Starting phenix.real_space_refine on Thu Sep 26 19:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/09_2024/7s0f_24789_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/09_2024/7s0f_24789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/09_2024/7s0f_24789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/09_2024/7s0f_24789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/09_2024/7s0f_24789_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/09_2024/7s0f_24789_trim.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.053 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 52 5.16 5 C 4461 2.51 5 N 1192 2.21 5 O 1293 1.98 5 H 6887 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13885 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4273 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5098 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3540 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 959 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.22, per 1000 atoms: 0.52 Number of scatterers: 13885 At special positions: 0 Unit cell: (85.88, 98.762, 132.041, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1293 8.00 N 1192 7.00 C 4461 6.00 H 6887 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 199 " distance=2.03 Simple disulfide: pdb=" SG CYS R 192 " - pdb=" SG CYS R 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 46.9% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'R' and resid 46 through 69 removed outlier: 3.985A pdb=" N LEU R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 105 removed outlier: 3.783A pdb=" N PHE R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 109 through 145 removed outlier: 4.087A pdb=" N LEU R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS R 133 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 154 through 179 removed outlier: 4.144A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 189 through 195 Processing helix chain 'R' and resid 204 through 216 Processing helix chain 'R' and resid 216 through 239 Processing helix chain 'R' and resid 284 through 316 removed outlier: 3.523A pdb=" N LEU R 289 " --> pdb=" O GLU R 285 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 305 - end of helix removed outlier: 3.617A pdb=" N VAL R 309 " --> pdb=" O PRO R 305 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 311 " --> pdb=" O PHE R 307 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE R 315 " --> pdb=" O ILE R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 344 removed outlier: 3.646A pdb=" N VAL R 326 " --> pdb=" O ASP R 322 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER R 336 " --> pdb=" O GLY R 332 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA R 337 " --> pdb=" O TYR R 333 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 346 through 356 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.921A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.664A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.530A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.564A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.450A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.841A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.997A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.533A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.516A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.538A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.586A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.870A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1092 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: 5.00 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6859 1.03 - 1.23: 30 1.23 - 1.42: 3002 1.42 - 1.62: 4062 1.62 - 1.81: 72 Bond restraints: 14025 Sorted by residual: bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.437 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.417 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.491 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" CAE 5FW R 401 " pdb=" CAH 5FW R 401 " ideal model delta sigma weight residual 1.515 1.546 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" CAG 5FW R 401 " pdb=" CAJ 5FW R 401 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 14020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 24021 1.09 - 2.19: 1201 2.19 - 3.28: 25 3.28 - 4.38: 20 4.38 - 5.47: 1 Bond angle restraints: 25268 Sorted by residual: angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 109.05 5.47 3.00e+00 1.11e-01 3.33e+00 angle pdb=" C LEU R 175 " pdb=" CA LEU R 175 " pdb=" CB LEU R 175 " ideal model delta sigma weight residual 113.49 110.32 3.17 1.82e+00 3.02e-01 3.04e+00 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 116.66 -3.06 1.90e+00 2.77e-01 2.60e+00 angle pdb=" C GLN B 9 " pdb=" N GLU B 10 " pdb=" CA GLU B 10 " ideal model delta sigma weight residual 120.28 118.02 2.26 1.44e+00 4.82e-01 2.47e+00 angle pdb=" C HIS A 188 " pdb=" N PHE A 189 " pdb=" CA PHE A 189 " ideal model delta sigma weight residual 121.85 119.23 2.62 1.77e+00 3.19e-01 2.19e+00 ... (remaining 25263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 5990 16.39 - 32.78: 438 32.78 - 49.17: 123 49.17 - 65.56: 36 65.56 - 81.95: 11 Dihedral angle restraints: 6598 sinusoidal: 3503 harmonic: 3095 Sorted by residual: dihedral pdb=" CA LYS B 127 " pdb=" C LYS B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR B 128 " pdb=" C THR B 128 " pdb=" N ARG B 129 " pdb=" CA ARG B 129 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP A 193 " pdb=" CB ASP A 193 " pdb=" CG ASP A 193 " pdb=" OD1 ASP A 193 " ideal model delta sinusoidal sigma weight residual -30.00 -84.11 54.11 1 2.00e+01 2.50e-03 9.93e+00 ... (remaining 6595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 975 0.058 - 0.115: 120 0.115 - 0.173: 13 0.173 - 0.231: 0 0.231 - 0.289: 1 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.58 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1106 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 218 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO R 219 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 219 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 219 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 95 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO R 96 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 96 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 96 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO A 282 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.014 5.00e-02 4.00e+02 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 925 2.22 - 2.81: 29471 2.81 - 3.41: 36220 3.41 - 4.00: 48683 4.00 - 4.60: 75421 Nonbonded interactions: 190720 Sorted by model distance: nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.623 2.450 nonbonded pdb=" HE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 1.653 2.450 nonbonded pdb=" O LEU R 72 " pdb="HD22 ASN R 77 " model vdw 1.689 2.450 nonbonded pdb=" OE1 GLU A 298 " pdb=" H GLU A 298 " model vdw 1.713 2.450 nonbonded pdb=" O VAL R 160 " pdb=" HG1 THR R 164 " model vdw 1.723 2.450 ... (remaining 190715 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: 0.860 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: 0.330 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 0.084 7138 Z= 0.195 Angle : 0.449 5.474 9675 Z= 0.261 Chirality : 0.039 0.289 1109 Planarity : 0.002 0.030 1223 Dihedral : 13.976 81.945 2550 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.74 % Allowed : 13.50 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 880 helix: -0.02 (0.24), residues: 380 sheet: -1.28 (0.32), residues: 181 loop : -2.36 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.006 0.001 TYR B 105 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 ARG cc_start: 0.6946 (ttm110) cc_final: 0.6077 (ttt-90) REVERT: R 233 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6728 (mm-30) REVERT: R 236 GLU cc_start: 0.7471 (tt0) cc_final: 0.7086 (tt0) REVERT: R 240 LYS cc_start: 0.6338 (mmtt) cc_final: 0.5972 (mmtp) REVERT: B 18 ILE cc_start: 0.7565 (mt) cc_final: 0.7319 (mt) REVERT: B 42 ARG cc_start: 0.7522 (mmm160) cc_final: 0.7281 (tpt-90) REVERT: B 172 GLU cc_start: 0.7788 (tt0) cc_final: 0.7569 (tt0) REVERT: B 226 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 258 ASP cc_start: 0.7932 (t0) cc_final: 0.7731 (t0) REVERT: B 331 SER cc_start: 0.9120 (t) cc_final: 0.8665 (t) REVERT: B 333 ASP cc_start: 0.7904 (p0) cc_final: 0.7688 (p0) REVERT: A 17 LYS cc_start: 0.7205 (mtpp) cc_final: 0.6967 (mtmm) REVERT: A 29 LYS cc_start: 0.8309 (tttt) cc_final: 0.7988 (tmtm) REVERT: A 205 ARG cc_start: 0.7033 (mtm110) cc_final: 0.6689 (tmm-80) REVERT: A 230 TYR cc_start: 0.8963 (p90) cc_final: 0.8572 (p90) REVERT: A 247 MET cc_start: 0.8194 (mtt) cc_final: 0.7970 (mmm) REVERT: A 248 LYS cc_start: 0.7490 (mttp) cc_final: 0.7043 (mttt) REVERT: A 251 ASP cc_start: 0.7494 (t0) cc_final: 0.7233 (t0) REVERT: A 257 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8537 (ptmt) REVERT: A 330 LYS cc_start: 0.7173 (mttt) cc_final: 0.6791 (mtmm) REVERT: G 47 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7348 (mt-10) REVERT: G 58 GLU cc_start: 0.7553 (mp0) cc_final: 0.7352 (mp0) REVERT: G 64 LYS cc_start: 0.6833 (mmmt) cc_final: 0.6404 (mmmm) outliers start: 13 outliers final: 7 residues processed: 254 average time/residue: 1.8925 time to fit residues: 513.0931 Evaluate side-chains 193 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 238 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 329 ASN R 339 ASN B 36 ASN B 239 ASN A 52 GLN A 304 GLN A 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7138 Z= 0.175 Angle : 0.459 4.608 9675 Z= 0.253 Chirality : 0.039 0.137 1109 Planarity : 0.003 0.039 1223 Dihedral : 5.219 56.710 978 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.67 % Allowed : 22.46 % Favored : 74.87 % 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: 880 helix: 1.32 (0.26), residues: 382 sheet: -0.77 (0.35), residues: 176 loop : -1.85 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.010 0.001 PHE A 189 TYR 0.007 0.001 TYR R 207 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: R 117 TRP cc_start: 0.8221 (t60) cc_final: 0.7923 (t60) REVERT: R 223 MET cc_start: 0.8186 (mtp) cc_final: 0.7981 (mtp) REVERT: R 233 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6639 (mm-30) REVERT: R 236 GLU cc_start: 0.7393 (tt0) cc_final: 0.7029 (tt0) REVERT: B 18 ILE cc_start: 0.7558 (mt) cc_final: 0.7288 (mt) REVERT: B 42 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7114 (tpt-90) REVERT: B 219 ARG cc_start: 0.7783 (mmt90) cc_final: 0.7507 (mtt-85) REVERT: B 226 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7531 (mt-10) REVERT: B 260 GLU cc_start: 0.6907 (tt0) cc_final: 0.6704 (tt0) REVERT: B 331 SER cc_start: 0.9188 (t) cc_final: 0.8476 (t) REVERT: B 333 ASP cc_start: 0.7791 (p0) cc_final: 0.7536 (p0) REVERT: A 17 LYS cc_start: 0.7265 (mtpp) cc_final: 0.6960 (mtmm) REVERT: A 29 LYS cc_start: 0.8365 (tttt) cc_final: 0.8113 (tptm) REVERT: A 205 ARG cc_start: 0.7101 (mtm110) cc_final: 0.6746 (tmm-80) REVERT: A 230 TYR cc_start: 0.8966 (p90) cc_final: 0.8613 (p90) REVERT: A 247 MET cc_start: 0.8240 (mtt) cc_final: 0.7952 (mmm) REVERT: A 248 LYS cc_start: 0.7570 (mttp) cc_final: 0.7138 (mttt) REVERT: A 257 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8456 (ptmt) REVERT: A 273 LEU cc_start: 0.7170 (tp) cc_final: 0.6941 (tp) REVERT: A 330 LYS cc_start: 0.7163 (mttt) cc_final: 0.6757 (mtmm) REVERT: G 28 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8066 (pp) REVERT: G 47 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7446 (mt-10) REVERT: G 58 GLU cc_start: 0.7544 (mp0) cc_final: 0.7307 (mp0) REVERT: G 64 LYS cc_start: 0.6832 (mmmt) cc_final: 0.6578 (mmmt) outliers start: 20 outliers final: 8 residues processed: 208 average time/residue: 1.9257 time to fit residues: 428.3431 Evaluate side-chains 203 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN B 35 ASN B 239 ASN A 52 GLN A 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7138 Z= 0.191 Angle : 0.454 3.994 9675 Z= 0.249 Chirality : 0.038 0.138 1109 Planarity : 0.003 0.044 1223 Dihedral : 4.392 43.247 972 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.39 % Favored : 97.50 % Rotamer: Outliers : 3.61 % Allowed : 23.26 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 880 helix: 1.98 (0.27), residues: 383 sheet: -0.58 (0.36), residues: 171 loop : -1.73 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.009 0.001 TYR R 207 ARG 0.004 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: R 117 TRP cc_start: 0.8213 (t60) cc_final: 0.7919 (t60) REVERT: R 223 MET cc_start: 0.8202 (mtp) cc_final: 0.7977 (mtp) REVERT: R 233 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6603 (mm-30) REVERT: R 236 GLU cc_start: 0.7371 (tt0) cc_final: 0.6979 (tt0) REVERT: B 18 ILE cc_start: 0.7570 (mt) cc_final: 0.7345 (mt) REVERT: B 226 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 331 SER cc_start: 0.9197 (t) cc_final: 0.8509 (t) REVERT: B 333 ASP cc_start: 0.7858 (p0) cc_final: 0.7582 (p0) REVERT: A 17 LYS cc_start: 0.7272 (mtpp) cc_final: 0.6970 (mtmm) REVERT: A 29 LYS cc_start: 0.8386 (tttt) cc_final: 0.8183 (tptm) REVERT: A 205 ARG cc_start: 0.7140 (mtm110) cc_final: 0.6798 (tmm-80) REVERT: A 230 TYR cc_start: 0.8995 (p90) cc_final: 0.8669 (p90) REVERT: A 247 MET cc_start: 0.8265 (mtt) cc_final: 0.7982 (mmm) REVERT: A 248 LYS cc_start: 0.7529 (mttp) cc_final: 0.7117 (mttt) REVERT: A 257 LYS cc_start: 0.8693 (ptpp) cc_final: 0.8373 (ptmt) REVERT: A 273 LEU cc_start: 0.7166 (tp) cc_final: 0.6956 (tp) REVERT: A 330 LYS cc_start: 0.7173 (mttt) cc_final: 0.6769 (mtmm) REVERT: G 28 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8149 (pp) REVERT: G 47 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7479 (mt-10) REVERT: G 58 GLU cc_start: 0.7551 (mp0) cc_final: 0.7302 (mp0) REVERT: G 64 LYS cc_start: 0.6732 (mmmt) cc_final: 0.6482 (mmmt) outliers start: 27 outliers final: 12 residues processed: 212 average time/residue: 1.7661 time to fit residues: 402.0414 Evaluate side-chains 206 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 77 ASN R 339 ASN B 239 ASN A 52 GLN A 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7138 Z= 0.180 Angle : 0.451 3.881 9675 Z= 0.246 Chirality : 0.038 0.139 1109 Planarity : 0.003 0.044 1223 Dihedral : 4.319 40.031 972 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.27 % Favored : 97.61 % Rotamer: Outliers : 3.48 % Allowed : 24.20 % Favored : 72.33 % 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: 0.52 (0.29), residues: 880 helix: 2.29 (0.27), residues: 383 sheet: -0.47 (0.36), residues: 171 loop : -1.63 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE A 189 TYR 0.009 0.001 TYR R 207 ARG 0.003 0.000 ARG R 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: R 117 TRP cc_start: 0.8220 (t60) cc_final: 0.7931 (t60) REVERT: R 223 MET cc_start: 0.8220 (mtp) cc_final: 0.7919 (mtp) REVERT: R 233 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6603 (mm-30) REVERT: R 236 GLU cc_start: 0.7311 (tt0) cc_final: 0.6937 (tt0) REVERT: R 240 LYS cc_start: 0.6196 (mmtp) cc_final: 0.5930 (mmtp) REVERT: B 18 ILE cc_start: 0.7602 (mt) cc_final: 0.7387 (mt) REVERT: B 226 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7591 (mt-10) REVERT: B 331 SER cc_start: 0.9167 (t) cc_final: 0.8486 (t) REVERT: B 333 ASP cc_start: 0.7870 (p0) cc_final: 0.7609 (p0) REVERT: A 17 LYS cc_start: 0.7260 (mtpp) cc_final: 0.6957 (mtmm) REVERT: A 18 MET cc_start: 0.7445 (tpp) cc_final: 0.7078 (tpp) REVERT: A 29 LYS cc_start: 0.8382 (tttt) cc_final: 0.8128 (tptm) REVERT: A 53 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6964 (mmt) REVERT: A 209 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8169 (ttpp) REVERT: A 230 TYR cc_start: 0.9008 (p90) cc_final: 0.8681 (p90) REVERT: A 247 MET cc_start: 0.8271 (mtt) cc_final: 0.7990 (mmm) REVERT: A 248 LYS cc_start: 0.7588 (mttp) cc_final: 0.7192 (mttt) REVERT: A 257 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8483 (ptmt) REVERT: A 330 LYS cc_start: 0.7169 (mttt) cc_final: 0.6766 (mtmm) REVERT: G 28 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8181 (pp) REVERT: G 47 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7469 (mt-10) REVERT: G 58 GLU cc_start: 0.7549 (mp0) cc_final: 0.7290 (mp0) REVERT: G 64 LYS cc_start: 0.6712 (mmmt) cc_final: 0.6463 (mmmt) outliers start: 26 outliers final: 18 residues processed: 209 average time/residue: 1.8536 time to fit residues: 416.0617 Evaluate side-chains 207 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN B 239 ASN A 52 GLN A 256 ASN A 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7138 Z= 0.220 Angle : 0.462 4.322 9675 Z= 0.254 Chirality : 0.039 0.139 1109 Planarity : 0.003 0.045 1223 Dihedral : 4.337 36.249 972 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 4.28 % Allowed : 23.80 % Favored : 71.93 % 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: 0.67 (0.29), residues: 880 helix: 2.41 (0.27), residues: 383 sheet: -0.33 (0.37), residues: 169 loop : -1.58 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR R 207 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: R 117 TRP cc_start: 0.8292 (t60) cc_final: 0.7990 (t60) REVERT: R 181 TRP cc_start: 0.6273 (OUTLIER) cc_final: 0.5683 (m-10) REVERT: R 223 MET cc_start: 0.8287 (mtp) cc_final: 0.7998 (mtp) REVERT: R 233 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6574 (mm-30) REVERT: R 236 GLU cc_start: 0.7256 (tt0) cc_final: 0.6883 (tt0) REVERT: B 226 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 258 ASP cc_start: 0.8046 (t0) cc_final: 0.7703 (t0) REVERT: B 331 SER cc_start: 0.9202 (t) cc_final: 0.8567 (t) REVERT: B 333 ASP cc_start: 0.7940 (p0) cc_final: 0.7685 (p0) REVERT: A 17 LYS cc_start: 0.7283 (mtpp) cc_final: 0.6976 (mtmm) REVERT: A 18 MET cc_start: 0.7414 (tpp) cc_final: 0.7067 (tpp) REVERT: A 53 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7000 (mmt) REVERT: A 247 MET cc_start: 0.8257 (mtt) cc_final: 0.8034 (mmm) REVERT: A 248 LYS cc_start: 0.7514 (mttp) cc_final: 0.7112 (mttt) REVERT: A 257 LYS cc_start: 0.8771 (ptpp) cc_final: 0.8463 (ptmt) REVERT: A 314 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6713 (mmmm) REVERT: A 330 LYS cc_start: 0.7175 (mttt) cc_final: 0.6774 (mtmm) REVERT: G 28 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8175 (pp) REVERT: G 47 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7521 (mt-10) REVERT: G 58 GLU cc_start: 0.7553 (mp0) cc_final: 0.7264 (mp0) outliers start: 32 outliers final: 19 residues processed: 208 average time/residue: 1.7875 time to fit residues: 398.2576 Evaluate side-chains 207 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 181 TRP Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 GLN R 339 ASN B 239 ASN A 256 ASN A 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 7138 Z= 0.482 Angle : 0.592 6.387 9675 Z= 0.329 Chirality : 0.044 0.154 1109 Planarity : 0.004 0.049 1223 Dihedral : 4.785 37.345 972 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.11 % Rotamer: Outliers : 4.68 % Allowed : 23.66 % Favored : 71.66 % 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: 0.22 (0.28), residues: 880 helix: 1.83 (0.26), residues: 385 sheet: -0.36 (0.36), residues: 177 loop : -1.70 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 330 HIS 0.004 0.002 HIS A 322 PHE 0.022 0.002 PHE B 151 TYR 0.010 0.002 TYR R 193 ARG 0.004 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: R 181 TRP cc_start: 0.6341 (OUTLIER) cc_final: 0.5717 (m-10) REVERT: R 223 MET cc_start: 0.8372 (mtp) cc_final: 0.8066 (mtp) REVERT: R 233 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6535 (mm-30) REVERT: R 240 LYS cc_start: 0.6347 (mmtp) cc_final: 0.6142 (mmtp) REVERT: B 226 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 258 ASP cc_start: 0.8068 (t0) cc_final: 0.7866 (t70) REVERT: B 331 SER cc_start: 0.9254 (t) cc_final: 0.8805 (t) REVERT: B 333 ASP cc_start: 0.8161 (p0) cc_final: 0.7912 (p0) REVERT: A 17 LYS cc_start: 0.7298 (mtpp) cc_final: 0.6998 (mtmm) REVERT: A 18 MET cc_start: 0.7420 (tpp) cc_final: 0.7048 (tpp) REVERT: A 33 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6863 (mm-30) REVERT: A 230 TYR cc_start: 0.9035 (p90) cc_final: 0.8749 (p90) REVERT: A 248 LYS cc_start: 0.7594 (mttp) cc_final: 0.7210 (mttt) REVERT: A 257 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8493 (ptmt) REVERT: A 314 LYS cc_start: 0.7098 (mmtt) cc_final: 0.6814 (mmmm) REVERT: A 330 LYS cc_start: 0.7170 (mttt) cc_final: 0.6806 (mtmm) REVERT: G 28 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8171 (pp) REVERT: G 29 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7304 (mttm) REVERT: G 47 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7609 (mt-10) REVERT: G 58 GLU cc_start: 0.7548 (mp0) cc_final: 0.7183 (mp0) outliers start: 35 outliers final: 24 residues processed: 210 average time/residue: 1.8581 time to fit residues: 419.3370 Evaluate side-chains 212 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 181 TRP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 311 ILE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 64 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN A 269 ASN A 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7138 Z= 0.180 Angle : 0.475 5.035 9675 Z= 0.259 Chirality : 0.039 0.144 1109 Planarity : 0.003 0.044 1223 Dihedral : 4.491 34.640 972 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.39 % Favored : 97.50 % Rotamer: Outliers : 3.88 % Allowed : 25.67 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 880 helix: 2.30 (0.27), residues: 384 sheet: -0.32 (0.36), residues: 169 loop : -1.55 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.001 TYR A 302 ARG 0.002 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: R 223 MET cc_start: 0.8336 (mtp) cc_final: 0.8119 (mtp) REVERT: R 233 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6489 (mm-30) REVERT: R 240 LYS cc_start: 0.6282 (mmtp) cc_final: 0.6079 (mmtp) REVERT: B 22 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7530 (mtm-85) REVERT: B 226 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7580 (mt-10) REVERT: B 331 SER cc_start: 0.9106 (t) cc_final: 0.8530 (t) REVERT: B 333 ASP cc_start: 0.7912 (p0) cc_final: 0.7680 (p0) REVERT: A 17 LYS cc_start: 0.7269 (mtpp) cc_final: 0.6959 (mtmm) REVERT: A 18 MET cc_start: 0.7421 (tpp) cc_final: 0.7051 (tpp) REVERT: A 33 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6712 (mm-30) REVERT: A 209 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8366 (ttpp) REVERT: A 248 LYS cc_start: 0.7682 (mttp) cc_final: 0.7296 (mttt) REVERT: A 257 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8466 (ptmt) REVERT: A 314 LYS cc_start: 0.7079 (mmtt) cc_final: 0.6789 (mmmm) REVERT: A 330 LYS cc_start: 0.7198 (mttt) cc_final: 0.6792 (mtmm) REVERT: G 28 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8160 (pp) REVERT: G 47 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7549 (mt-10) REVERT: G 58 GLU cc_start: 0.7521 (mp0) cc_final: 0.7192 (mp0) outliers start: 29 outliers final: 20 residues processed: 202 average time/residue: 1.7285 time to fit residues: 376.4061 Evaluate side-chains 203 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7138 Z= 0.188 Angle : 0.482 5.270 9675 Z= 0.262 Chirality : 0.039 0.140 1109 Planarity : 0.003 0.043 1223 Dihedral : 4.415 33.849 972 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 2.81 % Allowed : 26.47 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 880 helix: 2.41 (0.27), residues: 385 sheet: -0.25 (0.37), residues: 169 loop : -1.50 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 292 TYR 0.007 0.001 TYR R 207 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: R 223 MET cc_start: 0.8310 (mtp) cc_final: 0.7981 (mtp) REVERT: R 233 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6550 (mm-30) REVERT: R 240 LYS cc_start: 0.6270 (mmtp) cc_final: 0.6068 (mmtp) REVERT: B 226 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 331 SER cc_start: 0.9113 (t) cc_final: 0.8534 (t) REVERT: B 333 ASP cc_start: 0.7957 (p0) cc_final: 0.7616 (p0) REVERT: B 334 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8351 (p) REVERT: A 17 LYS cc_start: 0.7269 (mtpp) cc_final: 0.6948 (mtmm) REVERT: A 18 MET cc_start: 0.7416 (tpp) cc_final: 0.7042 (tpp) REVERT: A 33 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6712 (mm-30) REVERT: A 248 LYS cc_start: 0.7696 (mttp) cc_final: 0.7307 (mttt) REVERT: A 257 LYS cc_start: 0.8756 (ptpp) cc_final: 0.8454 (ptmt) REVERT: A 314 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6797 (mmmm) REVERT: A 330 LYS cc_start: 0.7191 (mttt) cc_final: 0.6786 (mtmm) REVERT: G 47 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7546 (mt-10) REVERT: G 58 GLU cc_start: 0.7525 (mp0) cc_final: 0.7204 (mp0) outliers start: 21 outliers final: 17 residues processed: 194 average time/residue: 1.7159 time to fit residues: 358.4837 Evaluate side-chains 201 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 77 ASN B 239 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7138 Z= 0.253 Angle : 0.496 5.294 9675 Z= 0.270 Chirality : 0.039 0.139 1109 Planarity : 0.003 0.045 1223 Dihedral : 4.447 33.863 972 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 3.34 % Allowed : 26.60 % Favored : 70.05 % 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: 0.70 (0.29), residues: 880 helix: 2.34 (0.26), residues: 385 sheet: -0.23 (0.37), residues: 169 loop : -1.52 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 117 HIS 0.002 0.001 HIS B 142 PHE 0.013 0.001 PHE B 151 TYR 0.008 0.001 TYR R 207 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: R 223 MET cc_start: 0.8387 (mtp) cc_final: 0.8068 (mtp) REVERT: R 233 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6509 (mm-30) REVERT: R 240 LYS cc_start: 0.6286 (mmtp) cc_final: 0.6083 (mmtp) REVERT: B 226 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 331 SER cc_start: 0.9165 (t) cc_final: 0.8549 (t) REVERT: B 333 ASP cc_start: 0.7973 (p0) cc_final: 0.7731 (p0) REVERT: A 17 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6961 (mtmm) REVERT: A 18 MET cc_start: 0.7419 (tpp) cc_final: 0.7044 (tpp) REVERT: A 33 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6795 (mm-30) REVERT: A 248 LYS cc_start: 0.7678 (mttp) cc_final: 0.7342 (mttp) REVERT: A 257 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8445 (ptmt) REVERT: A 314 LYS cc_start: 0.7273 (mmtt) cc_final: 0.6987 (mmmm) REVERT: A 330 LYS cc_start: 0.7200 (mttt) cc_final: 0.6824 (mtmm) REVERT: G 47 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7568 (mt-10) REVERT: G 58 GLU cc_start: 0.7519 (mp0) cc_final: 0.7198 (mp0) outliers start: 25 outliers final: 21 residues processed: 199 average time/residue: 1.6836 time to fit residues: 360.8097 Evaluate side-chains 207 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 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 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7138 Z= 0.207 Angle : 0.485 5.581 9675 Z= 0.263 Chirality : 0.039 0.140 1109 Planarity : 0.004 0.078 1223 Dihedral : 4.384 33.257 972 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.39 % Rotamer: Outliers : 2.94 % Allowed : 27.14 % Favored : 69.92 % 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: 0.83 (0.29), residues: 880 helix: 2.45 (0.26), residues: 385 sheet: -0.16 (0.37), residues: 169 loop : -1.44 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 117 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 292 TYR 0.007 0.001 TYR R 207 ARG 0.011 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: R 223 MET cc_start: 0.8365 (mtp) cc_final: 0.8050 (mtp) REVERT: R 233 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6483 (mm-30) REVERT: R 236 GLU cc_start: 0.7318 (tt0) cc_final: 0.6975 (tt0) REVERT: R 240 LYS cc_start: 0.6282 (mmtp) cc_final: 0.6076 (mmtp) REVERT: B 226 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 331 SER cc_start: 0.9115 (t) cc_final: 0.8524 (t) REVERT: B 333 ASP cc_start: 0.7937 (p0) cc_final: 0.7608 (p0) REVERT: B 334 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 17 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6952 (mtmm) REVERT: A 18 MET cc_start: 0.7425 (tpp) cc_final: 0.7045 (tpp) REVERT: A 33 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6732 (mm-30) REVERT: A 248 LYS cc_start: 0.7670 (mttp) cc_final: 0.7338 (mttp) REVERT: A 257 LYS cc_start: 0.8748 (ptpp) cc_final: 0.8432 (ptmt) REVERT: A 314 LYS cc_start: 0.7265 (mmtt) cc_final: 0.6977 (mmmm) REVERT: A 330 LYS cc_start: 0.7195 (mttt) cc_final: 0.6816 (mtmm) REVERT: G 47 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7557 (mt-10) REVERT: G 58 GLU cc_start: 0.7518 (mp0) cc_final: 0.7202 (mp0) outliers start: 22 outliers final: 19 residues processed: 195 average time/residue: 1.7036 time to fit residues: 357.8051 Evaluate side-chains 201 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102908 restraints weight = 23363.620| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.23 r_work: 0.2949 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7138 Z= 0.238 Angle : 0.494 5.437 9675 Z= 0.269 Chirality : 0.039 0.139 1109 Planarity : 0.004 0.072 1223 Dihedral : 4.403 32.859 972 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 3.34 % Allowed : 26.60 % Favored : 70.05 % 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: 0.77 (0.29), residues: 880 helix: 2.40 (0.26), residues: 385 sheet: -0.18 (0.37), residues: 170 loop : -1.49 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 117 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 151 TYR 0.007 0.001 TYR R 207 ARG 0.013 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7050.08 seconds wall clock time: 124 minutes 5.52 seconds (7445.52 seconds total)