Starting phenix.real_space_refine on Sat May 10 13:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m0d_63543/05_2025/9m0d_63543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m0d_63543/05_2025/9m0d_63543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m0d_63543/05_2025/9m0d_63543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m0d_63543/05_2025/9m0d_63543.map" model { file = "/net/cci-nas-00/data/ceres_data/9m0d_63543/05_2025/9m0d_63543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m0d_63543/05_2025/9m0d_63543.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 13 5.16 5 C 3928 2.51 5 N 1157 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6312 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1293 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 6, 'TRANS': 247} Chain breaks: 6 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 677 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 1, 'ARG:plan': 11, 'TYR:plan': 16, 'ASN:plan1': 11, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 414 Chain: "B" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2389 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 28, 'TRANS': 332} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 263 Chain: "D" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1371 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 11, 'TRANS': 207} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "Q" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1259 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 119} Link IDs: {'PTRANS': 11, 'TRANS': 198} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 179 Time building chain proxies: 4.39, per 1000 atoms: 0.70 Number of scatterers: 6312 At special positions: 0 Unit cell: (77.9, 95.94, 159.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 3 15.00 O 1211 8.00 N 1157 7.00 C 3928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS D 119 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 44 " - pdb=" SG CYS Q 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 978.7 milliseconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 16 sheets defined 26.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'R' and resid 60 through 90 removed outlier: 4.114A pdb=" N ARG R 90 " --> pdb=" O PHE R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 129 Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 141 through 171 Processing helix chain 'R' and resid 184 through 201 Processing helix chain 'R' and resid 230 through 265 Proline residue: R 248 - end of helix removed outlier: 4.001A pdb=" N VAL R 265 " --> pdb=" O ASN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 327 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 367 Proline residue: R 361 - end of helix removed outlier: 4.099A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 382 removed outlier: 3.732A pdb=" N LEU R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.652A pdb=" N GLN B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.873A pdb=" N SER B 162 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'Q' and resid 100 through 104 Processing helix chain 'Q' and resid 142 through 149 Processing helix chain 'Q' and resid 170 through 174 removed outlier: 3.533A pdb=" N ASN Q 173 " --> pdb=" O LYS Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 210 removed outlier: 3.580A pdb=" N GLU Q 208 " --> pdb=" O LYS Q 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 77 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 77 removed outlier: 3.857A pdb=" N TYR B 143 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 167 " --> pdb=" O TYR B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.950A pdb=" N ARG B 187 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 196 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 197 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 217 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 265 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 246 through 257 removed outlier: 6.538A pdb=" N VAL B 234 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET B 254 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 232 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 256 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 230 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 229 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 231 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 320 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 30 Processing sheet with id=AA7, first strand: chain 'D' and resid 33 through 35 removed outlier: 6.515A pdb=" N ILE D 57 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER D 73 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP D 59 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 33 through 35 removed outlier: 4.134A pdb=" N TYR D 132 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ARG D 123 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LEU D 130 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 152 through 154 removed outlier: 4.380A pdb=" N GLY D 169 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 180 through 184 Processing sheet with id=AB2, first strand: chain 'D' and resid 199 through 200 Processing sheet with id=AB3, first strand: chain 'Q' and resid 26 through 27 Processing sheet with id=AB4, first strand: chain 'Q' and resid 31 through 33 removed outlier: 6.387A pdb=" N VAL Q 54 " --> pdb=" O TYR Q 70 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR Q 70 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP Q 56 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 84 through 85 Processing sheet with id=AB6, first strand: chain 'Q' and resid 137 through 138 removed outlier: 6.304A pdb=" N TYR Q 194 " --> pdb=" O ASN Q 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 150 through 151 334 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.77 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: 2227 1.34 - 1.46: 1022 1.46 - 1.58: 3135 1.58 - 1.70: 3 1.70 - 1.82: 18 Bond restraints: 6405 Sorted by residual: bond pdb=" OG1 TPO R 407 " pdb=" P TPO R 407 " ideal model delta sigma weight residual 1.717 1.591 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" O3P SEP R 409 " pdb=" P SEP R 409 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" O2P SEP R 410 " pdb=" P SEP R 410 " ideal model delta sigma weight residual 1.610 1.512 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O3P SEP R 410 " pdb=" P SEP R 410 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" O2P SEP R 409 " pdb=" P SEP R 409 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 6400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 8622 1.80 - 3.59: 184 3.59 - 5.39: 27 5.39 - 7.18: 6 7.18 - 8.98: 4 Bond angle restraints: 8843 Sorted by residual: angle pdb=" C SEP R 409 " pdb=" N SEP R 410 " pdb=" CA SEP R 410 " ideal model delta sigma weight residual 121.70 114.99 6.71 1.80e+00 3.09e-01 1.39e+01 angle pdb=" CA PRO D 37 " pdb=" N PRO D 37 " pdb=" CD PRO D 37 " ideal model delta sigma weight residual 112.00 107.55 4.45 1.40e+00 5.10e-01 1.01e+01 angle pdb=" N PRO D 37 " pdb=" CD PRO D 37 " pdb=" CG PRO D 37 " ideal model delta sigma weight residual 103.20 98.81 4.39 1.50e+00 4.44e-01 8.55e+00 angle pdb=" CB SEP R 409 " pdb=" OG SEP R 409 " pdb=" P SEP R 409 " ideal model delta sigma weight residual 110.00 118.77 -8.77 3.00e+00 1.11e-01 8.54e+00 angle pdb=" N SEP R 409 " pdb=" CA SEP R 409 " pdb=" C SEP R 409 " ideal model delta sigma weight residual 111.20 103.25 7.95 2.80e+00 1.28e-01 8.07e+00 ... (remaining 8838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 3512 16.01 - 32.02: 174 32.02 - 48.03: 43 48.03 - 64.04: 20 64.04 - 80.05: 6 Dihedral angle restraints: 3755 sinusoidal: 719 harmonic: 3036 Sorted by residual: dihedral pdb=" CD ARG B 6 " pdb=" NE ARG B 6 " pdb=" CZ ARG B 6 " pdb=" NH1 ARG B 6 " ideal model delta sinusoidal sigma weight residual 0.00 46.15 -46.15 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" CB CYS D 45 " pdb=" SG CYS D 45 " pdb=" SG CYS D 119 " pdb=" CB CYS D 119 " ideal model delta sinusoidal sigma weight residual -86.00 -127.42 41.42 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA GLN D 105 " pdb=" C GLN D 105 " pdb=" N MET D 106 " pdb=" CA MET D 106 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 782 0.039 - 0.078: 227 0.078 - 0.117: 84 0.117 - 0.156: 10 0.156 - 0.195: 2 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CG LEU D 104 " pdb=" CB LEU D 104 " pdb=" CD1 LEU D 104 " pdb=" CD2 LEU D 104 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA SEP R 410 " pdb=" N SEP R 410 " pdb=" C SEP R 410 " pdb=" CB SEP R 410 " both_signs ideal model delta sigma weight residual False 2.50 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CB TPO R 407 " pdb=" CA TPO R 407 " pdb=" OG1 TPO R 407 " pdb=" CG2 TPO R 407 " both_signs ideal model delta sigma weight residual False 2.48 2.64 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1102 not shown) Planarity restraints: 1193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 6 " -0.785 9.50e-02 1.11e+02 3.52e-01 7.53e+01 pdb=" NE ARG B 6 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 6 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 6 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 6 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 196 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO D 197 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 197 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 197 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 180 " -0.038 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO B 181 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.032 5.00e-02 4.00e+02 ... (remaining 1190 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 65 2.63 - 3.20: 5755 3.20 - 3.77: 9505 3.77 - 4.33: 11860 4.33 - 4.90: 20645 Nonbonded interactions: 47830 Sorted by model distance: nonbonded pdb=" O PRO B 123 " pdb=" OH TYR B 143 " model vdw 2.064 3.040 nonbonded pdb=" CG1 VAL B 36 " pdb=" CB PHE B 116 " model vdw 2.100 3.860 nonbonded pdb=" O ALA B 262 " pdb=" OG SER B 265 " model vdw 2.248 3.040 nonbonded pdb=" O ASP Q 103 " pdb=" OH TYR Q 107 " model vdw 2.250 3.040 nonbonded pdb=" O ILE R 359 " pdb=" N LEU R 363 " model vdw 2.261 3.120 ... (remaining 47825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.005 0.126 6407 Z= 0.243 Angle : 0.664 8.980 8847 Z= 0.370 Chirality : 0.042 0.195 1105 Planarity : 0.011 0.352 1193 Dihedral : 12.641 80.051 1775 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.58 % Allowed : 20.18 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.27), residues: 1018 helix: 3.08 (0.31), residues: 237 sheet: -2.03 (0.30), residues: 281 loop : -1.78 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 70 HIS 0.004 0.001 HIS B 352 PHE 0.010 0.001 PHE B 267 TYR 0.009 0.001 TYR D 127 ARG 0.004 0.001 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.19159 ( 325) hydrogen bonds : angle 8.61366 ( 900) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.99718 ( 4) covalent geometry : bond 0.00479 ( 6405) covalent geometry : angle 0.66340 ( 8843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.691 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.1609 time to fit residues: 12.6082 Evaluate side-chains 53 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.0370 chunk 78 optimal weight: 0.2980 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 50.0000 chunk 31 optimal weight: 0.0670 chunk 49 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 406 HIS B 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.211945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.187937 restraints weight = 8625.673| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 1.27 r_work: 0.4178 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.4017 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6407 Z= 0.101 Angle : 0.495 6.642 8847 Z= 0.269 Chirality : 0.042 0.132 1105 Planarity : 0.004 0.053 1193 Dihedral : 5.699 83.483 1087 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.09 % Allowed : 17.25 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.27), residues: 1018 helix: 3.00 (0.30), residues: 243 sheet: -1.82 (0.33), residues: 255 loop : -1.61 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 70 HIS 0.004 0.001 HIS D 58 PHE 0.011 0.001 PHE Q 160 TYR 0.010 0.001 TYR B 143 ARG 0.014 0.001 ARG B 6 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 325) hydrogen bonds : angle 5.57013 ( 900) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.96875 ( 4) covalent geometry : bond 0.00196 ( 6405) covalent geometry : angle 0.49451 ( 8843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.644 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 57 average time/residue: 0.1505 time to fit residues: 12.3852 Evaluate side-chains 55 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 144 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 23 optimal weight: 50.0000 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 2 optimal weight: 50.0000 chunk 6 optimal weight: 40.0000 chunk 83 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.182344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144603 restraints weight = 8921.704| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.12 r_work: 0.3595 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 6407 Z= 0.330 Angle : 0.671 8.972 8847 Z= 0.362 Chirality : 0.047 0.155 1105 Planarity : 0.005 0.054 1193 Dihedral : 6.242 79.482 1085 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 6.14 % Allowed : 17.25 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.27), residues: 1018 helix: 3.33 (0.31), residues: 244 sheet: -2.32 (0.30), residues: 271 loop : -2.00 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP D 70 HIS 0.008 0.002 HIS D 58 PHE 0.026 0.003 PHE Q 92 TYR 0.024 0.002 TYR Q 112 ARG 0.008 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 325) hydrogen bonds : angle 5.98514 ( 900) SS BOND : bond 0.00851 ( 2) SS BOND : angle 1.29834 ( 4) covalent geometry : bond 0.00756 ( 6405) covalent geometry : angle 0.67107 ( 8843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.699 Fit side-chains REVERT: B 112 TYR cc_start: 0.7765 (m-80) cc_final: 0.7387 (m-80) outliers start: 21 outliers final: 19 residues processed: 63 average time/residue: 0.1279 time to fit residues: 12.1313 Evaluate side-chains 65 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 110 GLN Chi-restraints excluded: chain Q residue 144 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 50.0000 chunk 59 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 50.0000 chunk 80 optimal weight: 0.0040 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS Q 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.205006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.181445 restraints weight = 8742.261| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 1.31 r_work: 0.4075 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6407 Z= 0.120 Angle : 0.501 6.589 8847 Z= 0.269 Chirality : 0.042 0.131 1105 Planarity : 0.004 0.048 1193 Dihedral : 5.836 89.772 1085 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.68 % Allowed : 18.42 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.27), residues: 1018 helix: 3.48 (0.30), residues: 242 sheet: -2.13 (0.29), residues: 276 loop : -1.84 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 70 HIS 0.003 0.001 HIS D 58 PHE 0.014 0.001 PHE D 176 TYR 0.011 0.001 TYR D 127 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 325) hydrogen bonds : angle 4.96122 ( 900) SS BOND : bond 0.00353 ( 2) SS BOND : angle 1.32614 ( 4) covalent geometry : bond 0.00260 ( 6405) covalent geometry : angle 0.49987 ( 8843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: D 44 SER cc_start: 0.8264 (p) cc_final: 0.7956 (p) outliers start: 16 outliers final: 12 residues processed: 61 average time/residue: 0.1616 time to fit residues: 13.8940 Evaluate side-chains 60 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 10 optimal weight: 50.0000 chunk 68 optimal weight: 0.0030 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.185038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151187 restraints weight = 8855.363| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.03 r_work: 0.3632 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6407 Z= 0.184 Angle : 0.536 6.802 8847 Z= 0.288 Chirality : 0.043 0.138 1105 Planarity : 0.004 0.046 1193 Dihedral : 5.859 88.409 1085 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 7.02 % Allowed : 17.84 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.27), residues: 1018 helix: 3.69 (0.30), residues: 242 sheet: -2.19 (0.29), residues: 277 loop : -1.83 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 70 HIS 0.005 0.001 HIS D 58 PHE 0.015 0.002 PHE Q 92 TYR 0.023 0.002 TYR B 207 ARG 0.002 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 325) hydrogen bonds : angle 4.99193 ( 900) SS BOND : bond 0.00535 ( 2) SS BOND : angle 0.94359 ( 4) covalent geometry : bond 0.00414 ( 6405) covalent geometry : angle 0.53553 ( 8843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: D 44 SER cc_start: 0.8363 (p) cc_final: 0.8047 (p) outliers start: 24 outliers final: 21 residues processed: 68 average time/residue: 0.1530 time to fit residues: 14.7321 Evaluate side-chains 73 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 144 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 40.0000 chunk 100 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 50.0000 chunk 80 optimal weight: 0.1980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.184840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148398 restraints weight = 8830.105| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.07 r_work: 0.3630 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6407 Z= 0.177 Angle : 0.528 6.733 8847 Z= 0.284 Chirality : 0.043 0.134 1105 Planarity : 0.004 0.044 1193 Dihedral : 5.863 88.350 1085 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.76 % Favored : 92.14 % Rotamer: Outliers : 6.43 % Allowed : 18.71 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.27), residues: 1018 helix: 3.83 (0.30), residues: 242 sheet: -2.14 (0.30), residues: 280 loop : -1.84 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 70 HIS 0.004 0.001 HIS B 352 PHE 0.014 0.002 PHE D 176 TYR 0.025 0.002 TYR Q 76 ARG 0.004 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 325) hydrogen bonds : angle 4.83772 ( 900) SS BOND : bond 0.00513 ( 2) SS BOND : angle 1.08552 ( 4) covalent geometry : bond 0.00401 ( 6405) covalent geometry : angle 0.52754 ( 8843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.727 Fit side-chains REVERT: D 44 SER cc_start: 0.8371 (p) cc_final: 0.8059 (p) REVERT: Q 110 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8910 (tt0) REVERT: Q 160 PHE cc_start: 0.7978 (p90) cc_final: 0.7768 (p90) outliers start: 22 outliers final: 18 residues processed: 67 average time/residue: 0.1591 time to fit residues: 15.1116 Evaluate side-chains 68 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain Q residue 110 GLN Chi-restraints excluded: chain Q residue 144 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 25 optimal weight: 0.5980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.206583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.4335 r_free = 0.4335 target = 0.183460 restraints weight = 8757.148| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 1.16 r_work: 0.4122 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6407 Z= 0.102 Angle : 0.473 6.562 8847 Z= 0.252 Chirality : 0.041 0.126 1105 Planarity : 0.004 0.043 1193 Dihedral : 5.268 84.379 1085 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.83 % Rotamer: Outliers : 4.68 % Allowed : 20.76 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 1018 helix: 3.92 (0.29), residues: 242 sheet: -1.80 (0.31), residues: 267 loop : -1.77 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 70 HIS 0.003 0.001 HIS B 361 PHE 0.009 0.001 PHE Q 160 TYR 0.018 0.001 TYR Q 76 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 325) hydrogen bonds : angle 4.31495 ( 900) SS BOND : bond 0.00272 ( 2) SS BOND : angle 1.05714 ( 4) covalent geometry : bond 0.00219 ( 6405) covalent geometry : angle 0.47300 ( 8843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.708 Fit side-chains REVERT: D 44 SER cc_start: 0.8035 (p) cc_final: 0.7736 (p) REVERT: Q 52 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8157 (t) outliers start: 16 outliers final: 12 residues processed: 59 average time/residue: 0.1586 time to fit residues: 13.3420 Evaluate side-chains 58 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain Q residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 72 optimal weight: 0.0470 chunk 23 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.205038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.4316 r_free = 0.4316 target = 0.181819 restraints weight = 8700.642| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 1.15 r_work: 0.4099 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6407 Z= 0.132 Angle : 0.493 6.546 8847 Z= 0.263 Chirality : 0.042 0.131 1105 Planarity : 0.004 0.042 1193 Dihedral : 5.242 85.448 1085 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.44 % Rotamer: Outliers : 4.97 % Allowed : 20.18 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 1018 helix: 3.83 (0.30), residues: 248 sheet: -1.65 (0.31), residues: 266 loop : -1.73 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 70 HIS 0.003 0.001 HIS B 352 PHE 0.010 0.001 PHE B 267 TYR 0.019 0.001 TYR Q 76 ARG 0.003 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 325) hydrogen bonds : angle 4.28244 ( 900) SS BOND : bond 0.00343 ( 2) SS BOND : angle 0.78267 ( 4) covalent geometry : bond 0.00293 ( 6405) covalent geometry : angle 0.49264 ( 8843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.650 Fit side-chains REVERT: D 44 SER cc_start: 0.8035 (p) cc_final: 0.7766 (p) REVERT: Q 52 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8227 (t) outliers start: 17 outliers final: 15 residues processed: 57 average time/residue: 0.1403 time to fit residues: 11.7401 Evaluate side-chains 61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain Q residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.205382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.181618 restraints weight = 8724.822| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 1.36 r_work: 0.4003 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6407 Z= 0.102 Angle : 0.472 6.448 8847 Z= 0.251 Chirality : 0.041 0.124 1105 Planarity : 0.004 0.042 1193 Dihedral : 4.973 83.121 1085 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.39 % Allowed : 20.76 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.28), residues: 1018 helix: 3.91 (0.30), residues: 248 sheet: -1.47 (0.32), residues: 268 loop : -1.60 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 56 HIS 0.003 0.001 HIS B 361 PHE 0.008 0.001 PHE D 176 TYR 0.017 0.001 TYR Q 76 ARG 0.005 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.02669 ( 325) hydrogen bonds : angle 4.00379 ( 900) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.86936 ( 4) covalent geometry : bond 0.00222 ( 6405) covalent geometry : angle 0.47165 ( 8843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.732 Fit side-chains REVERT: D 44 SER cc_start: 0.8007 (p) cc_final: 0.7746 (p) outliers start: 15 outliers final: 15 residues processed: 56 average time/residue: 0.1452 time to fit residues: 11.9457 Evaluate side-chains 61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 14 optimal weight: 50.0000 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 50.0000 chunk 95 optimal weight: 5.9990 chunk 1 optimal weight: 40.0000 chunk 39 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.205519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.180047 restraints weight = 8742.371| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 1.33 r_work: 0.4051 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6407 Z= 0.108 Angle : 0.480 6.582 8847 Z= 0.255 Chirality : 0.041 0.130 1105 Planarity : 0.004 0.041 1193 Dihedral : 4.934 83.736 1085 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.39 % Allowed : 21.35 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 1018 helix: 4.01 (0.29), residues: 248 sheet: -1.33 (0.32), residues: 271 loop : -1.58 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 56 HIS 0.003 0.001 HIS B 361 PHE 0.009 0.001 PHE D 176 TYR 0.018 0.001 TYR Q 76 ARG 0.004 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.02625 ( 325) hydrogen bonds : angle 3.96317 ( 900) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.71821 ( 4) covalent geometry : bond 0.00236 ( 6405) covalent geometry : angle 0.47941 ( 8843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.704 Fit side-chains REVERT: D 44 SER cc_start: 0.8182 (p) cc_final: 0.7927 (p) outliers start: 15 outliers final: 15 residues processed: 57 average time/residue: 0.1470 time to fit residues: 12.3738 Evaluate side-chains 60 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 411 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 12 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 17 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 50.0000 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.148147 restraints weight = 9087.044| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.09 r_work: 0.3590 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6407 Z= 0.232 Angle : 0.584 6.885 8847 Z= 0.311 Chirality : 0.043 0.145 1105 Planarity : 0.004 0.043 1193 Dihedral : 5.614 87.505 1085 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.33 % Favored : 90.57 % Rotamer: Outliers : 4.97 % Allowed : 20.76 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 1018 helix: 4.05 (0.30), residues: 248 sheet: -1.65 (0.32), residues: 268 loop : -1.71 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 70 HIS 0.005 0.002 HIS B 352 PHE 0.015 0.002 PHE Q 92 TYR 0.023 0.002 TYR Q 76 ARG 0.006 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 325) hydrogen bonds : angle 4.68974 ( 900) SS BOND : bond 0.00608 ( 2) SS BOND : angle 0.97419 ( 4) covalent geometry : bond 0.00526 ( 6405) covalent geometry : angle 0.58371 ( 8843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.70 seconds wall clock time: 65 minutes 20.31 seconds (3920.31 seconds total)