHE R 222 " pdb=" CA PHE R 222 " ideal model delta sigma weight residual 120.68 114.20 6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CA CYS R 195 " pdb=" CB CYS R 195 " pdb=" SG CYS R 195 " ideal model delta sigma weight residual 114.40 122.04 -7.64 2.30e+00 1.89e-01 1.10e+01 angle pdb=" C VAL R 90 " pdb=" N VAL R 91 " pdb=" CA VAL R 91 " ideal model delta sigma weight residual 120.33 122.49 -2.16 8.00e-01 1.56e+00 7.28e+00 ... (remaining 10882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.75: 4398 19.75 - 39.50: 319 39.50 - 59.25: 38 59.25 - 79.00: 9 79.00 - 98.75: 6 Dihedral angle restraints: 4770 sinusoidal: 1794 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual 93.00 4.82 88.18 1 1.00e+01 1.00e-02 9.30e+01 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 93.00 147.93 -54.93 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 4767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 878 0.039 - 0.078: 281 0.078 - 0.117: 85 0.117 - 0.155: 13 0.155 - 0.194: 1 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CB THR A 315 " pdb=" CA THR A 315 " pdb=" OG1 THR A 315 " pdb=" CG2 THR A 315 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA ILE R 202 " pdb=" N ILE R 202 " pdb=" C ILE R 202 " pdb=" CB ILE R 202 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA PRO R 320 " pdb=" N PRO R 320 " pdb=" C PRO R 320 " pdb=" CB PRO R 320 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1255 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 342 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO R 343 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 343 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 343 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 341 " 0.013 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE R 341 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE R 341 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 341 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 341 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 341 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 341 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 319 " 0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO R 320 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 320 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 320 " 0.022 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 265 2.71 - 3.26: 7821 3.26 - 3.81: 12399 3.81 - 4.35: 15240 4.35 - 4.90: 26286 Nonbonded interactions: 62011 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.251 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.267 3.040 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.278 3.040 nonbonded pdb=" OD2 ASP B 258 " pdb=" NH1 ARG G 27 " model vdw 2.289 3.120 ... (remaining 62006 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.730 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.003 0.075 8008 Z= 0.224 Angle : 0.604 8.196 10887 Z= 0.323 Chirality : 0.042 0.194 1258 Planarity : 0.004 0.048 1394 Dihedral : 13.923 98.747 2832 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.25 (0.27), residues: 1011 helix: 0.90 (0.27), residues: 391 sheet: -0.97 (0.35), residues: 221 loop : -0.61 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 271 HIS 0.002 0.001 HIS B 183 PHE 0.031 0.002 PHE R 341 TYR 0.012 0.001 TYR R 204 ARG 0.008 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.7508 (p) cc_final: 0.7221 (t) REVERT: A 252 ASP cc_start: 0.8545 (t0) cc_final: 0.8222 (t0) REVERT: A 304 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 344 ASP cc_start: 0.6738 (m-30) cc_final: 0.6388 (p0) REVERT: B 145 TYR cc_start: 0.8429 (p90) cc_final: 0.8203 (p90) REVERT: B 156 GLN cc_start: 0.8681 (mm110) cc_final: 0.8090 (mm-40) REVERT: B 175 GLN cc_start: 0.7788 (pt0) cc_final: 0.7255 (mt0) REVERT: B 188 MET cc_start: 0.8138 (mmm) cc_final: 0.7212 (mmm) REVERT: B 262 MET cc_start: 0.7889 (mmm) cc_final: 0.7616 (mmp) REVERT: N 82 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7858 (tm-30) REVERT: N 84 ASN cc_start: 0.7226 (m-40) cc_final: 0.7004 (m-40) REVERT: R 235 LEU cc_start: 0.8159 (tt) cc_final: 0.7909 (tt) REVERT: G 19 LEU cc_start: 0.7467 (tp) cc_final: 0.6859 (tp) REVERT: G 21 MET cc_start: 0.6481 (ttm) cc_final: 0.6185 (ttp) REVERT: G 22 GLU cc_start: 0.5603 (mp0) cc_final: 0.4871 (mp0) REVERT: G 32 LYS cc_start: 0.8460 (ptpt) cc_final: 0.7588 (mmtt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1866 time to fit residues: 44.7122 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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: 3.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.0040 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8008 Z= 0.164 Angle : 0.582 7.790 10887 Z= 0.299 Chirality : 0.042 0.220 1258 Planarity : 0.004 0.045 1394 Dihedral : 5.162 84.967 1132 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.23 % Allowed : 10.66 % Favored : 88.11 % 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: 0.10 (0.26), residues: 1011 helix: 1.46 (0.27), residues: 386 sheet: -0.67 (0.37), residues: 203 loop : -0.80 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 347 PHE 0.028 0.002 PHE R 222 TYR 0.014 0.001 TYR B 264 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.998 Fit side-chains REVERT: A 252 ASP cc_start: 0.8581 (t0) cc_final: 0.8246 (t0) REVERT: A 304 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 344 ASP cc_start: 0.6633 (m-30) cc_final: 0.6244 (p0) REVERT: B 145 TYR cc_start: 0.8598 (p90) cc_final: 0.8133 (p90) REVERT: B 156 GLN cc_start: 0.8679 (mm110) cc_final: 0.8117 (mm-40) REVERT: B 175 GLN cc_start: 0.7787 (pt0) cc_final: 0.7262 (mt0) REVERT: B 188 MET cc_start: 0.8326 (mmm) cc_final: 0.8107 (mmm) REVERT: B 226 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8220 (mm-30) REVERT: B 301 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7437 (mmmt) REVERT: B 321 THR cc_start: 0.8029 (p) cc_final: 0.7770 (p) REVERT: N 1 GLN cc_start: 0.5799 (tt0) cc_final: 0.5594 (tt0) REVERT: N 82 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7658 (tm-30) REVERT: R 235 LEU cc_start: 0.8144 (tt) cc_final: 0.7937 (tt) REVERT: R 312 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8093 (m110) outliers start: 10 outliers final: 9 residues processed: 148 average time/residue: 0.1596 time to fit residues: 34.5866 Evaluate side-chains 134 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8008 Z= 0.181 Angle : 0.553 8.715 10887 Z= 0.283 Chirality : 0.041 0.163 1258 Planarity : 0.004 0.051 1394 Dihedral : 5.034 79.533 1132 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.45 % Allowed : 11.64 % Favored : 85.91 % 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: 0.29 (0.27), residues: 1011 helix: 1.63 (0.27), residues: 387 sheet: -0.62 (0.36), residues: 203 loop : -0.68 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.032 0.002 PHE B 235 TYR 0.015 0.001 TYR B 85 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.942 Fit side-chains REVERT: A 252 ASP cc_start: 0.8527 (t0) cc_final: 0.8154 (t0) REVERT: A 304 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 344 ASP cc_start: 0.6584 (m-30) cc_final: 0.6352 (p0) REVERT: B 57 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8265 (mtmt) REVERT: B 85 TYR cc_start: 0.8135 (m-80) cc_final: 0.7922 (m-80) REVERT: B 145 TYR cc_start: 0.8666 (p90) cc_final: 0.8132 (p90) REVERT: B 175 GLN cc_start: 0.7809 (pt0) cc_final: 0.7247 (mt0) REVERT: B 188 MET cc_start: 0.8384 (mmm) cc_final: 0.8093 (mmm) REVERT: B 321 THR cc_start: 0.8069 (p) cc_final: 0.7805 (p) REVERT: R 312 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (m110) REVERT: R 317 LEU cc_start: 0.7930 (mm) cc_final: 0.7279 (pp) outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 0.1761 time to fit residues: 37.6605 Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8008 Z= 0.147 Angle : 0.540 8.854 10887 Z= 0.272 Chirality : 0.041 0.236 1258 Planarity : 0.004 0.053 1394 Dihedral : 4.851 75.674 1132 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.06 % Allowed : 13.73 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1011 helix: 1.76 (0.27), residues: 387 sheet: -0.53 (0.36), residues: 203 loop : -0.70 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.024 0.001 PHE B 235 TYR 0.016 0.001 TYR N 80 ARG 0.002 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.938 Fit side-chains REVERT: A 252 ASP cc_start: 0.8500 (t0) cc_final: 0.8133 (t0) REVERT: A 304 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7351 (mm-30) REVERT: A 344 ASP cc_start: 0.6565 (m-30) cc_final: 0.6272 (p0) REVERT: B 145 TYR cc_start: 0.8659 (p90) cc_final: 0.8010 (p90) REVERT: B 175 GLN cc_start: 0.7737 (pt0) cc_final: 0.7205 (mt0) REVERT: B 188 MET cc_start: 0.8374 (mmm) cc_final: 0.7528 (mmm) REVERT: B 226 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 301 LYS cc_start: 0.7816 (mmtt) cc_final: 0.6982 (mmmt) REVERT: B 321 THR cc_start: 0.8038 (p) cc_final: 0.7755 (p) REVERT: R 312 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8074 (m110) REVERT: R 317 LEU cc_start: 0.7973 (mm) cc_final: 0.7260 (pp) outliers start: 25 outliers final: 16 residues processed: 151 average time/residue: 0.1737 time to fit residues: 37.8166 Evaluate side-chains 139 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 87 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8008 Z= 0.154 Angle : 0.537 7.253 10887 Z= 0.272 Chirality : 0.041 0.237 1258 Planarity : 0.004 0.054 1394 Dihedral : 4.754 71.843 1132 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.80 % Allowed : 13.36 % Favored : 82.84 % 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: 0.49 (0.27), residues: 1011 helix: 1.83 (0.27), residues: 387 sheet: -0.52 (0.37), residues: 204 loop : -0.61 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 271 HIS 0.004 0.001 HIS A 220 PHE 0.021 0.001 PHE B 235 TYR 0.014 0.001 TYR N 80 ARG 0.002 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.058 Fit side-chains REVERT: A 252 ASP cc_start: 0.8495 (t0) cc_final: 0.8103 (t0) REVERT: A 304 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 344 ASP cc_start: 0.6706 (m-30) cc_final: 0.6320 (p0) REVERT: B 145 TYR cc_start: 0.8650 (p90) cc_final: 0.8157 (p90) REVERT: B 175 GLN cc_start: 0.7761 (pt0) cc_final: 0.7205 (mt0) REVERT: B 188 MET cc_start: 0.8359 (mmm) cc_final: 0.7448 (mmm) REVERT: B 226 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 321 THR cc_start: 0.8016 (p) cc_final: 0.7761 (p) REVERT: N 82 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7544 (tm-30) REVERT: R 312 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8048 (m110) REVERT: R 317 LEU cc_start: 0.8006 (mm) cc_final: 0.7229 (pp) REVERT: G 61 PHE cc_start: 0.7827 (m-80) cc_final: 0.7494 (m-80) outliers start: 31 outliers final: 20 residues processed: 152 average time/residue: 0.1857 time to fit residues: 40.1161 Evaluate side-chains 144 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 312 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: 9.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8008 Z= 0.217 Angle : 0.555 6.689 10887 Z= 0.284 Chirality : 0.042 0.239 1258 Planarity : 0.004 0.053 1394 Dihedral : 4.876 71.257 1132 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.53 % Allowed : 13.11 % Favored : 82.35 % 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 (0.27), residues: 1011 helix: 1.70 (0.27), residues: 394 sheet: -0.64 (0.37), residues: 207 loop : -0.64 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.021 0.002 PHE B 235 TYR 0.014 0.002 TYR N 80 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.866 Fit side-chains REVERT: A 20 ARG cc_start: 0.7058 (mtm110) cc_final: 0.6754 (tpt170) REVERT: A 252 ASP cc_start: 0.8488 (t0) cc_final: 0.8134 (t0) REVERT: A 304 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 145 TYR cc_start: 0.8747 (p90) cc_final: 0.8304 (p90) REVERT: B 175 GLN cc_start: 0.7750 (pt0) cc_final: 0.7183 (mt0) REVERT: B 188 MET cc_start: 0.8347 (mmm) cc_final: 0.7713 (mmm) REVERT: B 321 THR cc_start: 0.7974 (p) cc_final: 0.7671 (p) REVERT: N 83 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7446 (mtp) REVERT: R 52 VAL cc_start: 0.7376 (t) cc_final: 0.7007 (p) REVERT: R 317 LEU cc_start: 0.7990 (mm) cc_final: 0.7202 (pp) outliers start: 37 outliers final: 29 residues processed: 161 average time/residue: 0.1778 time to fit residues: 41.2938 Evaluate side-chains 159 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain G residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8008 Z= 0.197 Angle : 0.553 7.039 10887 Z= 0.283 Chirality : 0.042 0.242 1258 Planarity : 0.004 0.053 1394 Dihedral : 4.856 69.525 1132 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.04 % Allowed : 13.85 % Favored : 82.11 % 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: 0.38 (0.27), residues: 1011 helix: 1.76 (0.27), residues: 393 sheet: -0.69 (0.37), residues: 209 loop : -0.65 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.003 0.001 HIS A 220 PHE 0.019 0.001 PHE B 235 TYR 0.015 0.001 TYR N 80 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.999 Fit side-chains REVERT: A 252 ASP cc_start: 0.8477 (t0) cc_final: 0.8104 (t0) REVERT: B 57 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8406 (pttm) REVERT: B 145 TYR cc_start: 0.8735 (p90) cc_final: 0.8347 (p90) REVERT: B 156 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8190 (mt0) REVERT: B 175 GLN cc_start: 0.7722 (pt0) cc_final: 0.7107 (mt0) REVERT: B 188 MET cc_start: 0.8246 (mmm) cc_final: 0.7755 (mmm) REVERT: B 226 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8469 (mm-30) REVERT: B 321 THR cc_start: 0.7951 (p) cc_final: 0.7655 (p) REVERT: N 82 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7590 (tm-30) REVERT: N 83 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7473 (mtp) REVERT: R 52 VAL cc_start: 0.7403 (t) cc_final: 0.6994 (p) REVERT: R 317 LEU cc_start: 0.8009 (mm) cc_final: 0.7198 (pp) outliers start: 33 outliers final: 27 residues processed: 153 average time/residue: 0.1719 time to fit residues: 38.0474 Evaluate side-chains 155 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8008 Z= 0.264 Angle : 0.590 7.745 10887 Z= 0.303 Chirality : 0.043 0.228 1258 Planarity : 0.004 0.053 1394 Dihedral : 5.034 69.617 1132 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.29 % Allowed : 14.46 % Favored : 81.25 % 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 (0.27), residues: 1011 helix: 1.70 (0.27), residues: 394 sheet: -0.56 (0.38), residues: 201 loop : -0.70 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.003 0.001 HIS A 220 PHE 0.021 0.002 PHE B 235 TYR 0.015 0.002 TYR B 59 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.916 Fit side-chains REVERT: A 20 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6788 (tpt170) REVERT: A 252 ASP cc_start: 0.8416 (t0) cc_final: 0.8058 (t0) REVERT: A 334 GLU cc_start: 0.8301 (tp30) cc_final: 0.8089 (tp30) REVERT: B 156 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8263 (mt0) REVERT: B 175 GLN cc_start: 0.7722 (pt0) cc_final: 0.7096 (mt0) REVERT: B 188 MET cc_start: 0.8263 (mmm) cc_final: 0.7853 (mmm) REVERT: N 83 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7552 (mtp) REVERT: R 52 VAL cc_start: 0.7513 (t) cc_final: 0.7111 (p) REVERT: R 317 LEU cc_start: 0.7868 (mm) cc_final: 0.7155 (pp) outliers start: 35 outliers final: 27 residues processed: 145 average time/residue: 0.1833 time to fit residues: 38.8643 Evaluate side-chains 150 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 0.0010 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8008 Z= 0.177 Angle : 0.563 8.174 10887 Z= 0.287 Chirality : 0.042 0.237 1258 Planarity : 0.004 0.054 1394 Dihedral : 4.882 67.326 1132 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.04 % Allowed : 15.20 % Favored : 80.76 % 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: 0.41 (0.27), residues: 1011 helix: 1.79 (0.27), residues: 393 sheet: -0.58 (0.37), residues: 205 loop : -0.71 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.018 0.001 PHE B 235 TYR 0.016 0.001 TYR N 80 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.951 Fit side-chains REVERT: A 252 ASP cc_start: 0.8361 (t0) cc_final: 0.8020 (t0) REVERT: A 334 GLU cc_start: 0.8140 (tp30) cc_final: 0.7900 (tp30) REVERT: A 358 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6865 (t70) REVERT: B 156 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8227 (mt0) REVERT: B 175 GLN cc_start: 0.7723 (pt0) cc_final: 0.7103 (mt0) REVERT: B 188 MET cc_start: 0.8264 (mmm) cc_final: 0.7915 (mmm) REVERT: R 52 VAL cc_start: 0.7460 (t) cc_final: 0.6997 (p) REVERT: R 317 LEU cc_start: 0.7853 (mm) cc_final: 0.7092 (pp) outliers start: 33 outliers final: 27 residues processed: 153 average time/residue: 0.1564 time to fit residues: 35.1930 Evaluate side-chains 151 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 0.0470 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 49 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8008 Z= 0.154 Angle : 0.559 10.168 10887 Z= 0.281 Chirality : 0.041 0.241 1258 Planarity : 0.004 0.056 1394 Dihedral : 4.700 65.065 1132 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.70 % Allowed : 16.79 % Favored : 80.51 % 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: 0.46 (0.27), residues: 1011 helix: 1.87 (0.27), residues: 393 sheet: -0.65 (0.36), residues: 219 loop : -0.66 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.018 0.001 PHE B 235 TYR 0.014 0.001 TYR N 80 ARG 0.002 0.000 ARG N 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.968 Fit side-chains REVERT: A 252 ASP cc_start: 0.8297 (t0) cc_final: 0.7955 (t0) REVERT: B 156 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8236 (mt0) REVERT: B 175 GLN cc_start: 0.7741 (pt0) cc_final: 0.7117 (mt0) REVERT: B 188 MET cc_start: 0.8252 (mmm) cc_final: 0.7856 (mmm) REVERT: B 321 THR cc_start: 0.7770 (p) cc_final: 0.7444 (p) REVERT: R 52 VAL cc_start: 0.7368 (t) cc_final: 0.6921 (p) REVERT: R 317 LEU cc_start: 0.7883 (mm) cc_final: 0.7163 (pp) outliers start: 22 outliers final: 19 residues processed: 140 average time/residue: 0.1576 time to fit residues: 32.1091 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115377 restraints weight = 10835.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117646 restraints weight = 7246.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119226 restraints weight = 5519.692| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8008 Z= 0.158 Angle : 0.553 9.715 10887 Z= 0.278 Chirality : 0.041 0.240 1258 Planarity : 0.004 0.056 1394 Dihedral : 4.640 64.073 1132 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.45 % Allowed : 17.16 % Favored : 80.39 % 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: 0.49 (0.27), residues: 1011 helix: 1.93 (0.27), residues: 393 sheet: -0.60 (0.36), residues: 214 loop : -0.71 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.018 0.001 PHE B 235 TYR 0.014 0.001 TYR N 80 ARG 0.005 0.000 ARG R 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.07 seconds wall clock time: 33 minutes 5.43 seconds (1985.43 seconds total)