Starting phenix.real_space_refine on Fri Aug 22 19:51:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frp_29404/08_2025/8frp_29404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frp_29404/08_2025/8frp_29404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8frp_29404/08_2025/8frp_29404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frp_29404/08_2025/8frp_29404.map" model { file = "/net/cci-nas-00/data/ceres_data/8frp_29404/08_2025/8frp_29404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frp_29404/08_2025/8frp_29404.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4861 2.51 5 N 1280 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7488 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1769 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1869 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 2 Time building chain proxies: 1.37, per 1000 atoms: 0.18 Number of scatterers: 7488 At special positions: 0 Unit cell: (68.475, 108.075, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1311 8.00 N 1280 7.00 C 4861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.52 Conformation dependent library (CDL) restraints added in 252.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 68.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.782A pdb=" N ILE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.506A pdb=" N GLN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 162 removed outlier: 3.804A pdb=" N ALA A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 4.268A pdb=" N GLY A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 235 through 242 removed outlier: 3.537A pdb=" N VAL A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.574A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.656A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.199A pdb=" N VAL B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 180 through 194 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.563A pdb=" N THR B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.523A pdb=" N UNK C 9 " --> pdb=" O UNK C 5 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK C 17 " --> pdb=" O UNK C 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 36 removed outlier: 3.722A pdb=" N ARG F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 55 through 82 removed outlier: 4.040A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 102 through 119 Processing helix chain 'F' and resid 119 through 132 Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.515A pdb=" N LEU F 251 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 262 through 274 Processing helix chain 'F' and resid 277 through 289 removed outlier: 3.566A pdb=" N ALA F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 288 " --> pdb=" O MET F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 325 removed outlier: 3.508A pdb=" N ALA F 305 " --> pdb=" O ARG F 301 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 308 " --> pdb=" O PRO F 304 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 348 removed outlier: 3.726A pdb=" N ALA F 335 " --> pdb=" O TRP F 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 Processing helix chain 'G' and resid 50 through 58 Processing helix chain 'G' and resid 58 through 85 Proline residue: G 68 - end of helix removed outlier: 3.565A pdb=" N LEU G 72 " --> pdb=" O PRO G 68 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 93 removed outlier: 4.023A pdb=" N VAL G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 123 removed outlier: 3.519A pdb=" N SER G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 135 removed outlier: 3.753A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 261 removed outlier: 3.662A pdb=" N TYR G 260 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 276 removed outlier: 3.556A pdb=" N ALA G 270 " --> pdb=" O THR G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 294 Processing helix chain 'G' and resid 300 through 327 removed outlier: 3.720A pdb=" N LEU G 327 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 354 removed outlier: 4.030A pdb=" N PHE G 336 " --> pdb=" O SER G 332 " (cutoff:3.500A) Proline residue: G 340 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 35 removed outlier: 6.505A pdb=" N LYS A 19 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 28 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 17 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 30 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS A 15 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 32 " --> pdb=" O CYS A 13 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N CYS A 13 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET A 34 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR A 11 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 17 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 65 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.662A pdb=" N ILE A 39 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR A 216 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY A 41 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL A 218 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 43 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 215 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 226 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 217 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 24 through 35 removed outlier: 5.998A pdb=" N VAL B 26 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASN B 20 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS B 28 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 18 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL B 30 " --> pdb=" O HIS B 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 16 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 17 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS B 65 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 91 removed outlier: 6.747A pdb=" N ILE B 39 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR B 216 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 41 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 218 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 43 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU B 226 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1353 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: 0.69 Time building geometry restraints manager: 0.65 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: 2398 1.34 - 1.46: 1039 1.46 - 1.57: 4126 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 7629 Sorted by residual: bond pdb=" CA ASN B 20 " pdb=" CB ASN B 20 " ideal model delta sigma weight residual 1.534 1.556 -0.022 2.33e-02 1.84e+03 8.96e-01 bond pdb=" CA ASN B 72 " pdb=" CB ASN B 72 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.70e-01 bond pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.05e-01 bond pdb=" CB ASN B 20 " pdb=" CG ASN B 20 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.19e-01 bond pdb=" CB GLU A 220 " pdb=" CG GLU A 220 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.42e-01 ... (remaining 7624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 10139 1.26 - 2.52: 138 2.52 - 3.77: 27 3.77 - 5.03: 14 5.03 - 6.29: 3 Bond angle restraints: 10321 Sorted by residual: angle pdb=" C ASP B 71 " pdb=" N ASN B 72 " pdb=" CA ASN B 72 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 angle pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " pdb=" CG GLU A 220 " ideal model delta sigma weight residual 114.10 118.59 -4.49 2.00e+00 2.50e-01 5.04e+00 angle pdb=" CA ASN B 72 " pdb=" CB ASN B 72 " pdb=" CG ASN B 72 " ideal model delta sigma weight residual 112.60 114.61 -2.01 1.00e+00 1.00e+00 4.02e+00 angle pdb=" C SER A 219 " pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta sigma weight residual 121.54 125.34 -3.80 1.91e+00 2.74e-01 3.96e+00 angle pdb=" C ASP A 71 " pdb=" N ASN A 72 " pdb=" CA ASN A 72 " ideal model delta sigma weight residual 122.07 124.40 -2.33 1.43e+00 4.89e-01 2.65e+00 ... (remaining 10316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4089 17.52 - 35.05: 403 35.05 - 52.57: 61 52.57 - 70.09: 9 70.09 - 87.62: 5 Dihedral angle restraints: 4567 sinusoidal: 1817 harmonic: 2750 Sorted by residual: dihedral pdb=" CA ASP B 246 " pdb=" CB ASP B 246 " pdb=" CG ASP B 246 " pdb=" OD1 ASP B 246 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA PHE A 98 " pdb=" C PHE A 98 " pdb=" N ARG A 99 " pdb=" CA ARG A 99 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 82 " pdb=" CG GLU A 82 " pdb=" CD GLU A 82 " pdb=" OE1 GLU A 82 " ideal model delta sinusoidal sigma weight residual 0.00 -87.62 87.62 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 4564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 691 0.026 - 0.053: 310 0.053 - 0.079: 127 0.079 - 0.105: 55 0.105 - 0.131: 17 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CA ASN B 72 " pdb=" N ASN B 72 " pdb=" C ASN B 72 " pdb=" CB ASN B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE A 14 " pdb=" N ILE A 14 " pdb=" C ILE A 14 " pdb=" CB ILE A 14 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 1197 not shown) Planarity restraints: 1289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 293 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO F 294 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 294 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 294 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 303 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO F 304 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 304 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 304 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 275 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO F 276 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 276 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 276 " -0.020 5.00e-02 4.00e+02 ... (remaining 1286 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2016 2.81 - 3.33: 7160 3.33 - 3.86: 11934 3.86 - 4.38: 14690 4.38 - 4.90: 25187 Nonbonded interactions: 60987 Sorted by model distance: nonbonded pdb=" NZ LYS G 265 " pdb=" O TYR G 329 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU F 268 " pdb=" NE ARG F 272 " model vdw 2.321 3.120 nonbonded pdb=" O VAL F 87 " pdb=" OG SER F 91 " model vdw 2.397 3.040 nonbonded pdb=" O ILE F 63 " pdb=" N GLY F 67 " model vdw 2.436 3.120 nonbonded pdb=" OD1 ASN A 190 " pdb=" NH2 ARG A 194 " model vdw 2.451 3.120 ... (remaining 60982 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 247) selection = chain 'B' } 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: 1.900 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.002 0.024 7629 Z= 0.078 Angle : 0.429 6.290 10321 Z= 0.219 Chirality : 0.038 0.131 1200 Planarity : 0.004 0.046 1289 Dihedral : 13.741 87.618 2795 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.26), residues: 918 helix: -0.66 (0.20), residues: 561 sheet: 1.17 (0.69), residues: 68 loop : -1.06 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.005 0.001 TYR F 333 PHE 0.005 0.001 PHE F 109 TRP 0.005 0.001 TRP F 331 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00162 ( 7629) covalent geometry : angle 0.42893 (10321) hydrogen bonds : bond 0.24164 ( 458) hydrogen bonds : angle 8.19072 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8811 (m-80) cc_final: 0.8591 (m-10) REVERT: A 108 MET cc_start: 0.8311 (tpt) cc_final: 0.7867 (tpp) REVERT: A 202 ASP cc_start: 0.7998 (t0) cc_final: 0.7522 (t70) REVERT: B 202 ASP cc_start: 0.8171 (t0) cc_final: 0.7905 (t0) REVERT: B 243 LEU cc_start: 0.7814 (mt) cc_final: 0.7507 (mt) REVERT: F 300 TYR cc_start: 0.6933 (t80) cc_final: 0.5911 (t80) REVERT: G 255 ASN cc_start: 0.6596 (m-40) cc_final: 0.6033 (m-40) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.0720 time to fit residues: 34.9723 Evaluate side-chains 218 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 121 GLN A 214 HIS B 81 HIS B 214 HIS G 85 ASN G 128 ASN G 249 GLN G 268 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113109 restraints weight = 13333.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116611 restraints weight = 7392.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118695 restraints weight = 4905.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120472 restraints weight = 3748.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121459 restraints weight = 3075.356| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7629 Z= 0.164 Angle : 0.696 10.743 10321 Z= 0.356 Chirality : 0.046 0.184 1200 Planarity : 0.005 0.046 1289 Dihedral : 3.909 14.808 1037 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.16 % Allowed : 16.31 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 918 helix: 0.70 (0.21), residues: 570 sheet: 1.90 (0.70), residues: 60 loop : -1.31 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 258 TYR 0.017 0.001 TYR G 64 PHE 0.023 0.002 PHE A 32 TRP 0.018 0.001 TRP G 57 HIS 0.006 0.001 HIS F 83 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7629) covalent geometry : angle 0.69624 (10321) hydrogen bonds : bond 0.05035 ( 458) hydrogen bonds : angle 5.03809 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8964 (m-80) cc_final: 0.8689 (m-10) REVERT: A 25 TRP cc_start: 0.8499 (m100) cc_final: 0.7994 (m100) REVERT: A 108 MET cc_start: 0.8137 (tpt) cc_final: 0.7826 (tpp) REVERT: A 217 ILE cc_start: 0.9217 (mm) cc_final: 0.8845 (tp) REVERT: B 111 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8689 (mm) REVERT: B 198 VAL cc_start: 0.9064 (t) cc_final: 0.8721 (m) REVERT: B 243 LEU cc_start: 0.7983 (mt) cc_final: 0.7581 (mt) REVERT: F 27 MET cc_start: 0.7932 (mtp) cc_final: 0.7500 (tmm) REVERT: F 120 MET cc_start: 0.8259 (mmm) cc_final: 0.7916 (mmm) outliers start: 25 outliers final: 15 residues processed: 255 average time/residue: 0.0636 time to fit residues: 22.3260 Evaluate side-chains 227 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 91 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN G 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109793 restraints weight = 13397.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113167 restraints weight = 7578.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115469 restraints weight = 5137.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116845 restraints weight = 3946.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117188 restraints weight = 3321.893| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7629 Z= 0.145 Angle : 0.636 9.617 10321 Z= 0.322 Chirality : 0.045 0.174 1200 Planarity : 0.005 0.048 1289 Dihedral : 3.943 14.485 1037 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.79 % Allowed : 19.97 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.27), residues: 918 helix: 1.15 (0.21), residues: 574 sheet: 1.65 (0.59), residues: 72 loop : -1.26 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 55 TYR 0.013 0.001 TYR F 80 PHE 0.022 0.002 PHE F 69 TRP 0.005 0.001 TRP G 57 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7629) covalent geometry : angle 0.63576 (10321) hydrogen bonds : bond 0.04308 ( 458) hydrogen bonds : angle 4.73334 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.8911 (t0) cc_final: 0.8685 (t0) REVERT: A 166 PHE cc_start: 0.8981 (m-80) cc_final: 0.8390 (m-10) REVERT: A 204 ASN cc_start: 0.8473 (t0) cc_final: 0.8233 (t0) REVERT: B 107 ILE cc_start: 0.9018 (mp) cc_final: 0.8695 (mp) REVERT: B 111 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8805 (mm) REVERT: F 27 MET cc_start: 0.8045 (mtp) cc_final: 0.7690 (tmm) REVERT: F 120 MET cc_start: 0.8263 (mmm) cc_final: 0.7889 (mmm) REVERT: F 271 TRP cc_start: 0.8880 (t-100) cc_final: 0.8481 (t-100) REVERT: F 289 LEU cc_start: 0.8730 (mt) cc_final: 0.8484 (mt) REVERT: G 253 PHE cc_start: 0.8645 (t80) cc_final: 0.7997 (t80) REVERT: G 254 MET cc_start: 0.8765 (mmm) cc_final: 0.8506 (mmm) REVERT: G 257 MET cc_start: 0.8971 (mtm) cc_final: 0.7517 (mtm) REVERT: G 337 VAL cc_start: 0.8931 (t) cc_final: 0.8679 (m) outliers start: 30 outliers final: 22 residues processed: 237 average time/residue: 0.0574 time to fit residues: 19.3604 Evaluate side-chains 219 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 319 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN G 85 ASN G 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107749 restraints weight = 14031.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111368 restraints weight = 7738.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113714 restraints weight = 5203.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115445 restraints weight = 4015.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116300 restraints weight = 3337.475| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7629 Z= 0.164 Angle : 0.658 9.569 10321 Z= 0.330 Chirality : 0.045 0.193 1200 Planarity : 0.004 0.049 1289 Dihedral : 3.986 14.849 1037 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.69 % Allowed : 19.97 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.27), residues: 918 helix: 1.23 (0.21), residues: 577 sheet: 1.71 (0.59), residues: 64 loop : -1.22 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 61 TYR 0.012 0.001 TYR F 80 PHE 0.014 0.001 PHE B 133 TRP 0.011 0.001 TRP F 271 HIS 0.004 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7629) covalent geometry : angle 0.65796 (10321) hydrogen bonds : bond 0.04085 ( 458) hydrogen bonds : angle 4.65074 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9046 (t0) cc_final: 0.8821 (t0) REVERT: A 108 MET cc_start: 0.8130 (tpt) cc_final: 0.7851 (tpp) REVERT: A 166 PHE cc_start: 0.9097 (m-80) cc_final: 0.8787 (m-10) REVERT: A 204 ASN cc_start: 0.8445 (t0) cc_final: 0.8126 (t0) REVERT: B 107 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 111 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8901 (mm) REVERT: F 27 MET cc_start: 0.8150 (mtp) cc_final: 0.7747 (tmm) REVERT: F 120 MET cc_start: 0.8185 (mmm) cc_final: 0.7944 (mmm) REVERT: F 123 TRP cc_start: 0.6968 (t60) cc_final: 0.6500 (t60) REVERT: F 271 TRP cc_start: 0.8776 (t-100) cc_final: 0.8543 (t-100) REVERT: G 266 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8980 (t) outliers start: 45 outliers final: 31 residues processed: 236 average time/residue: 0.0576 time to fit residues: 19.2981 Evaluate side-chains 227 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** 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 = 0.3605 r_free = 0.3605 target = 0.128664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103406 restraints weight = 14009.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106788 restraints weight = 7987.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109085 restraints weight = 5508.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110405 restraints weight = 4283.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111608 restraints weight = 3656.229| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7629 Z= 0.224 Angle : 0.690 9.269 10321 Z= 0.350 Chirality : 0.046 0.189 1200 Planarity : 0.005 0.052 1289 Dihedral : 4.052 16.143 1037 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 6.32 % Allowed : 20.73 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.27), residues: 918 helix: 1.22 (0.21), residues: 575 sheet: 1.22 (0.56), residues: 64 loop : -1.16 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 61 TYR 0.013 0.001 TYR F 6 PHE 0.016 0.002 PHE F 59 TRP 0.010 0.001 TRP G 99 HIS 0.004 0.001 HIS F 83 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 7629) covalent geometry : angle 0.68988 (10321) hydrogen bonds : bond 0.04157 ( 458) hydrogen bonds : angle 4.63707 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8562 (t0) cc_final: 0.8202 (t0) REVERT: B 33 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: F 120 MET cc_start: 0.8211 (mmm) cc_final: 0.7842 (mmm) REVERT: F 123 TRP cc_start: 0.6902 (t60) cc_final: 0.6637 (t60) REVERT: G 66 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8027 (tp) REVERT: G 67 LEU cc_start: 0.8289 (mt) cc_final: 0.7942 (mt) REVERT: G 254 MET cc_start: 0.8933 (mmm) cc_final: 0.8621 (mmm) outliers start: 50 outliers final: 39 residues processed: 218 average time/residue: 0.0585 time to fit residues: 17.8349 Evaluate side-chains 220 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.0030 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 85 ASN ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106962 restraints weight = 13944.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110396 restraints weight = 7737.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112665 restraints weight = 5229.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114259 restraints weight = 4042.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115211 restraints weight = 3373.462| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7629 Z= 0.134 Angle : 0.633 9.004 10321 Z= 0.315 Chirality : 0.045 0.181 1200 Planarity : 0.004 0.051 1289 Dihedral : 4.015 14.342 1037 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.55 % Allowed : 23.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 918 helix: 1.30 (0.21), residues: 575 sheet: 1.19 (0.59), residues: 64 loop : -1.15 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 61 TYR 0.016 0.001 TYR F 340 PHE 0.017 0.001 PHE G 52 TRP 0.008 0.001 TRP F 331 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7629) covalent geometry : angle 0.63312 (10321) hydrogen bonds : bond 0.03730 ( 458) hydrogen bonds : angle 4.48778 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8477 (t0) cc_final: 0.8211 (t0) REVERT: B 111 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8977 (mm) REVERT: B 202 ASP cc_start: 0.7714 (t0) cc_final: 0.7451 (t0) REVERT: G 254 MET cc_start: 0.8930 (mmm) cc_final: 0.8441 (mmm) outliers start: 36 outliers final: 23 residues processed: 227 average time/residue: 0.0790 time to fit residues: 25.2157 Evaluate side-chains 215 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 73 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN G 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105607 restraints weight = 13916.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109032 restraints weight = 7803.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111212 restraints weight = 5292.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112893 restraints weight = 4109.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113806 restraints weight = 3425.086| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7629 Z= 0.158 Angle : 0.661 10.770 10321 Z= 0.326 Chirality : 0.045 0.163 1200 Planarity : 0.005 0.108 1289 Dihedral : 3.994 14.763 1037 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.80 % Allowed : 25.41 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.28), residues: 918 helix: 1.33 (0.21), residues: 575 sheet: 1.12 (0.59), residues: 64 loop : -1.15 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 61 TYR 0.016 0.001 TYR F 340 PHE 0.025 0.001 PHE G 321 TRP 0.010 0.001 TRP F 271 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7629) covalent geometry : angle 0.66130 (10321) hydrogen bonds : bond 0.03729 ( 458) hydrogen bonds : angle 4.50132 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8498 (t0) cc_final: 0.8211 (t0) REVERT: B 33 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7617 (pp20) REVERT: B 62 ARG cc_start: 0.8297 (mmm160) cc_final: 0.8089 (mmm160) REVERT: B 111 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9006 (mm) REVERT: B 202 ASP cc_start: 0.7792 (t0) cc_final: 0.7533 (t0) REVERT: G 85 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8107 (t0) REVERT: G 253 PHE cc_start: 0.8687 (t80) cc_final: 0.8197 (t80) REVERT: G 254 MET cc_start: 0.8974 (mmm) cc_final: 0.8742 (mmm) REVERT: G 319 GLN cc_start: 0.8680 (pp30) cc_final: 0.8358 (pp30) REVERT: G 352 LEU cc_start: 0.8729 (mt) cc_final: 0.8245 (mt) outliers start: 38 outliers final: 28 residues processed: 218 average time/residue: 0.0795 time to fit residues: 24.2141 Evaluate side-chains 219 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN F 258 ASN G 85 ASN G 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106515 restraints weight = 14034.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109978 restraints weight = 7805.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112342 restraints weight = 5268.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113757 restraints weight = 4046.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114867 restraints weight = 3419.210| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7629 Z= 0.143 Angle : 0.674 12.440 10321 Z= 0.331 Chirality : 0.044 0.163 1200 Planarity : 0.004 0.052 1289 Dihedral : 3.912 14.581 1037 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.68 % Allowed : 25.54 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.28), residues: 918 helix: 1.40 (0.21), residues: 574 sheet: 0.97 (0.57), residues: 70 loop : -1.13 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 126 TYR 0.015 0.001 TYR F 340 PHE 0.013 0.001 PHE A 32 TRP 0.011 0.001 TRP F 271 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7629) covalent geometry : angle 0.67379 (10321) hydrogen bonds : bond 0.03622 ( 458) hydrogen bonds : angle 4.46387 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8479 (t0) cc_final: 0.8229 (t0) REVERT: B 62 ARG cc_start: 0.8296 (mmm160) cc_final: 0.7996 (mmp80) REVERT: F 252 PRO cc_start: 0.8168 (Cg_endo) cc_final: 0.7952 (Cg_exo) REVERT: F 271 TRP cc_start: 0.8810 (t-100) cc_final: 0.8300 (t-100) REVERT: G 85 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.7990 (t0) REVERT: G 253 PHE cc_start: 0.8680 (t80) cc_final: 0.8200 (t80) REVERT: G 352 LEU cc_start: 0.8727 (mt) cc_final: 0.8293 (mt) outliers start: 37 outliers final: 25 residues processed: 222 average time/residue: 0.0771 time to fit residues: 24.0426 Evaluate side-chains 219 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 chunk 86 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 258 ASN G 85 ASN G 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107008 restraints weight = 13894.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110474 restraints weight = 7812.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112835 restraints weight = 5285.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114266 restraints weight = 4064.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115348 restraints weight = 3432.690| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7629 Z= 0.145 Angle : 0.695 12.167 10321 Z= 0.341 Chirality : 0.045 0.169 1200 Planarity : 0.005 0.087 1289 Dihedral : 3.955 14.917 1037 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.30 % Allowed : 27.43 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.28), residues: 918 helix: 1.45 (0.21), residues: 574 sheet: 0.91 (0.57), residues: 70 loop : -1.16 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 61 TYR 0.018 0.001 TYR F 340 PHE 0.028 0.001 PHE G 321 TRP 0.011 0.001 TRP F 271 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7629) covalent geometry : angle 0.69516 (10321) hydrogen bonds : bond 0.03663 ( 458) hydrogen bonds : angle 4.49129 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8491 (t0) cc_final: 0.8253 (t0) REVERT: B 62 ARG cc_start: 0.8295 (mmm160) cc_final: 0.8002 (mmp80) REVERT: F 326 ASP cc_start: 0.6068 (t0) cc_final: 0.5833 (t0) REVERT: G 85 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8015 (t0) REVERT: G 87 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 253 PHE cc_start: 0.8679 (t80) cc_final: 0.8199 (t80) REVERT: G 254 MET cc_start: 0.8921 (mmm) cc_final: 0.8612 (mmm) outliers start: 34 outliers final: 28 residues processed: 219 average time/residue: 0.0785 time to fit residues: 24.0962 Evaluate side-chains 220 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 0.0070 chunk 1 optimal weight: 0.0670 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN B 214 HIS F 258 ASN G 85 ASN G 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107447 restraints weight = 13880.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110894 restraints weight = 7804.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113290 restraints weight = 5293.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114649 restraints weight = 4046.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115783 restraints weight = 3421.153| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7629 Z= 0.140 Angle : 0.700 13.092 10321 Z= 0.343 Chirality : 0.045 0.169 1200 Planarity : 0.005 0.053 1289 Dihedral : 3.960 16.928 1037 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.17 % Allowed : 27.69 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.28), residues: 918 helix: 1.48 (0.22), residues: 572 sheet: 0.93 (0.58), residues: 70 loop : -1.11 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 61 TYR 0.019 0.001 TYR F 340 PHE 0.027 0.001 PHE G 321 TRP 0.019 0.001 TRP F 271 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7629) covalent geometry : angle 0.69958 (10321) hydrogen bonds : bond 0.03618 ( 458) hydrogen bonds : angle 4.50727 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8473 (t0) cc_final: 0.8259 (t0) REVERT: B 62 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7989 (mmp80) REVERT: F 271 TRP cc_start: 0.8861 (t-100) cc_final: 0.8221 (t-100) REVERT: F 296 GLN cc_start: 0.8418 (mm110) cc_final: 0.8110 (mm110) REVERT: G 85 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7994 (t0) REVERT: G 87 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7791 (mt-10) REVERT: G 253 PHE cc_start: 0.8683 (t80) cc_final: 0.8205 (t80) REVERT: G 254 MET cc_start: 0.8921 (mmm) cc_final: 0.8599 (mmm) REVERT: G 352 LEU cc_start: 0.8645 (mt) cc_final: 0.8413 (mt) outliers start: 33 outliers final: 29 residues processed: 207 average time/residue: 0.0809 time to fit residues: 23.2890 Evaluate side-chains 216 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS F 258 ASN G 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106934 restraints weight = 14026.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110343 restraints weight = 7885.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112506 restraints weight = 5335.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114228 restraints weight = 4140.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114999 restraints weight = 3435.224| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7629 Z= 0.154 Angle : 0.703 12.195 10321 Z= 0.344 Chirality : 0.045 0.172 1200 Planarity : 0.004 0.053 1289 Dihedral : 3.956 16.622 1037 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.30 % Allowed : 27.94 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.28), residues: 918 helix: 1.45 (0.22), residues: 574 sheet: 0.95 (0.58), residues: 70 loop : -1.12 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 126 TYR 0.018 0.001 TYR F 340 PHE 0.026 0.001 PHE G 321 TRP 0.016 0.001 TRP F 271 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7629) covalent geometry : angle 0.70274 (10321) hydrogen bonds : bond 0.03631 ( 458) hydrogen bonds : angle 4.49891 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1273.00 seconds wall clock time: 22 minutes 39.55 seconds (1359.55 seconds total)